Starting phenix.real_space_refine on Thu Jan 23 14:00:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uxk_42767/01_2025/8uxk_42767.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uxk_42767/01_2025/8uxk_42767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uxk_42767/01_2025/8uxk_42767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uxk_42767/01_2025/8uxk_42767.map" model { file = "/net/cci-nas-00/data/ceres_data/8uxk_42767/01_2025/8uxk_42767.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uxk_42767/01_2025/8uxk_42767.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 148 5.16 5 C 44511 2.51 5 N 12432 2.21 5 O 15281 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 72372 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "B" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "C" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "D" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "E" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "F" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "G" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "H" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "I" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "J" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "K" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "L" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "M" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "N" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "O" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "P" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "Q" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "R" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "S" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "T" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "U" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "V" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "W" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "X" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "Y" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "Z" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "a" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "b" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "c" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "d" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "e" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "f" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "g" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "h" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "i" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "j" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "k" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Time building chain proxies: 30.44, per 1000 atoms: 0.42 Number of scatterers: 72372 At special positions: 0 Unit cell: (138.444, 135.942, 331.098, 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 148 16.00 O 15281 8.00 N 12432 7.00 C 44511 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.25 Conformation dependent library (CDL) restraints added in 7.6 seconds 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18722 Finding SS restraints... Secondary structure from input PDB file: 276 helices and 38 sheets defined 77.3% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.26 Creating SS restraints... Processing helix chain 'A' and resid 8 through 35 removed outlier: 3.934A pdb=" N LEU A 12 " --> pdb=" O ASN A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 101 removed outlier: 3.796A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASN A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N SER A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 129 Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.626A pdb=" N GLY A 169 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 233 removed outlier: 4.083A pdb=" N ALA A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 263 removed outlier: 3.763A pdb=" N GLU A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 271 removed outlier: 3.513A pdb=" N LEU A 268 " --> pdb=" O GLN A 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 35 removed outlier: 3.629A pdb=" N LEU B 12 " --> pdb=" O ASN B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 100 removed outlier: 4.456A pdb=" N ASN B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N SER B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 129 removed outlier: 3.502A pdb=" N LYS B 125 " --> pdb=" O ASP B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 169 removed outlier: 3.571A pdb=" N GLY B 169 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 233 removed outlier: 4.031A pdb=" N ALA B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 263 removed outlier: 3.864A pdb=" N GLU B 239 " --> pdb=" O ASP B 235 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLN B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 271 Processing helix chain 'C' and resid 8 through 35 removed outlier: 3.546A pdb=" N LEU C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 60 Processing helix chain 'C' and resid 60 through 101 removed outlier: 4.073A pdb=" N VAL C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 129 Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.647A pdb=" N GLY C 169 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 233 removed outlier: 4.085A pdb=" N ALA C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 262 removed outlier: 3.500A pdb=" N GLU C 239 " --> pdb=" O ASP C 235 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 241 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLN C 244 " --> pdb=" O SER C 240 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 271 Processing helix chain 'D' and resid 8 through 35 removed outlier: 3.863A pdb=" N LEU D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 100 removed outlier: 3.749A pdb=" N LEU D 61 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASN D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N SER D 63 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 129 Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.195A pdb=" N GLY D 134 " --> pdb=" O LYS D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 169 removed outlier: 3.640A pdb=" N GLY D 169 " --> pdb=" O THR D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 233 removed outlier: 4.148A pdb=" N ALA D 187 " --> pdb=" O LYS D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 262 removed outlier: 3.744A pdb=" N GLU D 239 " --> pdb=" O ASP D 235 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA D 241 " --> pdb=" O ALA D 237 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN D 262 " --> pdb=" O SER D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 271 removed outlier: 3.520A pdb=" N THR D 266 " --> pdb=" O THR D 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 35 Processing helix chain 'E' and resid 44 through 60 Processing helix chain 'E' and resid 60 through 101 removed outlier: 4.109A pdb=" N VAL E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP E 87 " --> pdb=" O ASP E 83 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP E 101 " --> pdb=" O LEU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 129 Processing helix chain 'E' and resid 164 through 169 removed outlier: 3.595A pdb=" N GLY E 169 " --> pdb=" O THR E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 233 removed outlier: 3.836A pdb=" N ALA E 187 " --> pdb=" O LYS E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 263 removed outlier: 3.588A pdb=" N ALA E 241 " --> pdb=" O ALA E 237 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLN E 244 " --> pdb=" O SER E 240 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN E 262 " --> pdb=" O SER E 258 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR E 263 " --> pdb=" O ILE E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 271 removed outlier: 4.094A pdb=" N LEU E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE E 271 " --> pdb=" O ILE E 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 266 through 271' Processing helix chain 'F' and resid 8 through 35 Processing helix chain 'F' and resid 44 through 60 Processing helix chain 'F' and resid 60 through 101 removed outlier: 4.091A pdb=" N VAL F 64 " --> pdb=" O SER F 60 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR F 84 " --> pdb=" O ALA F 80 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP F 87 " --> pdb=" O ASP F 83 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP F 101 " --> pdb=" O LEU F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 129 Processing helix chain 'F' and resid 164 through 169 removed outlier: 3.573A pdb=" N GLY F 169 " --> pdb=" O THR F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 233 removed outlier: 4.038A pdb=" N THR F 184 " --> pdb=" O ALA F 180 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA F 187 " --> pdb=" O LYS F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 263 removed outlier: 3.843A pdb=" N GLN F 244 " --> pdb=" O SER F 240 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN F 262 " --> pdb=" O SER F 258 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR F 263 " --> pdb=" O ILE F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 271 Processing helix chain 'G' and resid 8 through 35 Processing helix chain 'G' and resid 44 through 60 Processing helix chain 'G' and resid 60 through 100 removed outlier: 3.970A pdb=" N VAL G 64 " --> pdb=" O SER G 60 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR G 84 " --> pdb=" O ALA G 80 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP G 87 " --> pdb=" O ASP G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 129 Processing helix chain 'G' and resid 164 through 169 removed outlier: 3.552A pdb=" N GLY G 169 " --> pdb=" O THR G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 233 removed outlier: 3.976A pdb=" N THR G 184 " --> pdb=" O ALA G 180 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA G 187 " --> pdb=" O LYS G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 262 removed outlier: 3.639A pdb=" N ALA G 241 " --> pdb=" O ALA G 237 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN G 244 " --> pdb=" O SER G 240 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN G 262 " --> pdb=" O SER G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 265 No H-bonds generated for 'chain 'G' and resid 263 through 265' Processing helix chain 'G' and resid 266 through 271 removed outlier: 3.902A pdb=" N LEU G 270 " --> pdb=" O THR G 266 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE G 271 " --> pdb=" O ILE G 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 266 through 271' Processing helix chain 'H' and resid 8 through 35 Processing helix chain 'H' and resid 44 through 101 removed outlier: 3.595A pdb=" N TRP H 48 " --> pdb=" O ASN H 44 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU H 61 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER H 63 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL H 64 " --> pdb=" O SER H 60 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR H 84 " --> pdb=" O ALA H 80 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP H 101 " --> pdb=" O LEU H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 129 Processing helix chain 'H' and resid 178 through 233 removed outlier: 3.988A pdb=" N THR H 184 " --> pdb=" O ALA H 180 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA H 187 " --> pdb=" O LYS H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 262 removed outlier: 3.857A pdb=" N ALA H 241 " --> pdb=" O ALA H 237 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN H 244 " --> pdb=" O SER H 240 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN H 262 " --> pdb=" O SER H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 271 removed outlier: 3.815A pdb=" N SER H 269 " --> pdb=" O GLN H 265 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU H 270 " --> pdb=" O THR H 266 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE H 271 " --> pdb=" O ILE H 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 265 through 271' Processing helix chain 'I' and resid 8 through 35 Processing helix chain 'I' and resid 44 through 60 Processing helix chain 'I' and resid 60 through 100 removed outlier: 4.208A pdb=" N VAL I 64 " --> pdb=" O SER I 60 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR I 84 " --> pdb=" O ALA I 80 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP I 87 " --> pdb=" O ASP I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 129 Processing helix chain 'I' and resid 164 through 169 removed outlier: 3.644A pdb=" N GLY I 169 " --> pdb=" O THR I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 233 removed outlier: 3.796A pdb=" N ALA I 187 " --> pdb=" O LYS I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 235 through 263 removed outlier: 3.756A pdb=" N ALA I 241 " --> pdb=" O ALA I 237 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR I 248 " --> pdb=" O GLN I 244 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN I 262 " --> pdb=" O SER I 258 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR I 263 " --> pdb=" O ILE I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 271 removed outlier: 3.575A pdb=" N LEU I 268 " --> pdb=" O GLN I 265 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 35 removed outlier: 3.538A pdb=" N LEU J 12 " --> pdb=" O ASN J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 60 Processing helix chain 'J' and resid 60 through 100 removed outlier: 4.043A pdb=" N VAL J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR J 84 " --> pdb=" O ALA J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 129 Processing helix chain 'J' and resid 164 through 168 Processing helix chain 'J' and resid 178 through 233 removed outlier: 3.910A pdb=" N ALA J 187 " --> pdb=" O LYS J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 235 through 261 removed outlier: 4.035A pdb=" N ALA J 241 " --> pdb=" O ALA J 237 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR J 248 " --> pdb=" O GLN J 244 " (cutoff:3.500A) Processing helix chain 'J' and resid 262 through 271 Processing helix chain 'K' and resid 8 through 35 removed outlier: 3.961A pdb=" N LEU K 12 " --> pdb=" O ASN K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 100 removed outlier: 3.887A pdb=" N LEU K 61 " --> pdb=" O THR K 57 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN K 62 " --> pdb=" O ALA K 58 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER K 63 " --> pdb=" O SER K 59 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL K 64 " --> pdb=" O SER K 60 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR K 84 " --> pdb=" O ALA K 80 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP K 87 " --> pdb=" O ASP K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 129 Processing helix chain 'K' and resid 164 through 169 Processing helix chain 'K' and resid 178 through 233 removed outlier: 3.832A pdb=" N ALA K 187 " --> pdb=" O LYS K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 235 through 262 removed outlier: 3.831A pdb=" N ALA K 241 " --> pdb=" O ALA K 237 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR K 248 " --> pdb=" O GLN K 244 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN K 262 " --> pdb=" O SER K 258 " (cutoff:3.500A) Processing helix chain 'K' and resid 263 through 271 removed outlier: 3.625A pdb=" N THR K 266 " --> pdb=" O THR K 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 35 removed outlier: 3.739A pdb=" N LEU L 12 " --> pdb=" O ASN L 8 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 60 Processing helix chain 'L' and resid 60 through 100 removed outlier: 3.870A pdb=" N VAL L 64 " --> pdb=" O SER L 60 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR L 84 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 130 removed outlier: 3.882A pdb=" N ALA L 130 " --> pdb=" O ALA L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 168 Processing helix chain 'L' and resid 178 through 233 removed outlier: 3.825A pdb=" N ALA L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 235 through 263 removed outlier: 4.122A pdb=" N ALA L 241 " --> pdb=" O ALA L 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 271 removed outlier: 3.660A pdb=" N LEU L 270 " --> pdb=" O ILE L 267 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 35 removed outlier: 3.817A pdb=" N LEU M 12 " --> pdb=" O ASN M 8 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 100 removed outlier: 3.640A pdb=" N LEU M 61 " --> pdb=" O THR M 57 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN M 62 " --> pdb=" O ALA M 58 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N SER M 63 " --> pdb=" O SER M 59 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL M 64 " --> pdb=" O SER M 60 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR M 84 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 129 Processing helix chain 'M' and resid 164 through 169 removed outlier: 4.114A pdb=" N GLY M 169 " --> pdb=" O THR M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 178 through 233 removed outlier: 3.914A pdb=" N ALA M 187 " --> pdb=" O LYS M 183 " (cutoff:3.500A) Processing helix chain 'M' and resid 235 through 263 removed outlier: 4.074A pdb=" N ALA M 241 " --> pdb=" O ALA M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 271 Processing helix chain 'N' and resid 8 through 35 removed outlier: 3.673A pdb=" N LEU N 12 " --> pdb=" O ASN N 8 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 100 removed outlier: 3.939A pdb=" N LEU N 61 " --> pdb=" O THR N 57 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ASN N 62 " --> pdb=" O ALA N 58 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N SER N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL N 64 " --> pdb=" O SER N 60 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR N 84 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 130 removed outlier: 3.625A pdb=" N ALA N 130 " --> pdb=" O ALA N 126 " (cutoff:3.500A) Processing helix chain 'N' and resid 164 through 169 removed outlier: 3.987A pdb=" N GLY N 169 " --> pdb=" O THR N 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 178 through 233 removed outlier: 3.756A pdb=" N ALA N 187 " --> pdb=" O LYS N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 235 through 263 removed outlier: 4.052A pdb=" N ALA N 241 " --> pdb=" O ALA N 237 " (cutoff:3.500A) Processing helix chain 'N' and resid 264 through 271 removed outlier: 3.650A pdb=" N ILE N 267 " --> pdb=" O PRO N 264 " (cutoff:3.500A) Processing helix chain 'O' and resid 8 through 35 removed outlier: 3.638A pdb=" N LEU O 12 " --> pdb=" O ASN O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 100 removed outlier: 4.273A pdb=" N ASN O 62 " --> pdb=" O ALA O 58 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER O 63 " --> pdb=" O SER O 59 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL O 64 " --> pdb=" O SER O 60 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR O 84 " --> pdb=" O ALA O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 129 Processing helix chain 'O' and resid 165 through 169 removed outlier: 3.712A pdb=" N GLY O 169 " --> pdb=" O THR O 166 " (cutoff:3.500A) Processing helix chain 'O' and resid 178 through 233 removed outlier: 3.793A pdb=" N ALA O 187 " --> pdb=" O LYS O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 235 through 262 removed outlier: 4.071A pdb=" N ALA O 241 " --> pdb=" O ALA O 237 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN O 262 " --> pdb=" O SER O 258 " (cutoff:3.500A) Processing helix chain 'O' and resid 263 through 271 Processing helix chain 'P' and resid 9 through 35 Processing helix chain 'P' and resid 44 through 60 Processing helix chain 'P' and resid 60 through 100 removed outlier: 3.958A pdb=" N VAL P 64 " --> pdb=" O SER P 60 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR P 84 " --> pdb=" O ALA P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 130 removed outlier: 3.594A pdb=" N ASN P 129 " --> pdb=" O LYS P 125 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA P 130 " --> pdb=" O ALA P 126 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 169 removed outlier: 3.915A pdb=" N GLY P 169 " --> pdb=" O THR P 166 " (cutoff:3.500A) Processing helix chain 'P' and resid 178 through 233 removed outlier: 3.799A pdb=" N ALA P 187 " --> pdb=" O LYS P 183 " (cutoff:3.500A) Processing helix chain 'P' and resid 235 through 262 removed outlier: 3.927A pdb=" N ALA P 241 " --> pdb=" O ALA P 237 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN P 262 " --> pdb=" O SER P 258 " (cutoff:3.500A) Processing helix chain 'P' and resid 263 through 271 removed outlier: 3.511A pdb=" N ILE P 267 " --> pdb=" O PRO P 264 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 35 removed outlier: 3.734A pdb=" N LEU Q 12 " --> pdb=" O ASN Q 8 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 100 removed outlier: 3.827A pdb=" N LEU Q 61 " --> pdb=" O THR Q 57 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN Q 62 " --> pdb=" O ALA Q 58 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER Q 63 " --> pdb=" O SER Q 59 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR Q 84 " --> pdb=" O ALA Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 130 removed outlier: 3.799A pdb=" N ALA Q 130 " --> pdb=" O ALA Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 169 removed outlier: 3.984A pdb=" N GLY Q 169 " --> pdb=" O THR Q 166 " (cutoff:3.500A) Processing helix chain 'Q' and resid 178 through 233 removed outlier: 3.701A pdb=" N ALA Q 187 " --> pdb=" O LYS Q 183 " (cutoff:3.500A) Processing helix chain 'Q' and resid 235 through 262 removed outlier: 3.721A pdb=" N GLN Q 262 " --> pdb=" O SER Q 258 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 271 Processing helix chain 'R' and resid 8 through 35 removed outlier: 3.871A pdb=" N LEU R 12 " --> pdb=" O ASN R 8 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU R 24 " --> pdb=" O SER R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 101 removed outlier: 3.776A pdb=" N LEU R 61 " --> pdb=" O THR R 57 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASN R 62 " --> pdb=" O ALA R 58 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N SER R 63 " --> pdb=" O SER R 59 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL R 64 " --> pdb=" O SER R 60 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR R 84 " --> pdb=" O ALA R 80 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP R 101 " --> pdb=" O LEU R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 129 Processing helix chain 'R' and resid 164 through 169 removed outlier: 3.978A pdb=" N GLY R 169 " --> pdb=" O THR R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 233 removed outlier: 3.934A pdb=" N ALA R 187 " --> pdb=" O LYS R 183 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU R 231 " --> pdb=" O GLY R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 235 through 263 removed outlier: 3.652A pdb=" N GLU R 239 " --> pdb=" O ASP R 235 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 271 Processing helix chain 'S' and resid 8 through 35 removed outlier: 3.861A pdb=" N LEU S 12 " --> pdb=" O ASN S 8 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 60 Processing helix chain 'S' and resid 60 through 100 removed outlier: 3.925A pdb=" N VAL S 64 " --> pdb=" O SER S 60 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR S 84 " --> pdb=" O ALA S 80 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP S 87 " --> pdb=" O ASP S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 105 through 130 removed outlier: 3.638A pdb=" N ALA S 130 " --> pdb=" O ALA S 126 " (cutoff:3.500A) Processing helix chain 'S' and resid 178 through 233 removed outlier: 3.931A pdb=" N ALA S 187 " --> pdb=" O LYS S 183 " (cutoff:3.500A) Processing helix chain 'S' and resid 235 through 263 Processing helix chain 'S' and resid 264 through 271 removed outlier: 3.913A pdb=" N PHE S 271 " --> pdb=" O LEU S 268 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 35 removed outlier: 4.118A pdb=" N LEU T 12 " --> pdb=" O ASN T 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 60 Processing helix chain 'T' and resid 60 through 101 removed outlier: 3.818A pdb=" N VAL T 64 " --> pdb=" O SER T 60 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR T 84 " --> pdb=" O ALA T 80 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP T 87 " --> pdb=" O ASP T 83 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP T 101 " --> pdb=" O LEU T 97 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 130 removed outlier: 3.617A pdb=" N ALA T 130 " --> pdb=" O ALA T 126 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 169 removed outlier: 3.649A pdb=" N GLY T 169 " --> pdb=" O THR T 166 " (cutoff:3.500A) Processing helix chain 'T' and resid 178 through 233 removed outlier: 3.873A pdb=" N ALA T 187 " --> pdb=" O LYS T 183 " (cutoff:3.500A) Processing helix chain 'T' and resid 235 through 263 Processing helix chain 'T' and resid 266 through 271 removed outlier: 3.807A pdb=" N LEU T 270 " --> pdb=" O THR T 266 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE T 271 " --> pdb=" O ILE T 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 266 through 271' Processing helix chain 'U' and resid 9 through 35 Processing helix chain 'U' and resid 44 through 60 removed outlier: 3.920A pdb=" N SER U 60 " --> pdb=" O ALA U 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 60 through 100 removed outlier: 4.203A pdb=" N THR U 84 " --> pdb=" O ALA U 80 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP U 87 " --> pdb=" O ASP U 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 105 through 129 removed outlier: 3.526A pdb=" N ASN U 129 " --> pdb=" O LYS U 125 " (cutoff:3.500A) Processing helix chain 'U' and resid 164 through 169 removed outlier: 3.777A pdb=" N GLY U 169 " --> pdb=" O THR U 166 " (cutoff:3.500A) Processing helix chain 'U' and resid 178 through 233 removed outlier: 3.956A pdb=" N ALA U 187 " --> pdb=" O LYS U 183 " (cutoff:3.500A) Processing helix chain 'U' and resid 235 through 263 Processing helix chain 'U' and resid 264 through 271 removed outlier: 3.710A pdb=" N PHE U 271 " --> pdb=" O LEU U 268 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 34 removed outlier: 3.672A pdb=" N LEU V 12 " --> pdb=" O ASN V 8 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU V 24 " --> pdb=" O SER V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 60 Processing helix chain 'V' and resid 60 through 100 removed outlier: 3.951A pdb=" N VAL V 64 " --> pdb=" O SER V 60 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR V 84 " --> pdb=" O ALA V 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 105 through 130 removed outlier: 3.548A pdb=" N ASN V 129 " --> pdb=" O LYS V 125 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA V 130 " --> pdb=" O ALA V 126 " (cutoff:3.500A) Processing helix chain 'V' and resid 178 through 233 removed outlier: 4.030A pdb=" N ALA V 187 " --> pdb=" O LYS V 183 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN V 198 " --> pdb=" O GLN V 194 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP V 222 " --> pdb=" O GLY V 218 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU V 231 " --> pdb=" O GLY V 227 " (cutoff:3.500A) Processing helix chain 'V' and resid 235 through 263 removed outlier: 3.829A pdb=" N GLN V 251 " --> pdb=" O GLN V 247 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU V 252 " --> pdb=" O THR V 248 " (cutoff:3.500A) Processing helix chain 'V' and resid 264 through 271 Processing helix chain 'W' and resid 8 through 35 removed outlier: 3.606A pdb=" N LEU W 12 " --> pdb=" O ASN W 8 " (cutoff:3.500A) Processing helix chain 'W' and resid 44 through 60 Processing helix chain 'W' and resid 60 through 100 removed outlier: 3.935A pdb=" N VAL W 64 " --> pdb=" O SER W 60 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR W 84 " --> pdb=" O ALA W 80 " (cutoff:3.500A) Processing helix chain 'W' and resid 105 through 129 removed outlier: 3.559A pdb=" N ASN W 129 " --> pdb=" O LYS W 125 " (cutoff:3.500A) Processing helix chain 'W' and resid 164 through 169 removed outlier: 3.799A pdb=" N GLY W 169 " --> pdb=" O THR W 166 " (cutoff:3.500A) Processing helix chain 'W' and resid 178 through 233 removed outlier: 3.988A pdb=" N ALA W 187 " --> pdb=" O LYS W 183 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP W 222 " --> pdb=" O GLY W 218 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU W 231 " --> pdb=" O GLY W 227 " (cutoff:3.500A) Processing helix chain 'W' and resid 235 through 263 removed outlier: 3.790A pdb=" N GLN W 251 " --> pdb=" O GLN W 247 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU W 252 " --> pdb=" O THR W 248 " (cutoff:3.500A) Processing helix chain 'W' and resid 264 through 271 removed outlier: 3.889A pdb=" N LEU W 268 " --> pdb=" O GLN W 265 " (cutoff:3.500A) Processing helix chain 'X' and resid 8 through 35 removed outlier: 3.884A pdb=" N LEU X 12 " --> pdb=" O ASN X 8 " (cutoff:3.500A) Processing helix chain 'X' and resid 44 through 60 Processing helix chain 'X' and resid 60 through 100 removed outlier: 3.993A pdb=" N VAL X 64 " --> pdb=" O SER X 60 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR X 84 " --> pdb=" O ALA X 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 130 removed outlier: 3.648A pdb=" N ALA X 130 " --> pdb=" O ALA X 126 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 169 removed outlier: 3.843A pdb=" N GLY X 169 " --> pdb=" O THR X 166 " (cutoff:3.500A) Processing helix chain 'X' and resid 178 through 233 removed outlier: 3.869A pdb=" N ALA X 187 " --> pdb=" O LYS X 183 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN X 198 " --> pdb=" O GLN X 194 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP X 222 " --> pdb=" O GLY X 218 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU X 231 " --> pdb=" O GLY X 227 " (cutoff:3.500A) Processing helix chain 'X' and resid 235 through 263 removed outlier: 3.630A pdb=" N GLN X 251 " --> pdb=" O GLN X 247 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU X 252 " --> pdb=" O THR X 248 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 271 removed outlier: 3.629A pdb=" N LEU X 268 " --> pdb=" O GLN X 265 " (cutoff:3.500A) Processing helix chain 'Y' and resid 8 through 35 removed outlier: 3.770A pdb=" N LEU Y 12 " --> pdb=" O ASN Y 8 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 60 removed outlier: 3.778A pdb=" N TRP Y 48 " --> pdb=" O ASN Y 44 " (cutoff:3.500A) Processing helix chain 'Y' and resid 60 through 100 removed outlier: 4.125A pdb=" N VAL Y 64 " --> pdb=" O SER Y 60 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR Y 84 " --> pdb=" O ALA Y 80 " (cutoff:3.500A) Processing helix chain 'Y' and resid 105 through 130 removed outlier: 3.515A pdb=" N ALA Y 130 " --> pdb=" O ALA Y 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 164 through 168 Processing helix chain 'Y' and resid 178 through 233 removed outlier: 4.298A pdb=" N ALA Y 187 " --> pdb=" O LYS Y 183 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR Y 188 " --> pdb=" O THR Y 184 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP Y 222 " --> pdb=" O GLY Y 218 " (cutoff:3.500A) Processing helix chain 'Y' and resid 235 through 263 removed outlier: 3.964A pdb=" N ALA Y 241 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS Y 242 " --> pdb=" O LYS Y 238 " (cutoff:3.500A) Processing helix chain 'Y' and resid 264 through 271 removed outlier: 3.874A pdb=" N ILE Y 267 " --> pdb=" O PRO Y 264 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU Y 268 " --> pdb=" O GLN Y 265 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE Y 271 " --> pdb=" O LEU Y 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 8 through 35 removed outlier: 3.505A pdb=" N LEU Z 12 " --> pdb=" O ASN Z 8 " (cutoff:3.500A) Processing helix chain 'Z' and resid 44 through 100 removed outlier: 4.297A pdb=" N ASN Z 62 " --> pdb=" O ALA Z 58 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER Z 63 " --> pdb=" O SER Z 59 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL Z 64 " --> pdb=" O SER Z 60 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA Z 78 " --> pdb=" O THR Z 74 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR Z 84 " --> pdb=" O ALA Z 80 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP Z 87 " --> pdb=" O ASP Z 83 " (cutoff:3.500A) Processing helix chain 'Z' and resid 105 through 130 removed outlier: 3.646A pdb=" N ALA Z 130 " --> pdb=" O ALA Z 126 " (cutoff:3.500A) Processing helix chain 'Z' and resid 164 through 169 removed outlier: 3.859A pdb=" N GLY Z 169 " --> pdb=" O THR Z 166 " (cutoff:3.500A) Processing helix chain 'Z' and resid 178 through 233 removed outlier: 4.342A pdb=" N ALA Z 187 " --> pdb=" O LYS Z 183 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR Z 188 " --> pdb=" O THR Z 184 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP Z 222 " --> pdb=" O GLY Z 218 " (cutoff:3.500A) Processing helix chain 'Z' and resid 235 through 263 removed outlier: 3.811A pdb=" N ALA Z 241 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS Z 242 " --> pdb=" O LYS Z 238 " (cutoff:3.500A) Processing helix chain 'Z' and resid 264 through 271 removed outlier: 3.725A pdb=" N PHE Z 271 " --> pdb=" O LEU Z 268 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 35 removed outlier: 3.639A pdb=" N LEU a 12 " --> pdb=" O ASN a 8 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 99 removed outlier: 4.068A pdb=" N ASN a 62 " --> pdb=" O ALA a 58 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER a 63 " --> pdb=" O SER a 59 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL a 64 " --> pdb=" O SER a 60 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR a 84 " --> pdb=" O ALA a 80 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP a 87 " --> pdb=" O ASP a 83 " (cutoff:3.500A) Processing helix chain 'a' and resid 105 through 130 removed outlier: 3.504A pdb=" N GLN a 124 " --> pdb=" O ARG a 120 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN a 129 " --> pdb=" O LYS a 125 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA a 130 " --> pdb=" O ALA a 126 " (cutoff:3.500A) Processing helix chain 'a' and resid 178 through 233 removed outlier: 4.100A pdb=" N ALA a 187 " --> pdb=" O LYS a 183 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR a 188 " --> pdb=" O THR a 184 " (cutoff:3.500A) Processing helix chain 'a' and resid 235 through 263 removed outlier: 3.698A pdb=" N GLU a 239 " --> pdb=" O ASP a 235 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA a 241 " --> pdb=" O ALA a 237 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLN a 251 " --> pdb=" O GLN a 247 " (cutoff:3.500A) Processing helix chain 'a' and resid 264 through 271 removed outlier: 3.508A pdb=" N PHE a 271 " --> pdb=" O LEU a 268 " (cutoff:3.500A) Processing helix chain 'b' and resid 8 through 35 removed outlier: 4.031A pdb=" N LEU b 12 " --> pdb=" O ASN b 8 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 60 removed outlier: 3.744A pdb=" N SER b 60 " --> pdb=" O ALA b 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 60 through 100 removed outlier: 3.894A pdb=" N VAL b 64 " --> pdb=" O SER b 60 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL b 77 " --> pdb=" O SER b 73 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA b 78 " --> pdb=" O THR b 74 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP b 87 " --> pdb=" O ASP b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 105 through 129 Processing helix chain 'b' and resid 178 through 233 removed outlier: 3.811A pdb=" N ILE b 186 " --> pdb=" O ALA b 182 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA b 187 " --> pdb=" O LYS b 183 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR b 188 " --> pdb=" O THR b 184 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP b 222 " --> pdb=" O GLY b 218 " (cutoff:3.500A) Processing helix chain 'b' and resid 235 through 263 removed outlier: 4.285A pdb=" N ALA b 241 " --> pdb=" O ALA b 237 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS b 242 " --> pdb=" O LYS b 238 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN b 251 " --> pdb=" O GLN b 247 " (cutoff:3.500A) Processing helix chain 'b' and resid 264 through 271 Processing helix chain 'c' and resid 8 through 35 removed outlier: 3.631A pdb=" N LEU c 12 " --> pdb=" O ASN c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 60 removed outlier: 3.903A pdb=" N SER c 60 " --> pdb=" O ALA c 56 " (cutoff:3.500A) Processing helix chain 'c' and resid 60 through 99 removed outlier: 4.011A pdb=" N VAL c 64 " --> pdb=" O SER c 60 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR c 84 " --> pdb=" O ALA c 80 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP c 87 " --> pdb=" O ASP c 83 " (cutoff:3.500A) Processing helix chain 'c' and resid 105 through 129 removed outlier: 3.645A pdb=" N LYS c 125 " --> pdb=" O ASP c 121 " (cutoff:3.500A) Processing helix chain 'c' and resid 164 through 169 removed outlier: 3.638A pdb=" N GLY c 169 " --> pdb=" O THR c 166 " (cutoff:3.500A) Processing helix chain 'c' and resid 178 through 233 removed outlier: 4.094A pdb=" N ILE c 186 " --> pdb=" O ALA c 182 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA c 187 " --> pdb=" O LYS c 183 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR c 188 " --> pdb=" O THR c 184 " (cutoff:3.500A) Processing helix chain 'c' and resid 235 through 263 removed outlier: 4.308A pdb=" N ALA c 241 " --> pdb=" O ALA c 237 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS c 242 " --> pdb=" O LYS c 238 " (cutoff:3.500A) Processing helix chain 'c' and resid 264 through 271 removed outlier: 3.557A pdb=" N SER c 269 " --> pdb=" O THR c 266 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE c 271 " --> pdb=" O LEU c 268 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 35 removed outlier: 3.647A pdb=" N LEU d 12 " --> pdb=" O ASN d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 60 Processing helix chain 'd' and resid 61 through 99 removed outlier: 3.915A pdb=" N SER d 67 " --> pdb=" O SER d 63 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL d 77 " --> pdb=" O SER d 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA d 78 " --> pdb=" O THR d 74 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR d 84 " --> pdb=" O ALA d 80 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP d 87 " --> pdb=" O ASP d 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 129 removed outlier: 3.674A pdb=" N GLN d 124 " --> pdb=" O ARG d 120 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS d 125 " --> pdb=" O ASP d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 164 through 168 Processing helix chain 'd' and resid 178 through 233 removed outlier: 3.929A pdb=" N ILE d 186 " --> pdb=" O ALA d 182 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ALA d 187 " --> pdb=" O LYS d 183 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR d 188 " --> pdb=" O THR d 184 " (cutoff:3.500A) Processing helix chain 'd' and resid 235 through 263 removed outlier: 3.637A pdb=" N GLU d 239 " --> pdb=" O ASP d 235 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA d 241 " --> pdb=" O ALA d 237 " (cutoff:3.500A) Processing helix chain 'd' and resid 264 through 271 Processing helix chain 'e' and resid 8 through 35 removed outlier: 3.688A pdb=" N LEU e 12 " --> pdb=" O ASN e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 100 removed outlier: 4.589A pdb=" N ASN e 62 " --> pdb=" O ALA e 58 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N SER e 63 " --> pdb=" O SER e 59 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL e 64 " --> pdb=" O SER e 60 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA e 78 " --> pdb=" O THR e 74 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR e 84 " --> pdb=" O ALA e 80 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP e 87 " --> pdb=" O ASP e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 105 through 129 Processing helix chain 'e' and resid 164 through 169 Processing helix chain 'e' and resid 178 through 233 removed outlier: 4.602A pdb=" N ALA e 187 " --> pdb=" O LYS e 183 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR e 188 " --> pdb=" O THR e 184 " (cutoff:3.500A) Processing helix chain 'e' and resid 235 through 266 removed outlier: 4.230A pdb=" N ALA e 241 " --> pdb=" O ALA e 237 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS e 242 " --> pdb=" O LYS e 238 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN e 251 " --> pdb=" O GLN e 247 " (cutoff:3.500A) Proline residue: e 264 - end of helix Processing helix chain 'e' and resid 267 through 271 removed outlier: 3.589A pdb=" N PHE e 271 " --> pdb=" O LEU e 268 " (cutoff:3.500A) Processing helix chain 'f' and resid 8 through 35 removed outlier: 4.011A pdb=" N LEU f 12 " --> pdb=" O ASN f 8 " (cutoff:3.500A) Processing helix chain 'f' and resid 44 through 100 removed outlier: 4.508A pdb=" N ASN f 62 " --> pdb=" O ALA f 58 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N SER f 63 " --> pdb=" O SER f 59 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL f 64 " --> pdb=" O SER f 60 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR f 84 " --> pdb=" O ALA f 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP f 87 " --> pdb=" O ASP f 83 " (cutoff:3.500A) Processing helix chain 'f' and resid 105 through 129 Processing helix chain 'f' and resid 165 through 169 Processing helix chain 'f' and resid 178 through 233 removed outlier: 4.413A pdb=" N ALA f 187 " --> pdb=" O LYS f 183 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR f 188 " --> pdb=" O THR f 184 " (cutoff:3.500A) Processing helix chain 'f' and resid 235 through 263 removed outlier: 3.947A pdb=" N ALA f 241 " --> pdb=" O ALA f 237 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN f 251 " --> pdb=" O GLN f 247 " (cutoff:3.500A) Processing helix chain 'f' and resid 264 through 271 removed outlier: 3.567A pdb=" N PHE f 271 " --> pdb=" O LEU f 268 " (cutoff:3.500A) Processing helix chain 'g' and resid 8 through 35 removed outlier: 3.718A pdb=" N LEU g 12 " --> pdb=" O ASN g 8 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 61 Processing helix chain 'g' and resid 61 through 100 removed outlier: 3.542A pdb=" N SER g 67 " --> pdb=" O SER g 63 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR g 84 " --> pdb=" O ALA g 80 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP g 87 " --> pdb=" O ASP g 83 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER g 100 " --> pdb=" O ALA g 96 " (cutoff:3.500A) Processing helix chain 'g' and resid 105 through 129 Processing helix chain 'g' and resid 164 through 169 removed outlier: 3.520A pdb=" N GLY g 169 " --> pdb=" O THR g 166 " (cutoff:3.500A) Processing helix chain 'g' and resid 178 through 233 removed outlier: 4.292A pdb=" N ALA g 187 " --> pdb=" O LYS g 183 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR g 188 " --> pdb=" O THR g 184 " (cutoff:3.500A) Processing helix chain 'g' and resid 235 through 263 removed outlier: 3.911A pdb=" N ALA g 241 " --> pdb=" O ALA g 237 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN g 251 " --> pdb=" O GLN g 247 " (cutoff:3.500A) Processing helix chain 'g' and resid 264 through 271 Processing helix chain 'h' and resid 8 through 35 removed outlier: 4.021A pdb=" N LEU h 12 " --> pdb=" O ASN h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 44 through 60 removed outlier: 3.701A pdb=" N SER h 60 " --> pdb=" O ALA h 56 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 100 removed outlier: 3.951A pdb=" N THR h 84 " --> pdb=" O ALA h 80 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP h 87 " --> pdb=" O ASP h 83 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER h 100 " --> pdb=" O ALA h 96 " (cutoff:3.500A) Processing helix chain 'h' and resid 105 through 129 Processing helix chain 'h' and resid 164 through 169 removed outlier: 3.944A pdb=" N GLY h 169 " --> pdb=" O THR h 166 " (cutoff:3.500A) Processing helix chain 'h' and resid 178 through 233 removed outlier: 4.331A pdb=" N ALA h 187 " --> pdb=" O LYS h 183 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR h 188 " --> pdb=" O THR h 184 " (cutoff:3.500A) Processing helix chain 'h' and resid 235 through 263 removed outlier: 4.187A pdb=" N ALA h 241 " --> pdb=" O ALA h 237 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS h 242 " --> pdb=" O LYS h 238 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN h 251 " --> pdb=" O GLN h 247 " (cutoff:3.500A) Processing helix chain 'h' and resid 264 through 271 Processing helix chain 'i' and resid 8 through 35 removed outlier: 3.654A pdb=" N LEU i 12 " --> pdb=" O ASN i 8 " (cutoff:3.500A) Processing helix chain 'i' and resid 44 through 60 Processing helix chain 'i' and resid 60 through 101 removed outlier: 4.109A pdb=" N VAL i 64 " --> pdb=" O SER i 60 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR i 84 " --> pdb=" O ALA i 80 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP i 87 " --> pdb=" O ASP i 83 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP i 101 " --> pdb=" O LEU i 97 " (cutoff:3.500A) Processing helix chain 'i' and resid 105 through 129 removed outlier: 3.615A pdb=" N GLN i 124 " --> pdb=" O ARG i 120 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS i 125 " --> pdb=" O ASP i 121 " (cutoff:3.500A) Processing helix chain 'i' and resid 165 through 169 Processing helix chain 'i' and resid 178 through 233 removed outlier: 4.293A pdb=" N ALA i 187 " --> pdb=" O LYS i 183 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR i 188 " --> pdb=" O THR i 184 " (cutoff:3.500A) Processing helix chain 'i' and resid 235 through 263 removed outlier: 3.874A pdb=" N ALA i 241 " --> pdb=" O ALA i 237 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN i 251 " --> pdb=" O GLN i 247 " (cutoff:3.500A) Processing helix chain 'i' and resid 264 through 271 Processing helix chain 'j' and resid 8 through 35 removed outlier: 3.574A pdb=" N LEU j 12 " --> pdb=" O ASN j 8 " (cutoff:3.500A) Processing helix chain 'j' and resid 44 through 100 removed outlier: 4.413A pdb=" N ASN j 62 " --> pdb=" O ALA j 58 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N SER j 63 " --> pdb=" O SER j 59 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL j 64 " --> pdb=" O SER j 60 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR j 84 " --> pdb=" O ALA j 80 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP j 87 " --> pdb=" O ASP j 83 " (cutoff:3.500A) Processing helix chain 'j' and resid 105 through 129 Processing helix chain 'j' and resid 164 through 169 removed outlier: 3.699A pdb=" N GLY j 169 " --> pdb=" O THR j 166 " (cutoff:3.500A) Processing helix chain 'j' and resid 178 through 233 removed outlier: 3.866A pdb=" N ALA j 187 " --> pdb=" O LYS j 183 " (cutoff:3.500A) Processing helix chain 'j' and resid 235 through 263 removed outlier: 4.010A pdb=" N ALA j 241 " --> pdb=" O ALA j 237 " (cutoff:3.500A) Processing helix chain 'j' and resid 264 through 271 Processing helix chain 'k' and resid 8 through 35 Processing helix chain 'k' and resid 44 through 100 removed outlier: 3.778A pdb=" N LEU k 61 " --> pdb=" O THR k 57 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN k 62 " --> pdb=" O ALA k 58 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER k 63 " --> pdb=" O SER k 59 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL k 64 " --> pdb=" O SER k 60 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL k 77 " --> pdb=" O SER k 73 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA k 78 " --> pdb=" O THR k 74 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR k 84 " --> pdb=" O ALA k 80 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP k 87 " --> pdb=" O ASP k 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 105 through 129 Processing helix chain 'k' and resid 178 through 233 removed outlier: 4.084A pdb=" N ALA k 187 " --> pdb=" O LYS k 183 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR k 188 " --> pdb=" O THR k 184 " (cutoff:3.500A) Processing helix chain 'k' and resid 235 through 263 removed outlier: 4.275A pdb=" N ALA k 241 " --> pdb=" O ALA k 237 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS k 242 " --> pdb=" O LYS k 238 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN k 251 " --> pdb=" O GLN k 247 " (cutoff:3.500A) Processing helix chain 'k' and resid 264 through 271 removed outlier: 3.575A pdb=" N ILE k 267 " --> pdb=" O PRO k 264 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER k 269 " --> pdb=" O THR k 266 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE k 271 " --> pdb=" O LEU k 268 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 148 Processing sheet with id=AA2, first strand: chain 'B' and resid 144 through 148 Processing sheet with id=AA3, first strand: chain 'C' and resid 144 through 148 Processing sheet with id=AA4, first strand: chain 'D' and resid 144 through 148 Processing sheet with id=AA5, first strand: chain 'E' and resid 144 through 148 Processing sheet with id=AA6, first strand: chain 'F' and resid 144 through 148 Processing sheet with id=AA7, first strand: chain 'G' and resid 144 through 148 Processing sheet with id=AA8, first strand: chain 'H' and resid 144 through 148 removed outlier: 3.696A pdb=" N PHE H 147 " --> pdb=" O PHE H 156 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 144 through 148 Processing sheet with id=AB1, first strand: chain 'J' and resid 144 through 148 Processing sheet with id=AB2, first strand: chain 'K' and resid 144 through 148 Processing sheet with id=AB3, first strand: chain 'L' and resid 144 through 148 removed outlier: 3.557A pdb=" N LEU L 145 " --> pdb=" O VAL L 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 144 through 148 Processing sheet with id=AB5, first strand: chain 'N' and resid 144 through 148 Processing sheet with id=AB6, first strand: chain 'O' and resid 144 through 148 Processing sheet with id=AB7, first strand: chain 'P' and resid 144 through 148 Processing sheet with id=AB8, first strand: chain 'R' and resid 131 through 132 Processing sheet with id=AB9, first strand: chain 'R' and resid 144 through 148 Processing sheet with id=AC1, first strand: chain 'S' and resid 144 through 148 Processing sheet with id=AC2, first strand: chain 'T' and resid 144 through 148 Processing sheet with id=AC3, first strand: chain 'U' and resid 131 through 132 Processing sheet with id=AC4, first strand: chain 'U' and resid 144 through 148 Processing sheet with id=AC5, first strand: chain 'V' and resid 144 through 148 removed outlier: 3.758A pdb=" N PHE V 147 " --> pdb=" O PHE V 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'W' and resid 144 through 148 removed outlier: 3.538A pdb=" N PHE W 147 " --> pdb=" O PHE W 156 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'X' and resid 144 through 148 Processing sheet with id=AC8, first strand: chain 'Y' and resid 144 through 148 removed outlier: 3.825A pdb=" N PHE Y 147 " --> pdb=" O PHE Y 156 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Z' and resid 144 through 148 removed outlier: 3.561A pdb=" N PHE Z 147 " --> pdb=" O PHE Z 156 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'a' and resid 144 through 148 Processing sheet with id=AD2, first strand: chain 'b' and resid 144 through 148 Processing sheet with id=AD3, first strand: chain 'c' and resid 144 through 145 Processing sheet with id=AD4, first strand: chain 'd' and resid 144 through 145 Processing sheet with id=AD5, first strand: chain 'e' and resid 144 through 148 Processing sheet with id=AD6, first strand: chain 'f' and resid 144 through 148 Processing sheet with id=AD7, first strand: chain 'g' and resid 144 through 148 Processing sheet with id=AD8, first strand: chain 'h' and resid 144 through 145 Processing sheet with id=AD9, first strand: chain 'i' and resid 144 through 148 Processing sheet with id=AE1, first strand: chain 'j' and resid 144 through 148 Processing sheet with id=AE2, first strand: chain 'k' and resid 144 through 148 removed outlier: 3.518A pdb=" N PHE k 147 " --> pdb=" O PHE k 156 " (cutoff:3.500A) 6398 hydrogen bonds defined for protein. 18558 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: 28.44 Time building geometry restraints manager: 16.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 17005 1.33 - 1.45: 13224 1.45 - 1.58: 42291 1.58 - 1.70: 0 1.70 - 1.82: 296 Bond restraints: 72816 Sorted by residual: bond pdb=" N VAL R 232 " pdb=" CA VAL R 232 " ideal model delta sigma weight residual 1.460 1.503 -0.043 1.21e-02 6.83e+03 1.29e+01 bond pdb=" N VAL c 232 " pdb=" CA VAL c 232 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.11e+01 bond pdb=" N ASP R 233 " pdb=" CA ASP R 233 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.27e-02 6.20e+03 8.61e+00 bond pdb=" N ASP T 115 " pdb=" CA ASP T 115 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 6.99e+00 bond pdb=" N LEU R 231 " pdb=" CA LEU R 231 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.28e+00 ... (remaining 72811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 96798 1.84 - 3.69: 1635 3.69 - 5.53: 268 5.53 - 7.38: 39 7.38 - 9.22: 13 Bond angle restraints: 98753 Sorted by residual: angle pdb=" C LEU a 231 " pdb=" N VAL a 232 " pdb=" CA VAL a 232 " ideal model delta sigma weight residual 122.66 118.89 3.77 9.70e-01 1.06e+00 1.51e+01 angle pdb=" C ASN f 8 " pdb=" CA ASN f 8 " pdb=" CB ASN f 8 " ideal model delta sigma weight residual 110.02 115.79 -5.77 1.50e+00 4.44e-01 1.48e+01 angle pdb=" C ALA R 234 " pdb=" N ASP R 235 " pdb=" CA ASP R 235 " ideal model delta sigma weight residual 120.82 115.68 5.14 1.41e+00 5.03e-01 1.33e+01 angle pdb=" C LEU F 231 " pdb=" N VAL F 232 " pdb=" CA VAL F 232 " ideal model delta sigma weight residual 122.77 118.96 3.81 1.05e+00 9.07e-01 1.31e+01 angle pdb=" CA GLU c 117 " pdb=" CB GLU c 117 " pdb=" CG GLU c 117 " ideal model delta sigma weight residual 114.10 121.09 -6.99 2.00e+00 2.50e-01 1.22e+01 ... (remaining 98748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 40729 17.91 - 35.82: 3169 35.82 - 53.72: 479 53.72 - 71.63: 121 71.63 - 89.54: 87 Dihedral angle restraints: 44585 sinusoidal: 15910 harmonic: 28675 Sorted by residual: dihedral pdb=" CA GLU N 151 " pdb=" C GLU N 151 " pdb=" N ASP N 152 " pdb=" CA ASP N 152 " ideal model delta harmonic sigma weight residual 180.00 -155.92 -24.08 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA ASN S 155 " pdb=" C ASN S 155 " pdb=" N PHE S 156 " pdb=" CA PHE S 156 " ideal model delta harmonic sigma weight residual 180.00 157.23 22.77 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA ASN M 155 " pdb=" C ASN M 155 " pdb=" N PHE M 156 " pdb=" CA PHE M 156 " ideal model delta harmonic sigma weight residual 180.00 157.82 22.18 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 44582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 10937 0.052 - 0.105: 1693 0.105 - 0.157: 153 0.157 - 0.210: 16 0.210 - 0.262: 3 Chirality restraints: 12802 Sorted by residual: chirality pdb=" CA THR a 263 " pdb=" N THR a 263 " pdb=" C THR a 263 " pdb=" CB THR a 263 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB ILE T 85 " pdb=" CA ILE T 85 " pdb=" CG1 ILE T 85 " pdb=" CG2 ILE T 85 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB VAL R 232 " pdb=" CA VAL R 232 " pdb=" CG1 VAL R 232 " pdb=" CG2 VAL R 232 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 12799 not shown) Planarity restraints: 12617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP T 48 " -0.031 2.00e-02 2.50e+03 2.34e-02 1.36e+01 pdb=" CG TRP T 48 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP T 48 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP T 48 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP T 48 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP T 48 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP T 48 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP T 48 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP T 48 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP T 48 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN f 8 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.41e+00 pdb=" C ASN f 8 " -0.044 2.00e-02 2.50e+03 pdb=" O ASN f 8 " 0.016 2.00e-02 2.50e+03 pdb=" N PRO f 9 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN P 8 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO P 9 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO P 9 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO P 9 " -0.029 5.00e-02 4.00e+02 ... (remaining 12614 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 845 2.60 - 3.18: 67911 3.18 - 3.75: 120895 3.75 - 4.33: 158011 4.33 - 4.90: 262693 Nonbonded interactions: 610355 Sorted by model distance: nonbonded pdb=" OG SER f 245 " pdb=" O ILE i 5 " model vdw 2.027 3.040 nonbonded pdb=" OG SER f 4 " pdb=" OD2 ASP g 233 " model vdw 2.079 3.040 nonbonded pdb=" OG SER f 136 " pdb=" OD1 ASP f 139 " model vdw 2.083 3.040 nonbonded pdb=" OG SER D 4 " pdb=" O THR D 7 " model vdw 2.115 3.040 nonbonded pdb=" OE1 GLU h 117 " pdb=" NH2 ARG h 120 " model vdw 2.121 3.120 ... (remaining 610350 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' } 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: 14.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 2.140 Check model and map are aligned: 0.410 Set scattering table: 0.490 Process input model: 124.590 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.850 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: 0.020 Load rotamer database and sin/cos tables:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 0.003 0.055 72816 Z= 0.196 Angle : 0.632 9.224 98753 Z= 0.355 Chirality : 0.037 0.262 12802 Planarity : 0.004 0.052 12617 Dihedral : 13.863 89.541 25863 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.55 % Favored : 98.37 % Rotamer: Outliers : 0.08 % Allowed : 0.38 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.07), residues: 9916 helix: -0.26 (0.04), residues: 7363 sheet: -3.57 (0.22), residues: 370 loop : 1.66 (0.15), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP T 48 HIS 0.005 0.001 HIS Q 213 PHE 0.026 0.001 PHE J 156 ARG 0.007 0.001 ARG e 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1361 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1355 time to evaluate : 6.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ASP cc_start: 0.8213 (m-30) cc_final: 0.7904 (m-30) REVERT: B 233 ASP cc_start: 0.8364 (m-30) cc_final: 0.8163 (m-30) REVERT: G 8 ASN cc_start: 0.8642 (p0) cc_final: 0.8389 (p0) REVERT: G 50 MET cc_start: 0.9078 (mtp) cc_final: 0.8862 (mtp) REVERT: H 242 LYS cc_start: 0.8704 (tppt) cc_final: 0.8432 (tppt) REVERT: I 128 THR cc_start: 0.8724 (t) cc_final: 0.8466 (m) REVERT: J 254 VAL cc_start: 0.7720 (p) cc_final: 0.7188 (t) REVERT: K 83 ASP cc_start: 0.7109 (m-30) cc_final: 0.6905 (m-30) REVERT: K 117 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8656 (mt-10) REVERT: K 201 SER cc_start: 0.8766 (t) cc_final: 0.8375 (m) REVERT: K 252 LEU cc_start: 0.8635 (mm) cc_final: 0.8146 (tt) REVERT: K 270 LEU cc_start: 0.7778 (mt) cc_final: 0.7536 (tt) REVERT: L 116 PHE cc_start: 0.6797 (t80) cc_final: 0.6550 (t80) REVERT: L 117 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7355 (mm-30) REVERT: L 219 LYS cc_start: 0.7695 (mttp) cc_final: 0.7211 (tppt) REVERT: N 117 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7281 (mp0) REVERT: O 94 GLU cc_start: 0.5920 (mm-30) cc_final: 0.5121 (tt0) REVERT: P 15 LEU cc_start: 0.8114 (mt) cc_final: 0.7419 (tp) REVERT: P 201 SER cc_start: 0.9252 (t) cc_final: 0.9042 (p) REVERT: Q 175 THR cc_start: 0.8062 (t) cc_final: 0.7737 (m) REVERT: Q 262 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7802 (pp30) REVERT: R 94 GLU cc_start: 0.5613 (mm-30) cc_final: 0.4652 (mt-10) REVERT: S 122 GLN cc_start: 0.8718 (mt0) cc_final: 0.8021 (tp-100) REVERT: S 141 SER cc_start: 0.9007 (t) cc_final: 0.8677 (m) REVERT: W 17 ASN cc_start: 0.7401 (m-40) cc_final: 0.6916 (m110) REVERT: W 122 GLN cc_start: 0.8197 (mp10) cc_final: 0.7558 (mp10) REVERT: W 238 LYS cc_start: 0.6741 (mtpt) cc_final: 0.6231 (mptt) REVERT: X 42 LYS cc_start: 0.5285 (tptt) cc_final: 0.4673 (tppt) REVERT: Y 20 SER cc_start: 0.8617 (t) cc_final: 0.8199 (p) REVERT: Z 37 LYS cc_start: 0.7732 (mmtt) cc_final: 0.7262 (mptt) REVERT: Z 251 GLN cc_start: 0.8303 (mp10) cc_final: 0.7937 (mp10) REVERT: a 13 LEU cc_start: 0.7857 (mt) cc_final: 0.7467 (mt) REVERT: a 151 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6707 (tp30) REVERT: b 36 LYS cc_start: 0.7313 (mtpt) cc_final: 0.6702 (mmtt) REVERT: c 31 ARG cc_start: 0.8343 (mtm-85) cc_final: 0.8129 (mtm-85) REVERT: c 238 LYS cc_start: 0.8197 (ttmm) cc_final: 0.7994 (mttp) REVERT: f 84 THR cc_start: 0.8381 (m) cc_final: 0.8180 (m) REVERT: f 262 GLN cc_start: 0.8025 (tp40) cc_final: 0.7811 (tp40) REVERT: i 185 MET cc_start: 0.8123 (tpp) cc_final: 0.7717 (tpp) REVERT: j 2 LEU cc_start: 0.8703 (mp) cc_final: 0.8068 (tt) REVERT: j 115 ASP cc_start: 0.8260 (t70) cc_final: 0.8056 (t0) REVERT: j 262 GLN cc_start: 0.7849 (mt0) cc_final: 0.7573 (tp40) REVERT: k 94 GLU cc_start: 0.8699 (tp30) cc_final: 0.8374 (tp30) REVERT: k 194 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8239 (tp40) outliers start: 6 outliers final: 2 residues processed: 1359 average time/residue: 0.6016 time to fit residues: 1454.7406 Evaluate side-chains 1047 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1045 time to evaluate : 5.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain c residue 231 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 843 optimal weight: 4.9990 chunk 757 optimal weight: 4.9990 chunk 420 optimal weight: 9.9990 chunk 258 optimal weight: 10.0000 chunk 510 optimal weight: 5.9990 chunk 404 optimal weight: 4.9990 chunk 783 optimal weight: 6.9990 chunk 303 optimal weight: 9.9990 chunk 476 optimal weight: 6.9990 chunk 582 optimal weight: 9.9990 chunk 907 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN B 213 HIS C 6 ASN ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN D 230 ASN ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 ASN F 262 GLN G 29 GLN ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 GLN H 150 ASN I 247 GLN J 29 GLN ** J 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 251 GLN ** J 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 133 ASN K 155 ASN K 194 GLN K 198 ASN ** L 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 GLN M 198 ASN M 262 GLN N 3 ASN ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 194 GLN ** O 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 44 ASN ** P 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 29 GLN ** Q 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 155 ASN Q 255 GLN R 122 GLN S 22 ASN ** S 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 3 ASN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 122 GLN V 155 ASN W 29 GLN W 129 ASN X 262 GLN Y 6 ASN ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN ** Y 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 3 ASN Z 44 ASN a 122 GLN a 129 ASN ** b 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 150 ASN c 6 ASN ** c 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 124 GLN c 133 ASN d 6 ASN d 105 ASN d 250 GLN e 261 ASN ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 198 ASN h 129 ASN i 29 GLN i 72 GLN i 250 GLN j 230 ASN k 72 GLN k 110 ASN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.110620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.099811 restraints weight = 146927.499| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.02 r_work: 0.3420 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 72816 Z= 0.456 Angle : 0.691 11.014 98753 Z= 0.368 Chirality : 0.042 0.234 12802 Planarity : 0.004 0.055 12617 Dihedral : 4.567 46.714 10068 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.71 % Allowed : 8.61 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.08), residues: 9916 helix: 1.97 (0.06), residues: 7289 sheet: -3.31 (0.23), residues: 370 loop : 0.68 (0.14), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP T 48 HIS 0.007 0.002 HIS E 213 PHE 0.027 0.003 PHE b 109 ARG 0.007 0.001 ARG T 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 1013 time to evaluate : 6.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ASP cc_start: 0.8164 (m-30) cc_final: 0.7850 (m-30) REVERT: G 50 MET cc_start: 0.9110 (mtp) cc_final: 0.8764 (mtp) REVERT: G 267 ILE cc_start: 0.8779 (mm) cc_final: 0.8430 (mm) REVERT: H 242 LYS cc_start: 0.8927 (tppt) cc_final: 0.8538 (tppt) REVERT: K 31 ARG cc_start: 0.8706 (ttm-80) cc_final: 0.8406 (ttm-80) REVERT: K 252 LEU cc_start: 0.8716 (mm) cc_final: 0.8110 (tt) REVERT: K 270 LEU cc_start: 0.7709 (mt) cc_final: 0.7451 (tt) REVERT: L 219 LYS cc_start: 0.7880 (mttp) cc_final: 0.7205 (tppt) REVERT: N 115 ASP cc_start: 0.8235 (t0) cc_final: 0.8031 (t0) REVERT: P 201 SER cc_start: 0.9486 (t) cc_final: 0.9230 (p) REVERT: Q 230 ASN cc_start: 0.7757 (m-40) cc_final: 0.7364 (m-40) REVERT: Q 262 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7977 (pp30) REVERT: R 94 GLU cc_start: 0.5629 (mm-30) cc_final: 0.4613 (mt-10) REVERT: R 211 ASP cc_start: 0.8027 (m-30) cc_final: 0.7821 (m-30) REVERT: T 267 ILE cc_start: 0.8283 (mm) cc_final: 0.8050 (mt) REVERT: U 69 GLN cc_start: 0.8089 (tp40) cc_final: 0.7824 (tp40) REVERT: W 238 LYS cc_start: 0.7157 (mtpt) cc_final: 0.6523 (mptt) REVERT: W 239 GLU cc_start: 0.8450 (tp30) cc_final: 0.8146 (tp30) REVERT: X 38 VAL cc_start: 0.7524 (m) cc_final: 0.7154 (t) REVERT: X 42 LYS cc_start: 0.5173 (tptt) cc_final: 0.4427 (tppt) REVERT: Z 37 LYS cc_start: 0.7659 (mmtt) cc_final: 0.6857 (mptt) REVERT: Z 76 ASP cc_start: 0.7817 (t0) cc_final: 0.7615 (t0) REVERT: Z 251 GLN cc_start: 0.8347 (mp10) cc_final: 0.7863 (mp10) REVERT: a 255 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8394 (tp40) REVERT: c 117 GLU cc_start: 0.8149 (mp0) cc_final: 0.7739 (mp0) REVERT: i 185 MET cc_start: 0.8110 (tpp) cc_final: 0.7571 (tpp) REVERT: j 115 ASP cc_start: 0.8520 (t70) cc_final: 0.8107 (t0) REVERT: k 194 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8378 (mm-40) outliers start: 137 outliers final: 96 residues processed: 1099 average time/residue: 0.6160 time to fit residues: 1205.1973 Evaluate side-chains 1018 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 922 time to evaluate : 6.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain F residue 250 GLN Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain J residue 69 GLN Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 163 LEU Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 165 LEU Chi-restraints excluded: chain Q residue 255 GLN Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain R residue 15 LEU Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain T residue 135 VAL Chi-restraints excluded: chain V residue 47 ILE Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain X residue 266 THR Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 128 THR Chi-restraints excluded: chain Y residue 173 THR Chi-restraints excluded: chain Y residue 248 THR Chi-restraints excluded: chain Y residue 252 LEU Chi-restraints excluded: chain Y residue 259 ILE Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain Z residue 100 SER Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 232 VAL Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 87 ASP Chi-restraints excluded: chain a residue 261 ASN Chi-restraints excluded: chain b residue 32 ILE Chi-restraints excluded: chain b residue 177 THR Chi-restraints excluded: chain b residue 217 VAL Chi-restraints excluded: chain b residue 228 VAL Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain d residue 32 ILE Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain d residue 265 GLN Chi-restraints excluded: chain e residue 171 THR Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 265 GLN Chi-restraints excluded: chain e residue 270 LEU Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain g residue 4 SER Chi-restraints excluded: chain g residue 268 LEU Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 185 MET Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 265 GLN Chi-restraints excluded: chain h residue 266 THR Chi-restraints excluded: chain h residue 267 ILE Chi-restraints excluded: chain i residue 2 LEU Chi-restraints excluded: chain i residue 72 GLN Chi-restraints excluded: chain i residue 101 ASP Chi-restraints excluded: chain i residue 171 THR Chi-restraints excluded: chain j residue 263 THR Chi-restraints excluded: chain k residue 2 LEU Chi-restraints excluded: chain k residue 5 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 442 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 877 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 403 optimal weight: 0.9980 chunk 912 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 873 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 283 optimal weight: 0.2980 chunk 687 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 ASN ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 ASN F 262 GLN ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 124 GLN J 29 GLN J 62 ASN ** J 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 ASN L 124 GLN L 250 GLN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 262 GLN N 29 GLN N 124 GLN N 150 ASN O 6 ASN O 17 ASN ** O 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 29 GLN ** Q 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 198 ASN S 54 GLN ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 198 ASN U 29 GLN V 3 ASN V 29 GLN W 29 GLN ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 133 ASN Y 250 GLN Z 3 ASN b 17 ASN b 124 GLN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 122 GLN ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 54 GLN i 124 GLN i 250 GLN j 16 GLN ** k 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.116529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.105542 restraints weight = 143538.216| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.05 r_work: 0.3511 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 72816 Z= 0.159 Angle : 0.481 9.720 98753 Z= 0.261 Chirality : 0.034 0.219 12802 Planarity : 0.003 0.047 12617 Dihedral : 4.028 24.048 10066 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.18 % Allowed : 10.80 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.08), residues: 9916 helix: 2.90 (0.06), residues: 7400 sheet: -2.95 (0.24), residues: 370 loop : 0.27 (0.14), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP T 48 HIS 0.003 0.001 HIS X 213 PHE 0.016 0.001 PHE X 216 ARG 0.004 0.001 ARG L 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1306 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 1212 time to evaluate : 6.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.9036 (mmm) cc_final: 0.8786 (mmm) REVERT: C 139 ASP cc_start: 0.7929 (t0) cc_final: 0.7701 (t0) REVERT: F 242 LYS cc_start: 0.8292 (tttt) cc_final: 0.8065 (mtpp) REVERT: G 50 MET cc_start: 0.9010 (mtp) cc_final: 0.8787 (mtp) REVERT: G 267 ILE cc_start: 0.8603 (mm) cc_final: 0.8232 (mm) REVERT: H 242 LYS cc_start: 0.8841 (tppt) cc_final: 0.8479 (tppt) REVERT: I 76 ASP cc_start: 0.7771 (m-30) cc_final: 0.7489 (m-30) REVERT: I 97 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8146 (tt) REVERT: K 31 ARG cc_start: 0.8747 (ttm-80) cc_final: 0.8543 (ttm-80) REVERT: K 252 LEU cc_start: 0.8706 (mm) cc_final: 0.8062 (tt) REVERT: L 87 ASP cc_start: 0.8581 (m-30) cc_final: 0.8263 (m-30) REVERT: L 219 LYS cc_start: 0.7892 (mttp) cc_final: 0.7211 (tppt) REVERT: N 37 LYS cc_start: 0.8497 (ptpt) cc_final: 0.8244 (ptpt) REVERT: O 161 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7460 (mm-40) REVERT: P 185 MET cc_start: 0.9323 (tpp) cc_final: 0.9061 (tpp) REVERT: P 201 SER cc_start: 0.9439 (t) cc_final: 0.9194 (p) REVERT: Q 230 ASN cc_start: 0.7804 (m-40) cc_final: 0.7465 (m-40) REVERT: Q 262 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7721 (pp30) REVERT: R 43 ASP cc_start: 0.8098 (m-30) cc_final: 0.7829 (m-30) REVERT: R 94 GLU cc_start: 0.5579 (mm-30) cc_final: 0.4627 (mt-10) REVERT: S 122 GLN cc_start: 0.8569 (mt0) cc_final: 0.7895 (tp-100) REVERT: U 32 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7563 (mp) REVERT: W 17 ASN cc_start: 0.7397 (m-40) cc_final: 0.6880 (m110) REVERT: W 31 ARG cc_start: 0.8128 (ttm110) cc_final: 0.7852 (ttm110) REVERT: W 238 LYS cc_start: 0.6899 (mtpt) cc_final: 0.6299 (mptt) REVERT: X 38 VAL cc_start: 0.7172 (m) cc_final: 0.6700 (t) REVERT: X 42 LYS cc_start: 0.5071 (tptt) cc_final: 0.4427 (tppt) REVERT: X 230 ASN cc_start: 0.8436 (m-40) cc_final: 0.7782 (m-40) REVERT: Y 20 SER cc_start: 0.8758 (t) cc_final: 0.8190 (p) REVERT: Y 48 TRP cc_start: 0.7450 (t60) cc_final: 0.7191 (t60) REVERT: Y 133 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.7979 (t0) REVERT: Y 222 ASP cc_start: 0.6983 (t0) cc_final: 0.6505 (p0) REVERT: Z 37 LYS cc_start: 0.7508 (mmtt) cc_final: 0.6928 (mptt) REVERT: Z 244 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8095 (mp10) REVERT: Z 251 GLN cc_start: 0.8224 (mp10) cc_final: 0.7582 (mp10) REVERT: b 101 ASP cc_start: 0.8127 (t0) cc_final: 0.7841 (t70) REVERT: c 238 LYS cc_start: 0.8421 (ttmm) cc_final: 0.7848 (tptt) REVERT: h 255 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7072 (mp10) REVERT: i 185 MET cc_start: 0.8108 (tpp) cc_final: 0.7839 (tpp) REVERT: j 2 LEU cc_start: 0.8684 (mp) cc_final: 0.7953 (tt) REVERT: j 115 ASP cc_start: 0.8478 (t70) cc_final: 0.8269 (t0) REVERT: j 262 GLN cc_start: 0.7911 (mt0) cc_final: 0.7598 (tm-30) REVERT: k 94 GLU cc_start: 0.8558 (tp30) cc_final: 0.8271 (tp30) REVERT: k 117 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7770 (mt-10) outliers start: 94 outliers final: 48 residues processed: 1265 average time/residue: 0.6037 time to fit residues: 1362.2952 Evaluate side-chains 1072 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 1018 time to evaluate : 6.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain F residue 129 ASN Chi-restraints excluded: chain F residue 250 GLN Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 265 GLN Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 163 LEU Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain W residue 15 LEU Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 133 ASN Chi-restraints excluded: chain Y residue 252 LEU Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain Z residue 244 GLN Chi-restraints excluded: chain a residue 261 ASN Chi-restraints excluded: chain b residue 32 ILE Chi-restraints excluded: chain d residue 105 ASN Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 265 GLN Chi-restraints excluded: chain e residue 270 LEU Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain h residue 255 GLN Chi-restraints excluded: chain h residue 265 GLN Chi-restraints excluded: chain h residue 266 THR Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 117 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 923 optimal weight: 3.9990 chunk 739 optimal weight: 0.9990 chunk 887 optimal weight: 6.9990 chunk 962 optimal weight: 0.7980 chunk 395 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 790 optimal weight: 5.9990 chunk 404 optimal weight: 0.9980 chunk 605 optimal weight: 7.9990 chunk 737 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 133 ASN I 69 GLN I 247 GLN ** J 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 ASN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 262 GLN N 29 GLN N 150 ASN O 17 ASN O 29 GLN O 129 ASN O 155 ASN O 251 GLN ** Q 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 54 GLN ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 GLN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 29 GLN W 122 GLN X 150 ASN ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 265 GLN b 40 ASN b 124 GLN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 247 GLN i 124 GLN ** i 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 161 GLN i 250 GLN ** i 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.116384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.105402 restraints weight = 143407.247| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.04 r_work: 0.3508 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 72816 Z= 0.168 Angle : 0.477 8.964 98753 Z= 0.258 Chirality : 0.034 0.214 12802 Planarity : 0.002 0.039 12617 Dihedral : 3.885 23.615 10064 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.49 % Allowed : 12.27 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.09), residues: 9916 helix: 3.22 (0.06), residues: 7363 sheet: -2.68 (0.24), residues: 370 loop : 0.33 (0.14), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP T 48 HIS 0.003 0.001 HIS Q 213 PHE 0.024 0.001 PHE b 109 ARG 0.008 0.000 ARG a 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1256 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 1137 time to evaluate : 6.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.9018 (mmm) cc_final: 0.8716 (mmm) REVERT: E 210 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7992 (mp) REVERT: G 50 MET cc_start: 0.8977 (mtp) cc_final: 0.8727 (mtp) REVERT: G 119 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8754 (mp) REVERT: G 267 ILE cc_start: 0.8586 (mm) cc_final: 0.8220 (mm) REVERT: H 242 LYS cc_start: 0.8854 (tppt) cc_final: 0.8499 (tppt) REVERT: I 76 ASP cc_start: 0.7801 (m-30) cc_final: 0.7504 (m-30) REVERT: I 97 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8141 (tt) REVERT: K 31 ARG cc_start: 0.8721 (ttm-80) cc_final: 0.8506 (ttm-80) REVERT: K 252 LEU cc_start: 0.8734 (mm) cc_final: 0.8081 (tt) REVERT: L 15 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7271 (tt) REVERT: L 87 ASP cc_start: 0.8581 (m-30) cc_final: 0.8276 (m-30) REVERT: L 219 LYS cc_start: 0.7917 (mttp) cc_final: 0.7291 (tppt) REVERT: N 37 LYS cc_start: 0.8503 (ptpt) cc_final: 0.8266 (ptpt) REVERT: N 150 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7754 (m-40) REVERT: O 161 GLN cc_start: 0.8315 (mm-40) cc_final: 0.7493 (mm-40) REVERT: P 15 LEU cc_start: 0.8295 (mt) cc_final: 0.7657 (tp) REVERT: P 185 MET cc_start: 0.9362 (tpp) cc_final: 0.9084 (tpp) REVERT: P 201 SER cc_start: 0.9447 (t) cc_final: 0.9215 (p) REVERT: P 255 GLN cc_start: 0.8225 (tt0) cc_final: 0.8015 (tt0) REVERT: Q 230 ASN cc_start: 0.7610 (m-40) cc_final: 0.7210 (m-40) REVERT: Q 233 ASP cc_start: 0.8172 (m-30) cc_final: 0.7908 (m-30) REVERT: Q 262 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7677 (pp30) REVERT: R 94 GLU cc_start: 0.5577 (mm-30) cc_final: 0.4707 (mt-10) REVERT: T 210 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8248 (mp) REVERT: U 32 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7533 (mp) REVERT: U 235 ASP cc_start: 0.7454 (t0) cc_final: 0.7121 (t70) REVERT: W 175 THR cc_start: 0.8281 (t) cc_final: 0.8057 (m) REVERT: W 238 LYS cc_start: 0.7074 (mtpt) cc_final: 0.6425 (mptt) REVERT: X 42 LYS cc_start: 0.5171 (tptt) cc_final: 0.4479 (tppt) REVERT: Y 48 TRP cc_start: 0.7475 (t60) cc_final: 0.7247 (t60) REVERT: Y 93 LYS cc_start: 0.7741 (mtmt) cc_final: 0.6828 (mmtm) REVERT: Y 94 GLU cc_start: 0.7643 (mp0) cc_final: 0.7086 (tt0) REVERT: Y 222 ASP cc_start: 0.7022 (t0) cc_final: 0.6486 (p0) REVERT: Z 37 LYS cc_start: 0.7550 (mmtt) cc_final: 0.7040 (mptt) REVERT: Z 244 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8053 (mp10) REVERT: Z 251 GLN cc_start: 0.8210 (mp10) cc_final: 0.7657 (mp10) REVERT: b 54 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8099 (mp10) REVERT: b 101 ASP cc_start: 0.8103 (t0) cc_final: 0.7691 (t70) REVERT: b 185 MET cc_start: 0.7967 (tpt) cc_final: 0.7538 (tpp) REVERT: c 265 GLN cc_start: 0.8567 (tt0) cc_final: 0.8341 (pt0) REVERT: h 53 MET cc_start: 0.8403 (mmm) cc_final: 0.8125 (mmt) REVERT: h 255 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6903 (mp10) REVERT: i 185 MET cc_start: 0.8071 (tpp) cc_final: 0.7769 (tpp) REVERT: j 2 LEU cc_start: 0.8646 (mp) cc_final: 0.7916 (tt) REVERT: j 115 ASP cc_start: 0.8524 (t70) cc_final: 0.8085 (t0) REVERT: j 262 GLN cc_start: 0.7918 (mt0) cc_final: 0.7617 (tm-30) outliers start: 119 outliers final: 63 residues processed: 1215 average time/residue: 0.5937 time to fit residues: 1289.5672 Evaluate side-chains 1091 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 1019 time to evaluate : 6.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 250 GLN Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 163 LEU Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 150 ASN Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 210 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain T residue 210 LEU Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain V residue 92 MET Chi-restraints excluded: chain W residue 15 LEU Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 238 LYS Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 252 LEU Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain Z residue 244 GLN Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain a residue 261 ASN Chi-restraints excluded: chain b residue 32 ILE Chi-restraints excluded: chain c residue 92 MET Chi-restraints excluded: chain d residue 105 ASN Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 265 GLN Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 171 THR Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 265 GLN Chi-restraints excluded: chain e residue 270 LEU Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 255 GLN Chi-restraints excluded: chain h residue 265 GLN Chi-restraints excluded: chain h residue 266 THR Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 267 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 93 optimal weight: 2.9990 chunk 358 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 659 optimal weight: 2.9990 chunk 442 optimal weight: 6.9990 chunk 943 optimal weight: 2.9990 chunk 509 optimal weight: 0.2980 chunk 424 optimal weight: 8.9990 chunk 922 optimal weight: 0.5980 chunk 891 optimal weight: 20.0000 chunk 567 optimal weight: 0.0770 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 ASN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 29 GLN N 150 ASN N 262 GLN O 122 GLN ** Q 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 54 GLN ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 GLN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 29 GLN W 122 GLN X 250 GLN ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 133 ASN Y 250 GLN a 22 ASN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 72 GLN d 129 ASN ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 133 ASN i 250 GLN ** k 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.117969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.106947 restraints weight = 142957.470| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.05 r_work: 0.3533 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 72816 Z= 0.148 Angle : 0.457 9.047 98753 Z= 0.248 Chirality : 0.033 0.207 12802 Planarity : 0.002 0.060 12617 Dihedral : 3.777 21.927 10064 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.63 % Allowed : 13.10 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.74 (0.09), residues: 9916 helix: 3.36 (0.06), residues: 7400 sheet: -2.42 (0.25), residues: 370 loop : 0.04 (0.14), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP T 48 HIS 0.003 0.001 HIS Q 213 PHE 0.029 0.001 PHE i 132 ARG 0.008 0.000 ARG a 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1312 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 1182 time to evaluate : 6.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8981 (mmm) cc_final: 0.8676 (mmm) REVERT: A 83 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7568 (t0) REVERT: E 210 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7967 (mp) REVERT: F 242 LYS cc_start: 0.8716 (mtpp) cc_final: 0.8433 (mtpt) REVERT: G 50 MET cc_start: 0.8987 (mtp) cc_final: 0.8749 (mtp) REVERT: G 267 ILE cc_start: 0.8568 (mm) cc_final: 0.8207 (mm) REVERT: H 242 LYS cc_start: 0.8836 (tppt) cc_final: 0.8496 (tppt) REVERT: I 76 ASP cc_start: 0.7806 (m-30) cc_final: 0.7490 (m-30) REVERT: I 97 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8089 (tt) REVERT: K 31 ARG cc_start: 0.8733 (ttm-80) cc_final: 0.8526 (ttm-80) REVERT: K 252 LEU cc_start: 0.8726 (mm) cc_final: 0.8083 (tt) REVERT: L 15 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7235 (tt) REVERT: L 87 ASP cc_start: 0.8535 (m-30) cc_final: 0.8229 (m-30) REVERT: L 219 LYS cc_start: 0.7961 (mttp) cc_final: 0.7318 (tppt) REVERT: N 115 ASP cc_start: 0.8134 (t0) cc_final: 0.7868 (t0) REVERT: N 150 ASN cc_start: 0.7739 (OUTLIER) cc_final: 0.7450 (m-40) REVERT: O 94 GLU cc_start: 0.5547 (mm-30) cc_final: 0.4854 (tt0) REVERT: O 161 GLN cc_start: 0.8307 (mm-40) cc_final: 0.7477 (mm-40) REVERT: O 251 GLN cc_start: 0.8796 (mt0) cc_final: 0.8594 (mt0) REVERT: P 185 MET cc_start: 0.9355 (tpp) cc_final: 0.9081 (tpp) REVERT: P 201 SER cc_start: 0.9439 (t) cc_final: 0.9200 (p) REVERT: Q 230 ASN cc_start: 0.7505 (m-40) cc_final: 0.7012 (m-40) REVERT: Q 262 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7630 (pp30) REVERT: R 43 ASP cc_start: 0.8078 (m-30) cc_final: 0.7815 (m-30) REVERT: R 94 GLU cc_start: 0.5519 (mm-30) cc_final: 0.4630 (mt-10) REVERT: R 151 GLU cc_start: 0.8309 (pm20) cc_final: 0.8075 (pm20) REVERT: S 258 SER cc_start: 0.8598 (t) cc_final: 0.8254 (p) REVERT: T 210 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8168 (mp) REVERT: U 32 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.7299 (mp) REVERT: U 94 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: U 151 GLU cc_start: 0.5439 (tp30) cc_final: 0.5172 (tm-30) REVERT: U 235 ASP cc_start: 0.7595 (t0) cc_final: 0.7267 (t70) REVERT: V 5 ILE cc_start: 0.8393 (tp) cc_final: 0.8074 (tp) REVERT: V 233 ASP cc_start: 0.6215 (m-30) cc_final: 0.5864 (m-30) REVERT: W 238 LYS cc_start: 0.6718 (mtpt) cc_final: 0.6109 (mptt) REVERT: X 42 LYS cc_start: 0.5001 (tptt) cc_final: 0.4260 (tppt) REVERT: X 175 THR cc_start: 0.8723 (t) cc_final: 0.8416 (m) REVERT: Y 20 SER cc_start: 0.8744 (t) cc_final: 0.8180 (p) REVERT: Y 94 GLU cc_start: 0.7646 (mp0) cc_final: 0.7084 (tt0) REVERT: Y 131 LYS cc_start: 0.7870 (ptpp) cc_final: 0.7635 (ptpp) REVERT: Y 222 ASP cc_start: 0.6950 (t0) cc_final: 0.6413 (p0) REVERT: Y 252 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7706 (mt) REVERT: Z 37 LYS cc_start: 0.7433 (mmtt) cc_final: 0.6956 (mptt) REVERT: Z 244 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8010 (mp10) REVERT: Z 251 GLN cc_start: 0.8189 (mp10) cc_final: 0.7601 (mp10) REVERT: b 101 ASP cc_start: 0.8094 (t0) cc_final: 0.7697 (t70) REVERT: b 116 PHE cc_start: 0.7108 (t80) cc_final: 0.6819 (m-80) REVERT: b 185 MET cc_start: 0.7999 (tpt) cc_final: 0.7754 (tpp) REVERT: c 109 PHE cc_start: 0.7996 (t80) cc_final: 0.7789 (t80) REVERT: c 265 GLN cc_start: 0.8581 (tt0) cc_final: 0.8353 (pt0) REVERT: d 194 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7708 (mt0) REVERT: e 88 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8076 (tt) REVERT: e 95 LYS cc_start: 0.8439 (mmtm) cc_final: 0.8042 (mtpp) REVERT: h 53 MET cc_start: 0.8483 (mmm) cc_final: 0.8199 (mmt) REVERT: h 255 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.6997 (mp10) REVERT: i 152 ASP cc_start: 0.7903 (m-30) cc_final: 0.7622 (p0) REVERT: i 185 MET cc_start: 0.7995 (tpp) cc_final: 0.7686 (tpp) REVERT: j 2 LEU cc_start: 0.8594 (mp) cc_final: 0.7885 (tt) REVERT: j 115 ASP cc_start: 0.8509 (t70) cc_final: 0.8081 (t0) REVERT: j 262 GLN cc_start: 0.7937 (mt0) cc_final: 0.7624 (tm-30) outliers start: 130 outliers final: 83 residues processed: 1254 average time/residue: 0.6051 time to fit residues: 1345.6562 Evaluate side-chains 1139 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 1044 time to evaluate : 6.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 250 GLN Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 150 ASN Chi-restraints excluded: chain N residue 230 ASN Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 210 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain T residue 210 LEU Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 94 GLU Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain U residue 146 SER Chi-restraints excluded: chain V residue 92 MET Chi-restraints excluded: chain W residue 15 LEU Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain Y residue 250 GLN Chi-restraints excluded: chain Y residue 252 LEU Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 244 GLN Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain a residue 261 ASN Chi-restraints excluded: chain b residue 32 ILE Chi-restraints excluded: chain b residue 252 LEU Chi-restraints excluded: chain c residue 92 MET Chi-restraints excluded: chain d residue 32 ILE Chi-restraints excluded: chain d residue 105 ASN Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 265 GLN Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 88 LEU Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 97 LEU Chi-restraints excluded: chain e residue 171 THR Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 265 GLN Chi-restraints excluded: chain e residue 270 LEU Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain g residue 232 VAL Chi-restraints excluded: chain g residue 268 LEU Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 255 GLN Chi-restraints excluded: chain h residue 265 GLN Chi-restraints excluded: chain h residue 266 THR Chi-restraints excluded: chain i residue 101 ASP Chi-restraints excluded: chain i residue 133 ASN Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 267 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 699 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 730 optimal weight: 6.9990 chunk 646 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 933 optimal weight: 9.9990 chunk 67 optimal weight: 0.0670 chunk 662 optimal weight: 0.8980 chunk 358 optimal weight: 4.9990 chunk 841 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 261 ASN L 33 ASN L 150 ASN ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 150 ASN ** N 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 262 GLN O 122 GLN ** Q 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 54 GLN S 262 GLN ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 GLN U 265 GLN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 122 GLN W 261 ASN ** X 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 250 GLN ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 150 ASN b 40 ASN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 124 GLN ** e 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 250 GLN g 255 GLN ** i 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 250 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.117269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.106236 restraints weight = 143120.575| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.05 r_work: 0.3522 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 72816 Z= 0.168 Angle : 0.472 13.346 98753 Z= 0.255 Chirality : 0.034 0.230 12802 Planarity : 0.002 0.069 12617 Dihedral : 3.759 21.669 10064 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 1.83 % Allowed : 14.15 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.76 (0.08), residues: 9916 helix: 3.38 (0.06), residues: 7400 sheet: -2.29 (0.25), residues: 370 loop : -0.00 (0.14), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP T 48 HIS 0.004 0.001 HIS U 213 PHE 0.027 0.001 PHE Y 216 ARG 0.009 0.000 ARG a 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1249 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 1103 time to evaluate : 6.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 139 ASP cc_start: 0.7991 (t0) cc_final: 0.7775 (t0) REVERT: D 129 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7951 (t0) REVERT: E 210 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7995 (mp) REVERT: F 242 LYS cc_start: 0.8725 (mtpp) cc_final: 0.8479 (mtpt) REVERT: G 50 MET cc_start: 0.8996 (mtp) cc_final: 0.8746 (mtp) REVERT: G 267 ILE cc_start: 0.8578 (mm) cc_final: 0.8224 (mm) REVERT: H 242 LYS cc_start: 0.8841 (tppt) cc_final: 0.8486 (tppt) REVERT: I 97 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8137 (tt) REVERT: K 31 ARG cc_start: 0.8732 (ttm-80) cc_final: 0.8514 (ttm-80) REVERT: K 94 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: K 252 LEU cc_start: 0.8738 (mm) cc_final: 0.8086 (tt) REVERT: L 15 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7256 (tt) REVERT: L 87 ASP cc_start: 0.8559 (m-30) cc_final: 0.8245 (m-30) REVERT: L 219 LYS cc_start: 0.7916 (mttp) cc_final: 0.7296 (tppt) REVERT: N 150 ASN cc_start: 0.7884 (OUTLIER) cc_final: 0.7573 (m-40) REVERT: O 94 GLU cc_start: 0.5523 (mm-30) cc_final: 0.4850 (tt0) REVERT: O 161 GLN cc_start: 0.8322 (mm-40) cc_final: 0.7489 (mm-40) REVERT: P 201 SER cc_start: 0.9431 (t) cc_final: 0.9200 (p) REVERT: Q 230 ASN cc_start: 0.7482 (m-40) cc_final: 0.7088 (m-40) REVERT: Q 262 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7632 (pp30) REVERT: R 43 ASP cc_start: 0.8076 (m-30) cc_final: 0.7810 (m-30) REVERT: R 94 GLU cc_start: 0.5563 (mm-30) cc_final: 0.4710 (mt-10) REVERT: S 150 ASN cc_start: 0.8760 (t0) cc_final: 0.8485 (t0) REVERT: S 258 SER cc_start: 0.8620 (t) cc_final: 0.8255 (p) REVERT: T 210 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8193 (mp) REVERT: U 24 GLU cc_start: 0.8476 (tp30) cc_final: 0.8130 (mm-30) REVERT: U 32 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7280 (mp) REVERT: U 94 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: U 151 GLU cc_start: 0.5526 (tp30) cc_final: 0.5187 (tm-30) REVERT: U 235 ASP cc_start: 0.7716 (t0) cc_final: 0.7390 (t70) REVERT: V 5 ILE cc_start: 0.8410 (tp) cc_final: 0.8094 (tp) REVERT: V 233 ASP cc_start: 0.6224 (m-30) cc_final: 0.5862 (m-30) REVERT: W 238 LYS cc_start: 0.6901 (mtpt) cc_final: 0.6294 (mptt) REVERT: X 42 LYS cc_start: 0.5173 (tptt) cc_final: 0.4417 (tppt) REVERT: X 175 THR cc_start: 0.8731 (t) cc_final: 0.8427 (m) REVERT: Y 94 GLU cc_start: 0.7659 (mp0) cc_final: 0.7022 (tt0) REVERT: Y 131 LYS cc_start: 0.7844 (ptpp) cc_final: 0.7587 (ptpp) REVERT: Y 222 ASP cc_start: 0.6939 (t0) cc_final: 0.6408 (p0) REVERT: Y 248 THR cc_start: 0.8555 (m) cc_final: 0.8319 (p) REVERT: Z 37 LYS cc_start: 0.7421 (mmtt) cc_final: 0.6927 (mptt) REVERT: Z 251 GLN cc_start: 0.8220 (mp10) cc_final: 0.7620 (mp10) REVERT: b 101 ASP cc_start: 0.8078 (t0) cc_final: 0.7670 (t70) REVERT: b 185 MET cc_start: 0.7980 (tpt) cc_final: 0.7512 (tpp) REVERT: c 109 PHE cc_start: 0.7985 (t80) cc_final: 0.7722 (t80) REVERT: c 117 GLU cc_start: 0.7826 (mp0) cc_final: 0.7506 (mp0) REVERT: c 265 GLN cc_start: 0.8573 (tt0) cc_final: 0.8350 (pt0) REVERT: d 194 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7675 (mt0) REVERT: e 76 ASP cc_start: 0.8069 (m-30) cc_final: 0.7850 (m-30) REVERT: e 88 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8152 (tt) REVERT: e 95 LYS cc_start: 0.8461 (mmtm) cc_final: 0.8050 (mtpp) REVERT: e 185 MET cc_start: 0.6821 (OUTLIER) cc_final: 0.6620 (tpp) REVERT: h 53 MET cc_start: 0.8485 (mmm) cc_final: 0.8233 (mmt) REVERT: h 255 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.6973 (mp10) REVERT: i 152 ASP cc_start: 0.7920 (m-30) cc_final: 0.7629 (p0) REVERT: i 185 MET cc_start: 0.8006 (tpp) cc_final: 0.7676 (tpp) REVERT: j 2 LEU cc_start: 0.8606 (mp) cc_final: 0.7981 (tt) REVERT: j 115 ASP cc_start: 0.8558 (t70) cc_final: 0.8115 (t0) REVERT: j 262 GLN cc_start: 0.7933 (mt0) cc_final: 0.7641 (tm-30) outliers start: 146 outliers final: 101 residues processed: 1190 average time/residue: 0.5939 time to fit residues: 1263.9633 Evaluate side-chains 1155 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 1042 time to evaluate : 6.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 250 GLN Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain J residue 243 LEU Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 263 THR Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 150 ASN Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain P residue 83 ASP Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 210 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain T residue 210 LEU Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 94 GLU Chi-restraints excluded: chain U residue 146 SER Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 92 MET Chi-restraints excluded: chain W residue 15 LEU Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 173 THR Chi-restraints excluded: chain Y residue 252 LEU Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 244 GLN Chi-restraints excluded: chain a residue 115 ASP Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain a residue 261 ASN Chi-restraints excluded: chain a residue 263 THR Chi-restraints excluded: chain b residue 32 ILE Chi-restraints excluded: chain b residue 252 LEU Chi-restraints excluded: chain b residue 268 LEU Chi-restraints excluded: chain c residue 92 MET Chi-restraints excluded: chain d residue 32 ILE Chi-restraints excluded: chain d residue 105 ASN Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 265 GLN Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 88 LEU Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 97 LEU Chi-restraints excluded: chain e residue 117 GLU Chi-restraints excluded: chain e residue 171 THR Chi-restraints excluded: chain e residue 185 MET Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 265 GLN Chi-restraints excluded: chain e residue 270 LEU Chi-restraints excluded: chain f residue 158 VAL Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain g residue 232 VAL Chi-restraints excluded: chain g residue 268 LEU Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 255 GLN Chi-restraints excluded: chain h residue 265 GLN Chi-restraints excluded: chain h residue 266 THR Chi-restraints excluded: chain i residue 101 ASP Chi-restraints excluded: chain k residue 2 LEU Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 267 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 103 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 417 optimal weight: 10.0000 chunk 691 optimal weight: 0.1980 chunk 931 optimal weight: 0.9990 chunk 637 optimal weight: 10.0000 chunk 438 optimal weight: 1.9990 chunk 842 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 993 optimal weight: 7.9990 chunk 330 optimal weight: 3.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** J 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 19 ASN L 33 ASN ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 150 ASN ** N 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 262 GLN O 122 GLN O 251 GLN ** Q 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 155 ASN S 54 GLN ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 GLN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 122 GLN ** X 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 124 GLN ** e 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 255 GLN ** i 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 124 GLN i 133 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.116151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.105135 restraints weight = 143538.263| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.05 r_work: 0.3505 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 72816 Z= 0.194 Angle : 0.490 12.060 98753 Z= 0.264 Chirality : 0.035 0.238 12802 Planarity : 0.003 0.049 12617 Dihedral : 3.796 21.669 10064 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.86 % Allowed : 14.64 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.77 (0.09), residues: 9916 helix: 3.38 (0.06), residues: 7363 sheet: -2.20 (0.25), residues: 370 loop : 0.12 (0.14), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP T 48 HIS 0.004 0.001 HIS U 213 PHE 0.028 0.002 PHE Y 216 ARG 0.009 0.001 ARG a 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 1087 time to evaluate : 6.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 210 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8011 (mp) REVERT: F 242 LYS cc_start: 0.8711 (mtpp) cc_final: 0.8478 (mtpt) REVERT: G 50 MET cc_start: 0.9015 (mtp) cc_final: 0.8748 (mtp) REVERT: G 267 ILE cc_start: 0.8603 (mm) cc_final: 0.8257 (mm) REVERT: H 242 LYS cc_start: 0.8873 (tppt) cc_final: 0.8519 (tppt) REVERT: I 97 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8164 (tt) REVERT: I 151 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6993 (tp30) REVERT: K 31 ARG cc_start: 0.8715 (ttm-80) cc_final: 0.8475 (ttm-80) REVERT: K 94 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: K 252 LEU cc_start: 0.8743 (mm) cc_final: 0.8086 (tt) REVERT: L 15 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7293 (tt) REVERT: L 87 ASP cc_start: 0.8541 (m-30) cc_final: 0.8226 (m-30) REVERT: L 219 LYS cc_start: 0.7976 (mttp) cc_final: 0.7310 (tppt) REVERT: N 115 ASP cc_start: 0.8125 (t0) cc_final: 0.7875 (t0) REVERT: N 150 ASN cc_start: 0.7920 (OUTLIER) cc_final: 0.7239 (p0) REVERT: O 94 GLU cc_start: 0.5639 (mm-30) cc_final: 0.4923 (tt0) REVERT: O 161 GLN cc_start: 0.8294 (mm-40) cc_final: 0.7455 (mm-40) REVERT: P 201 SER cc_start: 0.9438 (t) cc_final: 0.9204 (p) REVERT: P 262 GLN cc_start: 0.8554 (mp10) cc_final: 0.8038 (mp10) REVERT: Q 230 ASN cc_start: 0.7452 (m-40) cc_final: 0.7028 (m-40) REVERT: Q 262 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7703 (pp30) REVERT: R 94 GLU cc_start: 0.5605 (mm-30) cc_final: 0.4745 (mt-10) REVERT: S 122 GLN cc_start: 0.8733 (mt0) cc_final: 0.8066 (tp-100) REVERT: T 85 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8452 (mp) REVERT: T 210 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8230 (mp) REVERT: T 235 ASP cc_start: 0.8324 (t0) cc_final: 0.7829 (t70) REVERT: U 24 GLU cc_start: 0.8506 (tp30) cc_final: 0.8144 (mm-30) REVERT: U 32 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7260 (mp) REVERT: U 151 GLU cc_start: 0.5675 (tp30) cc_final: 0.5290 (tm-30) REVERT: U 235 ASP cc_start: 0.7690 (t0) cc_final: 0.7379 (t70) REVERT: V 233 ASP cc_start: 0.6217 (m-30) cc_final: 0.5871 (m-30) REVERT: W 238 LYS cc_start: 0.6937 (mtpt) cc_final: 0.6272 (mptt) REVERT: X 42 LYS cc_start: 0.5202 (tptt) cc_final: 0.4434 (tppt) REVERT: X 175 THR cc_start: 0.8789 (t) cc_final: 0.8461 (m) REVERT: Y 94 GLU cc_start: 0.7667 (mp0) cc_final: 0.7012 (tt0) REVERT: Y 222 ASP cc_start: 0.6949 (t0) cc_final: 0.6414 (p0) REVERT: Y 248 THR cc_start: 0.8599 (m) cc_final: 0.8354 (p) REVERT: Z 37 LYS cc_start: 0.7429 (mmtt) cc_final: 0.6945 (mptt) REVERT: Z 251 GLN cc_start: 0.8207 (mp10) cc_final: 0.7614 (mp10) REVERT: b 101 ASP cc_start: 0.8113 (t0) cc_final: 0.7693 (t70) REVERT: b 185 MET cc_start: 0.7996 (tpt) cc_final: 0.7529 (tpp) REVERT: c 109 PHE cc_start: 0.7985 (t80) cc_final: 0.7762 (t80) REVERT: c 117 GLU cc_start: 0.7879 (mp0) cc_final: 0.7640 (mp0) REVERT: d 194 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7689 (mt0) REVERT: e 88 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8135 (tt) REVERT: e 95 LYS cc_start: 0.8438 (mmtm) cc_final: 0.8022 (mtpp) REVERT: e 185 MET cc_start: 0.6776 (tpp) cc_final: 0.6568 (tpp) REVERT: h 53 MET cc_start: 0.8493 (mmm) cc_final: 0.8253 (mmt) REVERT: h 255 GLN cc_start: 0.7217 (OUTLIER) cc_final: 0.6770 (mp10) REVERT: i 152 ASP cc_start: 0.7935 (m-30) cc_final: 0.7607 (p0) REVERT: i 185 MET cc_start: 0.8010 (tpp) cc_final: 0.7667 (tpp) REVERT: j 2 LEU cc_start: 0.8613 (mp) cc_final: 0.8002 (tt) REVERT: j 115 ASP cc_start: 0.8555 (t70) cc_final: 0.8099 (t0) REVERT: j 262 GLN cc_start: 0.8016 (mt0) cc_final: 0.7701 (tm-30) outliers start: 149 outliers final: 110 residues processed: 1179 average time/residue: 0.5913 time to fit residues: 1252.0924 Evaluate side-chains 1140 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 1019 time to evaluate : 6.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 250 GLN Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain N residue 5 ILE Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 150 ASN Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 159 THR Chi-restraints excluded: chain P residue 83 ASP Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 210 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 85 ILE Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain T residue 158 VAL Chi-restraints excluded: chain T residue 210 LEU Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain U residue 146 SER Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 92 MET Chi-restraints excluded: chain W residue 15 LEU Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 173 THR Chi-restraints excluded: chain Y residue 252 LEU Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain Z residue 244 GLN Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 115 ASP Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain a residue 261 ASN Chi-restraints excluded: chain a residue 263 THR Chi-restraints excluded: chain b residue 32 ILE Chi-restraints excluded: chain b residue 252 LEU Chi-restraints excluded: chain b residue 268 LEU Chi-restraints excluded: chain c residue 266 THR Chi-restraints excluded: chain d residue 32 ILE Chi-restraints excluded: chain d residue 105 ASN Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 265 GLN Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 88 LEU Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 97 LEU Chi-restraints excluded: chain e residue 117 GLU Chi-restraints excluded: chain e residue 171 THR Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 265 GLN Chi-restraints excluded: chain e residue 270 LEU Chi-restraints excluded: chain f residue 15 LEU Chi-restraints excluded: chain f residue 158 VAL Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain g residue 232 VAL Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 255 GLN Chi-restraints excluded: chain h residue 265 GLN Chi-restraints excluded: chain h residue 266 THR Chi-restraints excluded: chain i residue 101 ASP Chi-restraints excluded: chain i residue 133 ASN Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain k residue 2 LEU Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 171 THR Chi-restraints excluded: chain k residue 267 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 618 optimal weight: 1.9990 chunk 696 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 810 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 295 optimal weight: 0.9980 chunk 429 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 268 optimal weight: 0.6980 chunk 841 optimal weight: 1.9990 chunk 566 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 250 GLN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 ASN ** N 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 262 GLN O 122 GLN ** Q 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 155 ASN S 54 GLN ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 GLN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 122 GLN ** X 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 40 ASN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 255 GLN i 124 GLN i 133 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.117815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.106753 restraints weight = 142549.488| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.05 r_work: 0.3530 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 72816 Z= 0.158 Angle : 0.473 11.124 98753 Z= 0.256 Chirality : 0.034 0.281 12802 Planarity : 0.002 0.041 12617 Dihedral : 3.734 20.663 10064 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.83 % Allowed : 15.05 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.77 (0.08), residues: 9916 helix: 3.42 (0.06), residues: 7400 sheet: -2.11 (0.25), residues: 370 loop : -0.13 (0.13), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP T 48 HIS 0.003 0.001 HIS Q 213 PHE 0.031 0.001 PHE Y 216 ARG 0.010 0.000 ARG a 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1263 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 1117 time to evaluate : 6.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7548 (t0) REVERT: E 210 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7996 (mp) REVERT: F 242 LYS cc_start: 0.8693 (mtpp) cc_final: 0.8432 (mtpt) REVERT: G 50 MET cc_start: 0.8982 (mtp) cc_final: 0.8744 (mtp) REVERT: G 267 ILE cc_start: 0.8583 (mm) cc_final: 0.8232 (mm) REVERT: H 242 LYS cc_start: 0.8846 (tppt) cc_final: 0.8503 (tppt) REVERT: I 97 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8112 (tt) REVERT: K 31 ARG cc_start: 0.8709 (ttm-80) cc_final: 0.8490 (ttm-80) REVERT: K 94 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: K 252 LEU cc_start: 0.8726 (mm) cc_final: 0.8090 (tt) REVERT: L 15 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7302 (tt) REVERT: L 87 ASP cc_start: 0.8455 (m-30) cc_final: 0.8144 (m-30) REVERT: L 219 LYS cc_start: 0.7962 (mttp) cc_final: 0.7303 (tppt) REVERT: M 161 GLN cc_start: 0.7993 (mp10) cc_final: 0.7664 (mp10) REVERT: N 115 ASP cc_start: 0.8115 (t0) cc_final: 0.7874 (t0) REVERT: N 150 ASN cc_start: 0.7692 (m-40) cc_final: 0.7220 (p0) REVERT: N 230 ASN cc_start: 0.8049 (OUTLIER) cc_final: 0.7733 (t0) REVERT: O 94 GLU cc_start: 0.5539 (mm-30) cc_final: 0.4878 (tt0) REVERT: O 161 GLN cc_start: 0.8300 (mm-40) cc_final: 0.7463 (mm-40) REVERT: P 201 SER cc_start: 0.9440 (t) cc_final: 0.9216 (p) REVERT: P 262 GLN cc_start: 0.8487 (mp10) cc_final: 0.7967 (mp10) REVERT: Q 230 ASN cc_start: 0.7439 (m-40) cc_final: 0.6970 (m-40) REVERT: Q 262 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7595 (pp30) REVERT: R 92 MET cc_start: 0.8937 (mtp) cc_final: 0.8716 (mtp) REVERT: R 94 GLU cc_start: 0.5530 (mm-30) cc_final: 0.4703 (mt-10) REVERT: S 122 GLN cc_start: 0.8661 (mt0) cc_final: 0.8040 (tp-100) REVERT: S 258 SER cc_start: 0.8664 (t) cc_final: 0.8282 (p) REVERT: T 85 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8455 (mp) REVERT: T 210 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8201 (mp) REVERT: T 235 ASP cc_start: 0.8289 (t0) cc_final: 0.7743 (t70) REVERT: U 24 GLU cc_start: 0.8456 (tp30) cc_final: 0.8081 (mm-30) REVERT: U 32 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7244 (mp) REVERT: U 151 GLU cc_start: 0.5535 (tp30) cc_final: 0.5178 (tm-30) REVERT: U 235 ASP cc_start: 0.7809 (t0) cc_final: 0.7527 (t70) REVERT: V 5 ILE cc_start: 0.8353 (tp) cc_final: 0.8048 (tp) REVERT: V 233 ASP cc_start: 0.6205 (m-30) cc_final: 0.5851 (m-30) REVERT: W 238 LYS cc_start: 0.6868 (mtpt) cc_final: 0.6220 (mptt) REVERT: X 42 LYS cc_start: 0.5169 (tptt) cc_final: 0.4381 (tppt) REVERT: X 175 THR cc_start: 0.8740 (t) cc_final: 0.8441 (m) REVERT: Y 20 SER cc_start: 0.8728 (t) cc_final: 0.8164 (p) REVERT: Y 94 GLU cc_start: 0.7610 (mp0) cc_final: 0.6982 (tt0) REVERT: Y 222 ASP cc_start: 0.6950 (t0) cc_final: 0.6430 (p0) REVERT: Y 248 THR cc_start: 0.8601 (m) cc_final: 0.8349 (p) REVERT: Z 251 GLN cc_start: 0.8205 (mp10) cc_final: 0.7607 (mp10) REVERT: b 31 ARG cc_start: 0.8481 (ttp-170) cc_final: 0.8201 (mtm110) REVERT: b 36 LYS cc_start: 0.7426 (mtpt) cc_final: 0.6308 (mmtt) REVERT: b 101 ASP cc_start: 0.8146 (t0) cc_final: 0.7736 (t70) REVERT: b 116 PHE cc_start: 0.7036 (t80) cc_final: 0.6738 (m-80) REVERT: b 185 MET cc_start: 0.7991 (tpt) cc_final: 0.7724 (tpp) REVERT: c 109 PHE cc_start: 0.7940 (t80) cc_final: 0.7723 (t80) REVERT: c 124 GLN cc_start: 0.7854 (tp-100) cc_final: 0.7318 (pt0) REVERT: d 194 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7688 (mt0) REVERT: e 88 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8179 (tt) REVERT: e 95 LYS cc_start: 0.8439 (mmtm) cc_final: 0.8029 (mtpp) REVERT: h 53 MET cc_start: 0.8488 (mmm) cc_final: 0.8259 (mmt) REVERT: h 255 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6938 (mp10) REVERT: i 152 ASP cc_start: 0.7879 (m-30) cc_final: 0.7624 (p0) REVERT: i 185 MET cc_start: 0.7979 (tpp) cc_final: 0.7639 (tpp) REVERT: j 2 LEU cc_start: 0.8603 (mp) cc_final: 0.8009 (tt) REVERT: j 115 ASP cc_start: 0.8532 (t70) cc_final: 0.8097 (t0) REVERT: j 262 GLN cc_start: 0.7960 (mt0) cc_final: 0.7720 (tm-30) outliers start: 146 outliers final: 112 residues processed: 1208 average time/residue: 0.5915 time to fit residues: 1276.2451 Evaluate side-chains 1181 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 1058 time to evaluate : 5.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 250 GLN Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain N residue 5 ILE Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 230 ASN Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 159 THR Chi-restraints excluded: chain P residue 83 ASP Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 210 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 85 ILE Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain T residue 210 LEU Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain U residue 146 SER Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 92 MET Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 150 ASN Chi-restraints excluded: chain Y residue 173 THR Chi-restraints excluded: chain Y residue 252 LEU Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 244 GLN Chi-restraints excluded: chain a residue 115 ASP Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain a residue 261 ASN Chi-restraints excluded: chain a residue 263 THR Chi-restraints excluded: chain b residue 32 ILE Chi-restraints excluded: chain b residue 33 ASN Chi-restraints excluded: chain b residue 252 LEU Chi-restraints excluded: chain c residue 92 MET Chi-restraints excluded: chain c residue 230 ASN Chi-restraints excluded: chain c residue 266 THR Chi-restraints excluded: chain d residue 32 ILE Chi-restraints excluded: chain d residue 105 ASN Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 265 GLN Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 88 LEU Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 97 LEU Chi-restraints excluded: chain e residue 117 GLU Chi-restraints excluded: chain e residue 171 THR Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 265 GLN Chi-restraints excluded: chain e residue 267 ILE Chi-restraints excluded: chain e residue 270 LEU Chi-restraints excluded: chain f residue 158 VAL Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain g residue 232 VAL Chi-restraints excluded: chain g residue 268 LEU Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 255 GLN Chi-restraints excluded: chain h residue 265 GLN Chi-restraints excluded: chain h residue 266 THR Chi-restraints excluded: chain i residue 101 ASP Chi-restraints excluded: chain i residue 133 ASN Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain i residue 269 SER Chi-restraints excluded: chain k residue 2 LEU Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 171 THR Chi-restraints excluded: chain k residue 267 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 285 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 892 optimal weight: 5.9990 chunk 686 optimal weight: 3.9990 chunk 651 optimal weight: 0.0570 chunk 661 optimal weight: 1.9990 chunk 886 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 498 optimal weight: 9.9990 chunk 666 optimal weight: 5.9990 chunk 458 optimal weight: 0.6980 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 247 GLN L 33 ASN M 3 ASN ** N 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 262 GLN Q 54 GLN ** S 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 44 ASN Z 133 ASN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 194 GLN e 262 GLN ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 255 GLN ** i 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 133 ASN ** k 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.118864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.107756 restraints weight = 142787.026| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.06 r_work: 0.3546 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 72816 Z= 0.151 Angle : 0.476 10.685 98753 Z= 0.257 Chirality : 0.034 0.283 12802 Planarity : 0.002 0.050 12617 Dihedral : 3.681 19.925 10064 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.63 % Allowed : 15.53 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.81 (0.09), residues: 9916 helix: 3.45 (0.06), residues: 7400 sheet: -1.99 (0.26), residues: 370 loop : -0.17 (0.13), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP T 48 HIS 0.003 0.001 HIS Q 213 PHE 0.034 0.001 PHE Y 216 ARG 0.013 0.001 ARG e 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1271 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 1141 time to evaluate : 6.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7570 (t0) REVERT: B 239 GLU cc_start: 0.7344 (mp0) cc_final: 0.7079 (mp0) REVERT: E 210 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7978 (mp) REVERT: F 242 LYS cc_start: 0.8720 (mtpp) cc_final: 0.8477 (mtpt) REVERT: G 50 MET cc_start: 0.9002 (mtp) cc_final: 0.8769 (mtp) REVERT: G 267 ILE cc_start: 0.8558 (mm) cc_final: 0.8215 (mm) REVERT: I 97 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8102 (tt) REVERT: K 31 ARG cc_start: 0.8717 (ttm-80) cc_final: 0.8505 (ttm-80) REVERT: K 252 LEU cc_start: 0.8702 (mm) cc_final: 0.8085 (tt) REVERT: L 15 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7300 (tt) REVERT: L 87 ASP cc_start: 0.8443 (m-30) cc_final: 0.8128 (m-30) REVERT: L 219 LYS cc_start: 0.7933 (mttp) cc_final: 0.7296 (tppt) REVERT: M 225 ASP cc_start: 0.7084 (m-30) cc_final: 0.6806 (m-30) REVERT: N 117 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7323 (mp0) REVERT: N 131 LYS cc_start: 0.8267 (ptpp) cc_final: 0.7883 (mtmm) REVERT: N 150 ASN cc_start: 0.7977 (m-40) cc_final: 0.7334 (p0) REVERT: N 230 ASN cc_start: 0.8130 (OUTLIER) cc_final: 0.7853 (t0) REVERT: O 94 GLU cc_start: 0.5494 (mm-30) cc_final: 0.4877 (tt0) REVERT: O 161 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7455 (mm-40) REVERT: P 201 SER cc_start: 0.9434 (t) cc_final: 0.9214 (p) REVERT: P 262 GLN cc_start: 0.8425 (mp10) cc_final: 0.7914 (mp10) REVERT: Q 52 LYS cc_start: 0.8513 (tppt) cc_final: 0.7747 (ttpt) REVERT: Q 94 GLU cc_start: 0.7866 (tp30) cc_final: 0.7297 (tp30) REVERT: Q 230 ASN cc_start: 0.7385 (m-40) cc_final: 0.6889 (m-40) REVERT: Q 262 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7524 (pp30) REVERT: R 92 MET cc_start: 0.8926 (mtp) cc_final: 0.8710 (mtp) REVERT: R 94 GLU cc_start: 0.5734 (mm-30) cc_final: 0.4878 (mt-10) REVERT: S 122 GLN cc_start: 0.8641 (mt0) cc_final: 0.7964 (tp-100) REVERT: S 258 SER cc_start: 0.8639 (t) cc_final: 0.8290 (p) REVERT: T 210 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8133 (mp) REVERT: T 235 ASP cc_start: 0.8313 (t0) cc_final: 0.7819 (t70) REVERT: U 24 GLU cc_start: 0.8489 (tp30) cc_final: 0.8103 (mm-30) REVERT: U 32 ILE cc_start: 0.7485 (OUTLIER) cc_final: 0.7198 (mp) REVERT: U 94 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7649 (mt-10) REVERT: U 151 GLU cc_start: 0.5513 (tp30) cc_final: 0.5167 (tm-30) REVERT: U 235 ASP cc_start: 0.7809 (t0) cc_final: 0.7524 (t70) REVERT: U 239 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6748 (mm-30) REVERT: V 5 ILE cc_start: 0.8342 (tp) cc_final: 0.8028 (tp) REVERT: V 233 ASP cc_start: 0.6218 (m-30) cc_final: 0.5864 (m-30) REVERT: W 15 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7716 (mt) REVERT: X 42 LYS cc_start: 0.5053 (tptt) cc_final: 0.4245 (tppt) REVERT: X 175 THR cc_start: 0.8643 (t) cc_final: 0.8374 (m) REVERT: Y 20 SER cc_start: 0.8723 (t) cc_final: 0.8162 (p) REVERT: Y 93 LYS cc_start: 0.7552 (mtmt) cc_final: 0.6817 (mmtt) REVERT: Y 94 GLU cc_start: 0.7620 (mp0) cc_final: 0.6971 (tt0) REVERT: Y 222 ASP cc_start: 0.6910 (t0) cc_final: 0.6464 (p0) REVERT: Y 248 THR cc_start: 0.8522 (m) cc_final: 0.8278 (p) REVERT: Z 251 GLN cc_start: 0.8200 (mp10) cc_final: 0.7599 (mp10) REVERT: a 252 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8225 (mt) REVERT: b 36 LYS cc_start: 0.7418 (mtpt) cc_final: 0.6330 (mmtt) REVERT: b 101 ASP cc_start: 0.8167 (t0) cc_final: 0.7743 (t70) REVERT: b 116 PHE cc_start: 0.7020 (OUTLIER) cc_final: 0.6725 (m-80) REVERT: b 150 ASN cc_start: 0.8012 (t0) cc_final: 0.7808 (t0) REVERT: b 185 MET cc_start: 0.7998 (tpt) cc_final: 0.7726 (tpp) REVERT: c 109 PHE cc_start: 0.7925 (t80) cc_final: 0.7718 (t80) REVERT: c 124 GLN cc_start: 0.7778 (tp-100) cc_final: 0.7315 (pt0) REVERT: d 194 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7627 (mt0) REVERT: e 88 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8169 (tt) REVERT: e 95 LYS cc_start: 0.8452 (mmtm) cc_final: 0.8001 (mtpp) REVERT: h 255 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6910 (mp10) REVERT: i 185 MET cc_start: 0.7890 (tpp) cc_final: 0.7551 (tpp) REVERT: j 2 LEU cc_start: 0.8552 (mp) cc_final: 0.7917 (tt) REVERT: j 115 ASP cc_start: 0.8525 (t70) cc_final: 0.8107 (t0) REVERT: j 262 GLN cc_start: 0.7883 (mt0) cc_final: 0.7674 (tm-30) outliers start: 130 outliers final: 100 residues processed: 1215 average time/residue: 0.5978 time to fit residues: 1294.7847 Evaluate side-chains 1181 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 1068 time to evaluate : 6.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 250 GLN Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain N residue 5 ILE Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 230 ASN Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 159 THR Chi-restraints excluded: chain P residue 83 ASP Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 210 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain T residue 210 LEU Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 94 GLU Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain U residue 146 SER Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 92 MET Chi-restraints excluded: chain W residue 15 LEU Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain Y residue 150 ASN Chi-restraints excluded: chain Y residue 252 LEU Chi-restraints excluded: chain Z residue 44 ASN Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain Z residue 104 LEU Chi-restraints excluded: chain Z residue 244 GLN Chi-restraints excluded: chain a residue 115 ASP Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain a residue 252 LEU Chi-restraints excluded: chain a residue 261 ASN Chi-restraints excluded: chain a residue 263 THR Chi-restraints excluded: chain b residue 32 ILE Chi-restraints excluded: chain b residue 116 PHE Chi-restraints excluded: chain b residue 252 LEU Chi-restraints excluded: chain c residue 92 MET Chi-restraints excluded: chain c residue 266 THR Chi-restraints excluded: chain d residue 105 ASN Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 265 GLN Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 88 LEU Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 97 LEU Chi-restraints excluded: chain e residue 117 GLU Chi-restraints excluded: chain e residue 171 THR Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 265 GLN Chi-restraints excluded: chain e residue 267 ILE Chi-restraints excluded: chain e residue 270 LEU Chi-restraints excluded: chain f residue 158 VAL Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain g residue 232 VAL Chi-restraints excluded: chain g residue 268 LEU Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 255 GLN Chi-restraints excluded: chain h residue 266 THR Chi-restraints excluded: chain i residue 101 ASP Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain i residue 269 SER Chi-restraints excluded: chain k residue 2 LEU Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 171 THR Chi-restraints excluded: chain k residue 267 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 114 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 839 optimal weight: 10.0000 chunk 981 optimal weight: 0.9990 chunk 753 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 843 optimal weight: 0.9980 chunk 811 optimal weight: 8.9990 chunk 253 optimal weight: 6.9990 chunk 206 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 GLN D 29 GLN ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 133 ASN ** J 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 ASN ** N 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 262 GLN O 122 GLN ** S 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 GLN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 150 ASN ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 54 GLN c 124 GLN e 262 GLN ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.118126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.107074 restraints weight = 142380.985| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.05 r_work: 0.3536 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 72816 Z= 0.173 Angle : 0.497 10.647 98753 Z= 0.268 Chirality : 0.035 0.319 12802 Planarity : 0.003 0.053 12617 Dihedral : 3.706 19.855 10064 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.58 % Allowed : 16.08 % Favored : 82.34 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.75 (0.09), residues: 9916 helix: 3.40 (0.06), residues: 7400 sheet: -1.96 (0.26), residues: 370 loop : -0.19 (0.13), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP Z 48 HIS 0.003 0.001 HIS U 213 PHE 0.031 0.001 PHE Y 216 ARG 0.013 0.001 ARG e 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1198 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 1072 time to evaluate : 6.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 239 GLU cc_start: 0.7339 (mp0) cc_final: 0.7081 (mp0) REVERT: D 235 ASP cc_start: 0.7508 (t0) cc_final: 0.7018 (t70) REVERT: E 210 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8005 (mp) REVERT: F 242 LYS cc_start: 0.8727 (mtpp) cc_final: 0.8501 (mtpt) REVERT: G 50 MET cc_start: 0.9045 (mtp) cc_final: 0.8807 (mtp) REVERT: G 267 ILE cc_start: 0.8575 (mm) cc_final: 0.8231 (mm) REVERT: H 242 LYS cc_start: 0.8865 (tppt) cc_final: 0.8492 (tppt) REVERT: I 97 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8136 (tt) REVERT: K 31 ARG cc_start: 0.8697 (ttm-80) cc_final: 0.8485 (ttm-80) REVERT: K 94 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: K 252 LEU cc_start: 0.8721 (mm) cc_final: 0.8093 (tt) REVERT: L 87 ASP cc_start: 0.8472 (m-30) cc_final: 0.8154 (m-30) REVERT: L 219 LYS cc_start: 0.7953 (mttp) cc_final: 0.7294 (tppt) REVERT: N 117 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7334 (mp0) REVERT: N 131 LYS cc_start: 0.8291 (ptpp) cc_final: 0.7926 (mtmm) REVERT: N 150 ASN cc_start: 0.7936 (m-40) cc_final: 0.7249 (p0) REVERT: N 230 ASN cc_start: 0.8047 (OUTLIER) cc_final: 0.7775 (t0) REVERT: O 94 GLU cc_start: 0.5520 (mm-30) cc_final: 0.4902 (tt0) REVERT: O 161 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7469 (mm-40) REVERT: P 201 SER cc_start: 0.9436 (t) cc_final: 0.9218 (p) REVERT: P 262 GLN cc_start: 0.8427 (mp10) cc_final: 0.7931 (mp10) REVERT: Q 52 LYS cc_start: 0.8499 (tppt) cc_final: 0.7693 (ttpt) REVERT: Q 94 GLU cc_start: 0.7851 (tp30) cc_final: 0.7318 (tp30) REVERT: Q 230 ASN cc_start: 0.7310 (m-40) cc_final: 0.7091 (m-40) REVERT: Q 262 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7550 (pp30) REVERT: R 94 GLU cc_start: 0.5742 (mm-30) cc_final: 0.4897 (mt-10) REVERT: S 122 GLN cc_start: 0.8636 (mt0) cc_final: 0.7962 (tp-100) REVERT: S 258 SER cc_start: 0.8641 (t) cc_final: 0.8279 (p) REVERT: T 210 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8153 (mp) REVERT: T 235 ASP cc_start: 0.8333 (t0) cc_final: 0.7735 (t70) REVERT: U 24 GLU cc_start: 0.8476 (tp30) cc_final: 0.8125 (mm-30) REVERT: U 32 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7216 (mp) REVERT: U 94 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7672 (mt-10) REVERT: U 151 GLU cc_start: 0.5579 (tp30) cc_final: 0.5238 (tm-30) REVERT: U 235 ASP cc_start: 0.7856 (t0) cc_final: 0.7594 (t70) REVERT: U 239 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6760 (mm-30) REVERT: V 233 ASP cc_start: 0.6252 (m-30) cc_final: 0.5892 (m-30) REVERT: W 15 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7718 (mt) REVERT: X 42 LYS cc_start: 0.4981 (tptt) cc_final: 0.4169 (tppt) REVERT: X 175 THR cc_start: 0.8689 (t) cc_final: 0.8408 (m) REVERT: X 265 GLN cc_start: 0.8151 (tp-100) cc_final: 0.7741 (mt0) REVERT: Y 20 SER cc_start: 0.8732 (t) cc_final: 0.8164 (p) REVERT: Y 38 VAL cc_start: 0.5321 (m) cc_final: 0.5071 (p) REVERT: Y 93 LYS cc_start: 0.7584 (mtmt) cc_final: 0.6836 (mmtt) REVERT: Y 94 GLU cc_start: 0.7631 (mp0) cc_final: 0.6954 (tt0) REVERT: Y 133 ASN cc_start: 0.8536 (t0) cc_final: 0.8187 (t0) REVERT: Y 222 ASP cc_start: 0.6866 (t0) cc_final: 0.6426 (p0) REVERT: Y 248 THR cc_start: 0.8607 (m) cc_final: 0.8362 (p) REVERT: Z 251 GLN cc_start: 0.8209 (mp10) cc_final: 0.7607 (mp10) REVERT: a 244 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8540 (mp10) REVERT: a 252 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8215 (mt) REVERT: b 101 ASP cc_start: 0.8154 (t0) cc_final: 0.7733 (t70) REVERT: b 116 PHE cc_start: 0.7036 (OUTLIER) cc_final: 0.6748 (m-80) REVERT: b 185 MET cc_start: 0.8029 (tpt) cc_final: 0.7723 (tpp) REVERT: c 124 GLN cc_start: 0.7753 (tp40) cc_final: 0.7546 (pt0) REVERT: d 194 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7636 (mt0) REVERT: e 88 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8225 (tt) REVERT: e 95 LYS cc_start: 0.8473 (mmtm) cc_final: 0.8027 (mtpp) REVERT: h 53 MET cc_start: 0.8483 (mmm) cc_final: 0.8213 (mmt) REVERT: h 255 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6917 (mp10) REVERT: i 185 MET cc_start: 0.7947 (tpp) cc_final: 0.7607 (tpp) REVERT: j 2 LEU cc_start: 0.8609 (mp) cc_final: 0.8030 (tt) REVERT: j 115 ASP cc_start: 0.8535 (t70) cc_final: 0.8099 (t0) REVERT: j 262 GLN cc_start: 0.7933 (mt0) cc_final: 0.7691 (tm-30) outliers start: 126 outliers final: 106 residues processed: 1148 average time/residue: 0.5926 time to fit residues: 1217.3685 Evaluate side-chains 1163 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 1045 time to evaluate : 5.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 250 GLN Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain N residue 5 ILE Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 230 ASN Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 159 THR Chi-restraints excluded: chain P residue 83 ASP Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 210 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain T residue 210 LEU Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 94 GLU Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain U residue 146 SER Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 92 MET Chi-restraints excluded: chain W residue 15 LEU Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain Y residue 150 ASN Chi-restraints excluded: chain Y residue 243 LEU Chi-restraints excluded: chain Y residue 252 LEU Chi-restraints excluded: chain Z residue 104 LEU Chi-restraints excluded: chain Z residue 244 GLN Chi-restraints excluded: chain a residue 115 ASP Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain a residue 252 LEU Chi-restraints excluded: chain a residue 261 ASN Chi-restraints excluded: chain a residue 263 THR Chi-restraints excluded: chain b residue 32 ILE Chi-restraints excluded: chain b residue 33 ASN Chi-restraints excluded: chain b residue 116 PHE Chi-restraints excluded: chain b residue 252 LEU Chi-restraints excluded: chain c residue 92 MET Chi-restraints excluded: chain c residue 266 THR Chi-restraints excluded: chain d residue 105 ASN Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 265 GLN Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 88 LEU Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 97 LEU Chi-restraints excluded: chain e residue 117 GLU Chi-restraints excluded: chain e residue 171 THR Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 265 GLN Chi-restraints excluded: chain e residue 267 ILE Chi-restraints excluded: chain e residue 270 LEU Chi-restraints excluded: chain f residue 158 VAL Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain g residue 232 VAL Chi-restraints excluded: chain g residue 268 LEU Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 255 GLN Chi-restraints excluded: chain h residue 266 THR Chi-restraints excluded: chain i residue 101 ASP Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain i residue 269 SER Chi-restraints excluded: chain k residue 2 LEU Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 171 THR Chi-restraints excluded: chain k residue 267 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 321 optimal weight: 0.9980 chunk 379 optimal weight: 4.9990 chunk 981 optimal weight: 1.9990 chunk 966 optimal weight: 0.8980 chunk 942 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 331 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 chunk 420 optimal weight: 9.9990 chunk 552 optimal weight: 9.9990 chunk 846 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 133 ASN ** J 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 262 GLN O 122 GLN ** S 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 GLN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 262 GLN ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 255 GLN i 54 GLN ** k 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.117208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.106149 restraints weight = 143475.162| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.05 r_work: 0.3521 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 72816 Z= 0.199 Angle : 0.517 10.580 98753 Z= 0.277 Chirality : 0.035 0.322 12802 Planarity : 0.003 0.055 12617 Dihedral : 3.745 20.088 10064 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.58 % Allowed : 16.23 % Favored : 82.19 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.76 (0.09), residues: 9916 helix: 3.39 (0.06), residues: 7363 sheet: -1.96 (0.26), residues: 370 loop : 0.00 (0.14), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP T 48 HIS 0.004 0.001 HIS U 213 PHE 0.034 0.002 PHE Y 216 ARG 0.014 0.001 ARG e 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35052.99 seconds wall clock time: 605 minutes 26.88 seconds (36326.88 seconds total)