Starting phenix.real_space_refine on Thu Jan 23 13:28:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cem_45504/01_2025/9cem_45504.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cem_45504/01_2025/9cem_45504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cem_45504/01_2025/9cem_45504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cem_45504/01_2025/9cem_45504.map" model { file = "/net/cci-nas-00/data/ceres_data/9cem_45504/01_2025/9cem_45504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cem_45504/01_2025/9cem_45504.cif" } resolution = 2.46 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= 0.003 sd= 0.106 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 363 residue(s): 0.16s 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: 30.61, per 1000 atoms: 0.42 Number of scatterers: 72372 At special positions: 0 Unit cell: (137.61, 137.61, 333.6, 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: 14.74 Conformation dependent library (CDL) restraints added in 8.0 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 37 sheets defined 77.3% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.22 Creating SS restraints... Processing helix chain 'A' and resid 8 through 35 removed outlier: 3.808A pdb=" N LEU A 12 " --> pdb=" O ASN A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 60 Processing helix chain 'A' and resid 60 through 101 removed outlier: 3.960A pdb=" N VAL A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.272A 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 168 Processing helix chain 'A' and resid 178 through 233 removed outlier: 4.316A pdb=" N ALA A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 263 removed outlier: 3.698A pdb=" N GLU A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 271 Processing helix chain 'B' and resid 8 through 35 removed outlier: 3.604A pdb=" N LEU B 12 " --> pdb=" O ASN B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 101 removed outlier: 4.562A pdb=" N ASN B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N SER B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 129 Processing helix chain 'B' and resid 165 through 169 removed outlier: 3.676A pdb=" N GLY B 169 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 233 removed outlier: 3.851A pdb=" N ALA B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 263 removed outlier: 3.934A pdb=" N GLU B 239 " --> pdb=" O ASP B 235 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 271 removed outlier: 3.608A pdb=" N ILE B 267 " --> pdb=" O PRO B 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 35 removed outlier: 3.572A pdb=" N LEU C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 101 removed outlier: 3.813A pdb=" N LEU C 61 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASN C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER C 63 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.775A 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 165 through 169 removed outlier: 3.622A pdb=" N GLY C 169 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 233 removed outlier: 3.927A pdb=" N ALA C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 263 removed outlier: 3.554A pdb=" N GLU C 239 " --> pdb=" O ASP C 235 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA C 241 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN C 244 " --> pdb=" O SER C 240 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 271 Processing helix chain 'D' and resid 8 through 35 removed outlier: 3.768A pdb=" N LEU D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 101 removed outlier: 3.804A pdb=" N LEU D 61 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASN D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N SER D 63 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 129 Processing helix chain 'D' and resid 178 through 233 removed outlier: 3.971A pdb=" N ALA D 187 " --> pdb=" O LYS D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 263 removed outlier: 3.587A pdb=" N GLU D 239 " --> pdb=" O ASP D 235 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA D 241 " --> pdb=" O ALA D 237 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN D 262 " --> pdb=" O SER D 258 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 271 removed outlier: 3.601A pdb=" N ILE D 267 " --> pdb=" O PRO D 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 35 Processing helix chain 'E' and resid 44 through 100 removed outlier: 3.902A pdb=" N LEU E 61 " --> pdb=" O THR E 57 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASN E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER E 63 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) removed outlier: 3.603A 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 165 through 169 Processing helix chain 'E' and resid 178 through 233 removed outlier: 3.974A pdb=" N ALA E 187 " --> pdb=" O LYS E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 263 removed outlier: 3.701A pdb=" N GLU E 239 " --> pdb=" O ASP E 235 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA E 241 " --> pdb=" O ALA E 237 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN E 244 " --> pdb=" O SER E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 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: 4.020A pdb=" N VAL F 64 " --> pdb=" O SER F 60 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR F 84 " --> pdb=" O ALA F 80 " (cutoff:3.500A) removed outlier: 4.061A 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 165 through 169 removed outlier: 3.545A pdb=" N GLY F 169 " --> pdb=" O THR F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 233 removed outlier: 4.052A pdb=" N ALA F 187 " --> pdb=" O LYS F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 263 removed outlier: 3.697A pdb=" N GLU F 239 " --> pdb=" O ASP F 235 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN F 244 " --> pdb=" O SER F 240 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN F 262 " --> pdb=" O SER F 258 " (cutoff:3.500A) removed outlier: 3.823A 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 removed outlier: 3.747A pdb=" N LEU G 12 " --> pdb=" O ASN G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 100 removed outlier: 3.762A pdb=" N LEU G 61 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASN G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N SER G 63 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL G 64 " --> pdb=" O SER G 60 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR G 84 " --> pdb=" O ALA G 80 " (cutoff:3.500A) removed outlier: 3.751A 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 165 through 169 Processing helix chain 'G' and resid 178 through 233 removed outlier: 3.950A pdb=" N ALA G 187 " --> pdb=" O LYS G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 263 removed outlier: 3.637A pdb=" N GLU G 239 " --> pdb=" O ASP G 235 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA G 241 " --> pdb=" O ALA G 237 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN G 244 " --> pdb=" O SER G 240 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN G 262 " --> pdb=" O SER G 258 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR G 263 " --> pdb=" O ILE G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 271 Processing helix chain 'H' and resid 8 through 35 Processing helix chain 'H' and resid 44 through 100 removed outlier: 4.247A pdb=" N ASN H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER H 63 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL H 64 " --> pdb=" O SER H 60 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR H 84 " --> pdb=" O ALA H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 129 Processing helix chain 'H' and resid 165 through 169 removed outlier: 3.748A pdb=" N GLY H 169 " --> pdb=" O THR H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 233 removed outlier: 3.972A pdb=" N ALA H 187 " --> pdb=" O LYS H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 263 removed outlier: 3.578A pdb=" N GLU H 239 " --> pdb=" O ASP H 235 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA H 241 " --> pdb=" O ALA H 237 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN H 244 " --> pdb=" O SER H 240 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN H 262 " --> pdb=" O SER H 258 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR H 263 " --> pdb=" O ILE H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 271 Processing helix chain 'I' and resid 8 through 35 Processing helix chain 'I' and resid 44 through 60 removed outlier: 3.659A pdb=" N TRP I 48 " --> pdb=" O ASN I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 101 removed outlier: 4.031A pdb=" N VAL I 64 " --> pdb=" O SER I 60 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR I 84 " --> pdb=" O ALA I 80 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP I 87 " --> pdb=" O ASP I 83 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP I 101 " --> pdb=" O LEU I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 129 Processing helix chain 'I' and resid 165 through 169 removed outlier: 3.733A pdb=" N GLY I 169 " --> pdb=" O THR I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 233 removed outlier: 3.872A pdb=" N ALA I 187 " --> pdb=" O LYS I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 235 through 263 removed outlier: 3.589A pdb=" N GLU I 239 " --> pdb=" O ASP I 235 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA I 241 " --> pdb=" O ALA I 237 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR I 248 " --> pdb=" O GLN I 244 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN I 262 " --> pdb=" O SER I 258 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR I 263 " --> pdb=" O ILE I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 271 removed outlier: 3.572A pdb=" N PHE I 271 " --> pdb=" O LEU I 268 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 35 Processing helix chain 'J' and resid 44 through 60 Processing helix chain 'J' and resid 60 through 101 removed outlier: 4.114A pdb=" N VAL J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR J 84 " --> pdb=" O ALA J 80 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP J 101 " --> pdb=" O LEU J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 129 Processing helix chain 'J' and resid 165 through 169 removed outlier: 3.670A pdb=" N GLY J 169 " --> pdb=" O THR J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 233 removed outlier: 3.986A pdb=" N ALA J 187 " --> pdb=" O LYS J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 235 through 263 removed outlier: 4.049A pdb=" N ALA J 241 " --> pdb=" O ALA J 237 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR J 248 " --> pdb=" O GLN J 244 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN J 262 " --> pdb=" O SER J 258 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR J 263 " --> pdb=" O ILE J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 271 Processing helix chain 'K' and resid 8 through 35 removed outlier: 3.996A pdb=" N LEU K 12 " --> pdb=" O ASN K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 60 Processing helix chain 'K' and resid 60 through 100 removed outlier: 4.113A pdb=" N VAL K 64 " --> pdb=" O SER K 60 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR K 84 " --> pdb=" O ALA K 80 " (cutoff:3.500A) removed outlier: 3.800A 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 165 through 169 removed outlier: 3.544A pdb=" N GLY K 169 " --> pdb=" O THR K 166 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 233 removed outlier: 4.106A pdb=" N ALA K 187 " --> pdb=" O LYS K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 235 through 262 removed outlier: 4.081A pdb=" N ALA K 241 " --> pdb=" O ALA K 237 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR K 248 " --> pdb=" O GLN K 244 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN K 262 " --> pdb=" O SER K 258 " (cutoff:3.500A) Processing helix chain 'K' and resid 263 through 271 Processing helix chain 'L' and resid 8 through 35 removed outlier: 3.812A 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 101 removed outlier: 4.111A pdb=" N VAL L 64 " --> pdb=" O SER L 60 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THR L 84 " --> pdb=" O ALA L 80 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP L 101 " --> pdb=" O LEU L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 129 Processing helix chain 'L' and resid 164 through 169 removed outlier: 3.750A pdb=" N GLY L 169 " --> pdb=" O THR L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 233 removed outlier: 4.093A pdb=" N ALA L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 235 through 263 Processing helix chain 'L' and resid 264 through 271 removed outlier: 3.564A pdb=" N PHE L 271 " --> pdb=" O LEU L 268 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 35 removed outlier: 3.937A pdb=" N LEU M 12 " --> pdb=" O ASN M 8 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 60 Processing helix chain 'M' and resid 60 through 100 removed outlier: 3.988A pdb=" N VAL M 64 " --> pdb=" O SER M 60 " (cutoff:3.500A) removed outlier: 3.985A 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 178 through 233 removed outlier: 3.872A pdb=" N ALA M 187 " --> pdb=" O LYS M 183 " (cutoff:3.500A) Processing helix chain 'M' and resid 235 through 263 removed outlier: 3.832A 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: 3.857A pdb=" N LEU N 12 " --> pdb=" O ASN N 8 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 60 Processing helix chain 'N' and resid 60 through 100 removed outlier: 4.067A pdb=" N VAL N 64 " --> pdb=" O SER N 60 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR N 84 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 129 Processing helix chain 'N' and resid 165 through 169 removed outlier: 3.588A pdb=" N GLY N 169 " --> pdb=" O THR N 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 178 through 233 removed outlier: 4.058A pdb=" N ALA N 187 " --> pdb=" O LYS N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 235 through 263 removed outlier: 3.745A pdb=" N ALA N 241 " --> pdb=" O ALA N 237 " (cutoff:3.500A) Processing helix chain 'N' and resid 264 through 271 Processing helix chain 'O' and resid 8 through 35 removed outlier: 4.018A pdb=" N LEU O 12 " --> pdb=" O ASN O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 100 removed outlier: 4.348A pdb=" N ASN O 62 " --> pdb=" O ALA O 58 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N SER O 63 " --> pdb=" O SER O 59 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL O 64 " --> pdb=" O SER O 60 " (cutoff:3.500A) removed outlier: 4.098A 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: 3.644A pdb=" N GLY O 169 " --> pdb=" O THR O 166 " (cutoff:3.500A) Processing helix chain 'O' and resid 178 through 233 removed outlier: 3.944A pdb=" N ALA O 187 " --> pdb=" O LYS O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 235 through 262 removed outlier: 3.953A pdb=" N GLN O 262 " --> pdb=" O SER O 258 " (cutoff:3.500A) Processing helix chain 'O' and resid 265 through 271 removed outlier: 4.222A pdb=" N SER O 269 " --> pdb=" O GLN O 265 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU O 270 " --> pdb=" O THR O 266 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE O 271 " --> pdb=" O ILE O 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 265 through 271' Processing helix chain 'P' and resid 8 through 35 removed outlier: 3.688A pdb=" N LEU P 12 " --> pdb=" O ASN P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 60 Processing helix chain 'P' and resid 60 through 100 removed outlier: 3.970A pdb=" N VAL P 64 " --> pdb=" O SER P 60 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR P 84 " --> pdb=" O ALA P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 129 removed outlier: 3.611A pdb=" N ASN P 129 " --> pdb=" O LYS P 125 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 169 removed outlier: 3.593A pdb=" N GLY P 169 " --> pdb=" O THR P 166 " (cutoff:3.500A) Processing helix chain 'P' and resid 178 through 233 removed outlier: 3.871A pdb=" N ALA P 187 " --> pdb=" O LYS P 183 " (cutoff:3.500A) Processing helix chain 'P' and resid 235 through 262 removed outlier: 3.843A pdb=" N GLN P 262 " --> pdb=" O SER P 258 " (cutoff:3.500A) Processing helix chain 'P' and resid 263 through 269 removed outlier: 3.569A pdb=" N THR P 266 " --> pdb=" O THR P 263 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER P 269 " --> pdb=" O THR P 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 35 removed outlier: 3.554A pdb=" N LEU Q 12 " --> pdb=" O ASN Q 8 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 100 removed outlier: 3.912A pdb=" N LEU Q 61 " --> pdb=" O THR Q 57 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN Q 62 " --> pdb=" O ALA Q 58 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER Q 63 " --> pdb=" O SER Q 59 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR Q 84 " --> pdb=" O ALA Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 129 Processing helix chain 'Q' and resid 164 through 169 removed outlier: 3.676A pdb=" N GLY Q 169 " --> pdb=" O THR Q 166 " (cutoff:3.500A) Processing helix chain 'Q' and resid 178 through 233 removed outlier: 3.869A pdb=" N ALA Q 187 " --> pdb=" O LYS Q 183 " (cutoff:3.500A) Processing helix chain 'Q' and resid 235 through 262 removed outlier: 3.777A pdb=" N GLN Q 262 " --> pdb=" O SER Q 258 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 271 removed outlier: 3.673A pdb=" N PHE Q 271 " --> pdb=" O LEU Q 268 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 35 removed outlier: 3.662A pdb=" N LEU R 12 " --> pdb=" O ASN R 8 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU R 24 " --> pdb=" O SER R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 60 Processing helix chain 'R' and resid 60 through 100 removed outlier: 4.052A pdb=" N VAL R 64 " --> pdb=" O SER R 60 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR R 84 " --> pdb=" O ALA R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 129 Processing helix chain 'R' and resid 164 through 169 removed outlier: 3.579A pdb=" N GLY R 169 " --> pdb=" O THR R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 233 removed outlier: 3.985A pdb=" N ALA R 187 " --> pdb=" O LYS R 183 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU R 231 " --> pdb=" O GLY R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 235 through 263 removed outlier: 3.769A 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: 3.724A 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: 4.230A pdb=" N VAL S 64 " --> pdb=" O SER S 60 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR S 84 " --> pdb=" O ALA S 80 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP S 87 " --> pdb=" O ASP S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 105 through 129 Processing helix chain 'S' and resid 164 through 169 removed outlier: 3.557A pdb=" N ILE S 168 " --> pdb=" O LEU S 165 " (cutoff:3.500A) Processing helix chain 'S' and resid 178 through 233 removed outlier: 4.023A pdb=" N ALA S 187 " --> pdb=" O LYS S 183 " (cutoff:3.500A) Processing helix chain 'S' and resid 235 through 263 removed outlier: 3.945A pdb=" N GLU S 239 " --> pdb=" O ASP S 235 " (cutoff:3.500A) Processing helix chain 'S' and resid 264 through 271 Processing helix chain 'T' and resid 8 through 35 removed outlier: 3.945A 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 100 removed outlier: 4.192A pdb=" N VAL T 64 " --> pdb=" O SER T 60 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR T 84 " --> pdb=" O ALA T 80 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP T 87 " --> pdb=" O ASP T 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 130 removed outlier: 3.822A pdb=" N ALA T 130 " --> pdb=" O ALA T 126 " (cutoff:3.500A) Processing helix chain 'T' and resid 178 through 233 removed outlier: 4.013A 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 265 through 271 removed outlier: 4.262A pdb=" N SER T 269 " --> pdb=" O GLN T 265 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE T 271 " --> pdb=" O ILE T 267 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 35 removed outlier: 4.027A pdb=" N LEU U 12 " --> pdb=" O ASN U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 101 removed outlier: 4.019A pdb=" N LEU U 61 " --> pdb=" O THR U 57 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASN U 62 " --> pdb=" O ALA U 58 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER U 63 " --> pdb=" O SER U 59 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR U 84 " --> pdb=" O ALA U 80 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP U 87 " --> pdb=" O ASP U 83 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP U 101 " --> pdb=" O LEU U 97 " (cutoff:3.500A) Processing helix chain 'U' and resid 105 through 130 removed outlier: 3.772A pdb=" N ALA U 130 " --> pdb=" O ALA U 126 " (cutoff:3.500A) Processing helix chain 'U' and resid 178 through 233 removed outlier: 3.978A pdb=" N ALA U 187 " --> pdb=" O LYS U 183 " (cutoff:3.500A) Processing helix chain 'U' and resid 235 through 263 removed outlier: 3.568A pdb=" N GLU U 239 " --> pdb=" O ASP U 235 " (cutoff:3.500A) Processing helix chain 'U' and resid 264 through 271 Processing helix chain 'V' and resid 8 through 35 removed outlier: 3.754A pdb=" N LEU V 12 " --> pdb=" O ASN V 8 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 60 Processing helix chain 'V' and resid 60 through 100 removed outlier: 4.053A pdb=" N VAL V 64 " --> pdb=" O SER V 60 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR V 84 " --> pdb=" O ALA V 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 105 through 129 Processing helix chain 'V' and resid 164 through 169 removed outlier: 3.772A pdb=" N GLY V 169 " --> pdb=" O THR V 166 " (cutoff:3.500A) Processing helix chain 'V' and resid 178 through 233 removed outlier: 3.936A pdb=" N ALA V 187 " --> pdb=" O LYS V 183 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP V 222 " --> pdb=" O GLY V 218 " (cutoff:3.500A) Processing helix chain 'V' and resid 235 through 263 removed outlier: 3.514A 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: 4.077A 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: 4.113A pdb=" N VAL W 64 " --> pdb=" O SER W 60 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR W 84 " --> pdb=" O ALA W 80 " (cutoff:3.500A) Processing helix chain 'W' and resid 105 through 129 Processing helix chain 'W' and resid 164 through 169 removed outlier: 3.670A pdb=" N GLY W 169 " --> pdb=" O THR W 166 " (cutoff:3.500A) Processing helix chain 'W' and resid 178 through 233 removed outlier: 4.036A pdb=" N ALA W 187 " --> pdb=" O LYS W 183 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP W 222 " --> pdb=" O GLY W 218 " (cutoff:3.500A) Processing helix chain 'W' and resid 235 through 263 removed outlier: 3.588A pdb=" N GLU W 239 " --> pdb=" O ASP W 235 " (cutoff:3.500A) Processing helix chain 'W' and resid 264 through 271 Processing helix chain 'X' and resid 8 through 35 removed outlier: 4.094A 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: 4.138A pdb=" N VAL X 64 " --> pdb=" O SER X 60 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR X 84 " --> pdb=" O ALA X 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 129 Processing helix chain 'X' and resid 164 through 169 removed outlier: 3.540A pdb=" N GLY X 169 " --> pdb=" O THR X 166 " (cutoff:3.500A) Processing helix chain 'X' and resid 178 through 233 removed outlier: 4.080A pdb=" N ALA X 187 " --> pdb=" O LYS X 183 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP X 222 " --> pdb=" O GLY X 218 " (cutoff:3.500A) Processing helix chain 'X' and resid 235 through 263 removed outlier: 3.536A pdb=" N GLU X 239 " --> pdb=" O ASP X 235 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 271 removed outlier: 4.002A pdb=" N PHE X 271 " --> pdb=" O LEU X 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 8 through 35 removed outlier: 3.827A pdb=" N LEU Y 12 " --> pdb=" O ASN Y 8 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 60 removed outlier: 3.565A pdb=" N TRP Y 48 " --> pdb=" O ASN Y 44 " (cutoff:3.500A) Processing helix chain 'Y' and resid 60 through 100 removed outlier: 4.357A pdb=" N VAL Y 64 " --> pdb=" O SER Y 60 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR Y 84 " --> pdb=" O ALA Y 80 " (cutoff:3.500A) Processing helix chain 'Y' and resid 105 through 129 Processing helix chain 'Y' and resid 164 through 169 removed outlier: 3.550A pdb=" N ILE Y 168 " --> pdb=" O LEU Y 165 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY Y 169 " --> pdb=" O THR Y 166 " (cutoff:3.500A) Processing helix chain 'Y' and resid 178 through 233 removed outlier: 4.250A pdb=" N ALA Y 187 " --> pdb=" O LYS Y 183 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR Y 188 " --> pdb=" O THR Y 184 " (cutoff:3.500A) Processing helix chain 'Y' and resid 235 through 263 removed outlier: 4.038A pdb=" N ALA Y 241 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 264 through 271 Processing helix chain 'Z' and resid 8 through 35 Processing helix chain 'Z' and resid 44 through 100 removed outlier: 4.631A pdb=" N ASN Z 62 " --> pdb=" O ALA Z 58 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N SER Z 63 " --> pdb=" O SER Z 59 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL Z 64 " --> pdb=" O SER Z 60 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA Z 78 " --> pdb=" O THR Z 74 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR Z 84 " --> pdb=" O ALA Z 80 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP Z 87 " --> pdb=" O ASP Z 83 " (cutoff:3.500A) Processing helix chain 'Z' and resid 105 through 129 Processing helix chain 'Z' and resid 165 through 169 removed outlier: 3.627A pdb=" N GLY Z 169 " --> pdb=" O THR Z 166 " (cutoff:3.500A) Processing helix chain 'Z' and resid 178 through 233 removed outlier: 3.984A pdb=" N ALA Z 187 " --> pdb=" O LYS Z 183 " (cutoff:3.500A) Processing helix chain 'Z' and resid 235 through 263 removed outlier: 3.632A pdb=" N GLU Z 239 " --> pdb=" O ASP Z 235 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA Z 241 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 264 through 271 Processing helix chain 'a' and resid 8 through 35 removed outlier: 3.822A pdb=" N LEU a 12 " --> pdb=" O ASN a 8 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 100 removed outlier: 4.631A pdb=" N ASN a 62 " --> pdb=" O ALA a 58 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N SER a 63 " --> pdb=" O SER a 59 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL a 64 " --> pdb=" O SER a 60 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR a 84 " --> pdb=" O ALA a 80 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP a 87 " --> pdb=" O ASP a 83 " (cutoff:3.500A) Processing helix chain 'a' and resid 105 through 129 Processing helix chain 'a' and resid 165 through 169 removed outlier: 3.653A pdb=" N GLY a 169 " --> pdb=" O THR a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 178 through 233 removed outlier: 4.051A pdb=" N ALA a 187 " --> pdb=" O LYS a 183 " (cutoff:3.500A) Processing helix chain 'a' and resid 235 through 263 removed outlier: 3.509A pdb=" N GLU a 239 " --> pdb=" O ASP a 235 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA a 241 " --> pdb=" O ALA a 237 " (cutoff:3.500A) Processing helix chain 'a' and resid 264 through 271 Processing helix chain 'b' and resid 8 through 35 removed outlier: 3.910A pdb=" N LEU b 12 " --> pdb=" O ASN b 8 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 60 Processing helix chain 'b' and resid 60 through 101 removed outlier: 4.053A pdb=" N VAL b 64 " --> pdb=" O SER b 60 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP b 101 " --> pdb=" O LEU b 97 " (cutoff:3.500A) Processing helix chain 'b' and resid 105 through 129 Processing helix chain 'b' and resid 164 through 169 Processing helix chain 'b' and resid 178 through 233 removed outlier: 4.578A pdb=" N ALA b 187 " --> pdb=" O LYS b 183 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR b 188 " --> pdb=" O THR b 184 " (cutoff:3.500A) Processing helix chain 'b' and resid 235 through 263 removed outlier: 4.529A pdb=" N ALA b 241 " --> pdb=" O ALA b 237 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS b 242 " --> pdb=" O LYS b 238 " (cutoff:3.500A) removed outlier: 3.615A 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: 3.812A 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 100 removed outlier: 4.020A pdb=" N VAL c 64 " --> pdb=" O SER c 60 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR c 84 " --> pdb=" O ALA c 80 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP c 87 " --> pdb=" O ASP c 83 " (cutoff:3.500A) Processing helix chain 'c' and resid 105 through 129 Processing helix chain 'c' and resid 165 through 169 removed outlier: 3.525A pdb=" N GLY c 169 " --> pdb=" O THR c 166 " (cutoff:3.500A) Processing helix chain 'c' and resid 178 through 233 removed outlier: 4.244A pdb=" N ALA c 187 " --> pdb=" O LYS c 183 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR c 188 " --> pdb=" O THR c 184 " (cutoff:3.500A) Processing helix chain 'c' and resid 235 through 263 removed outlier: 3.520A pdb=" N GLU c 239 " --> pdb=" O ASP c 235 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA c 241 " --> pdb=" O ALA c 237 " (cutoff:3.500A) Processing helix chain 'c' and resid 264 through 271 removed outlier: 3.519A pdb=" N ILE c 267 " --> pdb=" O PRO c 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 35 removed outlier: 3.783A 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 60 through 100 removed outlier: 3.961A pdb=" N VAL d 64 " --> pdb=" O SER d 60 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL d 77 " --> pdb=" O SER d 73 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA d 78 " --> pdb=" O THR d 74 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR d 84 " --> pdb=" O ALA d 80 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP d 87 " --> pdb=" O ASP d 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 129 removed outlier: 3.725A pdb=" N GLN d 124 " --> pdb=" O ARG d 120 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS d 125 " --> pdb=" O ASP d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 164 through 169 Processing helix chain 'd' and resid 178 through 233 removed outlier: 4.192A pdb=" N ALA d 187 " --> pdb=" O LYS d 183 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR d 188 " --> pdb=" O THR d 184 " (cutoff:3.500A) Processing helix chain 'd' and resid 235 through 263 removed outlier: 3.940A 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: 3.619A pdb=" N LEU e 12 " --> pdb=" O ASN e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 101 removed outlier: 4.452A pdb=" N ASN e 62 " --> pdb=" O ALA e 58 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N SER e 63 " --> pdb=" O SER e 59 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL e 64 " --> pdb=" O SER e 60 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR e 84 " --> pdb=" O ALA e 80 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP e 87 " --> pdb=" O ASP e 83 " (cutoff:3.500A) removed outlier: 4.019A 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 Processing helix chain 'e' and resid 178 through 233 removed outlier: 4.357A pdb=" N ALA e 187 " --> pdb=" O LYS e 183 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR e 188 " --> pdb=" O THR e 184 " (cutoff:3.500A) Processing helix chain 'e' and resid 235 through 263 removed outlier: 4.512A pdb=" N ALA e 241 " --> pdb=" O ALA e 237 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS e 242 " --> pdb=" O LYS e 238 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN e 251 " --> pdb=" O GLN e 247 " (cutoff:3.500A) Processing helix chain 'e' and resid 264 through 271 Processing helix chain 'f' and resid 8 through 35 removed outlier: 3.981A pdb=" N LEU f 12 " --> pdb=" O ASN f 8 " (cutoff:3.500A) Processing helix chain 'f' and resid 44 through 101 removed outlier: 4.465A pdb=" N ASN f 62 " --> pdb=" O ALA f 58 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N SER f 63 " --> pdb=" O SER f 59 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL f 64 " --> pdb=" O SER f 60 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR f 84 " --> pdb=" O ALA f 80 " (cutoff:3.500A) removed outlier: 3.944A 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 165 through 169 Processing helix chain 'f' and resid 178 through 233 removed outlier: 4.063A pdb=" N ALA f 187 " --> pdb=" O LYS f 183 " (cutoff:3.500A) Processing helix chain 'f' and resid 235 through 263 removed outlier: 3.584A pdb=" N GLU f 239 " --> pdb=" O ASP f 235 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA f 241 " --> pdb=" O ALA f 237 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN f 251 " --> pdb=" O GLN f 247 " (cutoff:3.500A) Processing helix chain 'f' and resid 264 through 271 Processing helix chain 'g' and resid 8 through 35 removed outlier: 3.714A pdb=" N LEU g 12 " --> pdb=" O ASN g 8 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 100 removed outlier: 4.514A pdb=" N ASN g 62 " --> pdb=" O ALA g 58 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N SER g 63 " --> pdb=" O SER g 59 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL g 64 " --> pdb=" O SER g 60 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR g 84 " --> pdb=" O ALA g 80 " (cutoff:3.500A) removed outlier: 3.767A 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 Processing helix chain 'g' and resid 178 through 233 removed outlier: 3.987A pdb=" N ALA g 187 " --> pdb=" O LYS g 183 " (cutoff:3.500A) Processing helix chain 'g' and resid 235 through 263 removed outlier: 4.138A pdb=" N ALA g 241 " --> pdb=" O ALA g 237 " (cutoff:3.500A) removed outlier: 3.604A 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: 3.900A pdb=" N LEU h 12 " --> pdb=" O ASN h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 44 through 60 Processing helix chain 'h' and resid 60 through 100 removed outlier: 4.117A pdb=" N VAL h 64 " --> pdb=" O SER h 60 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR h 84 " --> pdb=" O ALA h 80 " (cutoff:3.500A) removed outlier: 3.617A 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: 3.531A pdb=" N GLY h 169 " --> pdb=" O THR h 166 " (cutoff:3.500A) Processing helix chain 'h' and resid 178 through 233 removed outlier: 4.269A pdb=" N ALA h 187 " --> pdb=" O LYS h 183 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR h 188 " --> pdb=" O THR h 184 " (cutoff:3.500A) Processing helix chain 'h' and resid 235 through 263 removed outlier: 4.570A pdb=" N ALA h 241 " --> pdb=" O ALA h 237 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS h 242 " --> pdb=" O LYS h 238 " (cutoff:3.500A) removed outlier: 3.728A 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: 3.674A pdb=" N LEU i 12 " --> pdb=" O ASN i 8 " (cutoff:3.500A) Processing helix chain 'i' and resid 44 through 101 removed outlier: 3.809A pdb=" N LEU i 61 " --> pdb=" O THR i 57 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASN i 62 " --> pdb=" O ALA i 58 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N SER i 63 " --> pdb=" O SER i 59 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL i 64 " --> pdb=" O SER i 60 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR i 84 " --> pdb=" O ALA i 80 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP i 87 " --> pdb=" O ASP i 83 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP i 101 " --> pdb=" O LEU i 97 " (cutoff:3.500A) Processing helix chain 'i' and resid 105 through 129 removed outlier: 3.510A pdb=" N GLN i 124 " --> pdb=" O ARG i 120 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS i 125 " --> pdb=" O ASP i 121 " (cutoff:3.500A) Processing helix chain 'i' and resid 164 through 169 removed outlier: 3.736A pdb=" N GLY i 169 " --> pdb=" O THR i 166 " (cutoff:3.500A) Processing helix chain 'i' and resid 178 through 233 removed outlier: 4.615A pdb=" N ALA i 187 " --> pdb=" O LYS i 183 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR i 188 " --> pdb=" O THR i 184 " (cutoff:3.500A) Processing helix chain 'i' and resid 235 through 263 removed outlier: 4.009A pdb=" N ALA i 241 " --> pdb=" O ALA i 237 " (cutoff:3.500A) removed outlier: 3.760A 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: 3.709A pdb=" N LEU j 12 " --> pdb=" O ASN j 8 " (cutoff:3.500A) Processing helix chain 'j' and resid 44 through 101 removed outlier: 4.370A pdb=" N ASN j 62 " --> pdb=" O ALA j 58 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N SER j 63 " --> pdb=" O SER j 59 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL j 64 " --> pdb=" O SER j 60 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR j 84 " --> pdb=" O ALA j 80 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP j 87 " --> pdb=" O ASP j 83 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP j 101 " --> pdb=" O LEU j 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 105 through 129 Processing helix chain 'j' and resid 165 through 169 removed outlier: 3.629A pdb=" N GLY j 169 " --> pdb=" O THR j 166 " (cutoff:3.500A) Processing helix chain 'j' and resid 178 through 233 removed outlier: 3.815A pdb=" N ALA j 187 " --> pdb=" O LYS j 183 " (cutoff:3.500A) Processing helix chain 'j' and resid 235 through 263 removed outlier: 3.536A pdb=" N GLU j 239 " --> pdb=" O ASP j 235 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA j 241 " --> pdb=" O ALA j 237 " (cutoff:3.500A) Processing helix chain 'j' and resid 264 through 271 removed outlier: 3.608A pdb=" N LEU j 268 " --> pdb=" O GLN j 265 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 35 Processing helix chain 'k' and resid 44 through 60 Processing helix chain 'k' and resid 60 through 101 removed outlier: 4.116A pdb=" N VAL k 64 " --> pdb=" O SER k 60 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR k 84 " --> pdb=" O ALA k 80 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP k 87 " --> pdb=" O ASP k 83 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP k 101 " --> pdb=" O LEU k 97 " (cutoff:3.500A) Processing helix chain 'k' and resid 105 through 129 Processing helix chain 'k' and resid 164 through 169 removed outlier: 3.562A pdb=" N GLY k 169 " --> pdb=" O THR k 166 " (cutoff:3.500A) Processing helix chain 'k' and resid 178 through 233 removed outlier: 4.326A pdb=" N ALA k 187 " --> pdb=" O LYS k 183 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR k 188 " --> pdb=" O THR k 184 " (cutoff:3.500A) Processing helix chain 'k' and resid 235 through 263 removed outlier: 4.423A pdb=" N ALA k 241 " --> pdb=" O ALA k 237 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS k 242 " --> pdb=" O LYS k 238 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN k 251 " --> pdb=" O GLN k 247 " (cutoff:3.500A) Processing helix chain 'k' and resid 264 through 271 removed outlier: 3.558A pdb=" N ILE k 267 " --> pdb=" O PRO k 264 " (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 145 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 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 removed outlier: 3.579A pdb=" N PHE K 147 " --> pdb=" O PHE K 156 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 144 through 145 Processing sheet with id=AB4, first strand: chain 'M' and resid 144 through 145 Processing sheet with id=AB5, first strand: chain 'N' and resid 144 through 145 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 145 Processing sheet with id=AB8, first strand: chain 'Q' and resid 144 through 148 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 145 Processing sheet with id=AC2, first strand: chain 'T' and resid 144 through 145 Processing sheet with id=AC3, first strand: chain 'U' and resid 144 through 148 Processing sheet with id=AC4, first strand: chain 'V' and resid 144 through 148 Processing sheet with id=AC5, first strand: chain 'W' and resid 144 through 148 Processing sheet with id=AC6, first strand: chain 'X' and resid 144 through 148 Processing sheet with id=AC7, first strand: chain 'Y' and resid 144 through 148 Processing sheet with id=AC8, first strand: chain 'Z' and resid 144 through 148 Processing sheet with id=AC9, first strand: chain 'a' and resid 144 through 148 Processing sheet with id=AD1, first strand: chain 'b' and resid 144 through 148 Processing sheet with id=AD2, first strand: chain 'c' and resid 144 through 148 Processing sheet with id=AD3, first strand: chain 'd' and resid 144 through 148 Processing sheet with id=AD4, first strand: chain 'e' and resid 144 through 145 Processing sheet with id=AD5, first strand: chain 'f' and resid 144 through 148 Processing sheet with id=AD6, first strand: chain 'g' and resid 144 through 148 Processing sheet with id=AD7, first strand: chain 'h' and resid 144 through 148 Processing sheet with id=AD8, first strand: chain 'i' and resid 144 through 148 Processing sheet with id=AD9, first strand: chain 'j' and resid 144 through 148 Processing sheet with id=AE1, first strand: chain 'k' and resid 144 through 148 removed outlier: 3.579A pdb=" N PHE k 147 " --> pdb=" O PHE k 156 " (cutoff:3.500A) 6454 hydrogen bonds defined for protein. 18705 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: 25.04 Time building geometry restraints manager: 17.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 17887 1.33 - 1.45: 11790 1.45 - 1.57: 42843 1.57 - 1.69: 0 1.69 - 1.81: 296 Bond restraints: 72816 Sorted by residual: bond pdb=" CA PHE I 156 " pdb=" CB PHE I 156 " ideal model delta sigma weight residual 1.526 1.567 -0.041 1.53e-02 4.27e+03 7.13e+00 bond pdb=" CA ALA X 130 " pdb=" CB ALA X 130 " ideal model delta sigma weight residual 1.527 1.504 0.023 1.30e-02 5.92e+03 3.24e+00 bond pdb=" CA ASN S 8 " pdb=" CB ASN S 8 " ideal model delta sigma weight residual 1.526 1.543 -0.017 1.20e-02 6.94e+03 1.93e+00 bond pdb=" CA ASN U 8 " pdb=" CB ASN U 8 " ideal model delta sigma weight residual 1.530 1.551 -0.021 1.58e-02 4.01e+03 1.78e+00 bond pdb=" CA THR M 263 " pdb=" C THR M 263 " ideal model delta sigma weight residual 1.522 1.537 -0.016 1.26e-02 6.30e+03 1.52e+00 ... (remaining 72811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 97334 2.01 - 4.02: 1242 4.02 - 6.04: 154 6.04 - 8.05: 19 8.05 - 10.06: 4 Bond angle restraints: 98753 Sorted by residual: angle pdb=" C ASN O 8 " pdb=" CA ASN O 8 " pdb=" CB ASN O 8 " ideal model delta sigma weight residual 110.16 115.14 -4.98 1.33e+00 5.65e-01 1.40e+01 angle pdb=" C ASN b 8 " pdb=" CA ASN b 8 " pdb=" CB ASN b 8 " ideal model delta sigma weight residual 110.13 115.07 -4.94 1.34e+00 5.57e-01 1.36e+01 angle pdb=" C ASN W 8 " pdb=" CA ASN W 8 " pdb=" CB ASN W 8 " ideal model delta sigma weight residual 109.65 114.38 -4.73 1.30e+00 5.92e-01 1.32e+01 angle pdb=" C LEU g 231 " pdb=" N VAL g 232 " pdb=" CA VAL g 232 " ideal model delta sigma weight residual 121.85 117.55 4.30 1.19e+00 7.06e-01 1.31e+01 angle pdb=" N GLU P 117 " pdb=" CA GLU P 117 " pdb=" CB GLU P 117 " ideal model delta sigma weight residual 110.28 115.84 -5.56 1.55e+00 4.16e-01 1.29e+01 ... (remaining 98748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 41227 17.97 - 35.94: 2740 35.94 - 53.91: 358 53.91 - 71.88: 165 71.88 - 89.85: 95 Dihedral angle restraints: 44585 sinusoidal: 15910 harmonic: 28675 Sorted by residual: dihedral pdb=" CA PRO M 264 " pdb=" C PRO M 264 " pdb=" N GLN M 265 " pdb=" CA GLN M 265 " ideal model delta harmonic sigma weight residual -180.00 -161.88 -18.12 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA VAL L 232 " pdb=" C VAL L 232 " pdb=" N ASP L 233 " pdb=" CA ASP L 233 " ideal model delta harmonic sigma weight residual -180.00 -161.93 -18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASP S 235 " pdb=" C ASP S 235 " pdb=" N LEU S 236 " pdb=" CA LEU S 236 " ideal model delta harmonic sigma weight residual -180.00 -161.97 -18.03 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 44582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 11338 0.060 - 0.119: 1335 0.119 - 0.179: 115 0.179 - 0.239: 12 0.239 - 0.298: 2 Chirality restraints: 12802 Sorted by residual: chirality pdb=" CG LEU Z 224 " pdb=" CB LEU Z 224 " pdb=" CD1 LEU Z 224 " pdb=" CD2 LEU Z 224 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CG LEU B 224 " pdb=" CB LEU B 224 " pdb=" CD1 LEU B 224 " pdb=" CD2 LEU B 224 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA THR J 263 " pdb=" N THR J 263 " pdb=" C THR J 263 " pdb=" CB THR J 263 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 12799 not shown) Planarity restraints: 12617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN K 8 " -0.015 2.00e-02 2.50e+03 2.87e-02 8.21e+00 pdb=" C ASN K 8 " 0.050 2.00e-02 2.50e+03 pdb=" O ASN K 8 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO K 9 " -0.017 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 2.64e-02 6.99e+00 pdb=" C ASN f 8 " 0.046 2.00e-02 2.50e+03 pdb=" O ASN f 8 " -0.017 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=" CB TRP Q 48 " -0.025 2.00e-02 2.50e+03 1.66e-02 6.91e+00 pdb=" CG TRP Q 48 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP Q 48 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP Q 48 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP Q 48 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP Q 48 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP Q 48 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP Q 48 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP Q 48 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP Q 48 " -0.000 2.00e-02 2.50e+03 ... (remaining 12614 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 548 2.60 - 3.17: 64800 3.17 - 3.75: 118924 3.75 - 4.32: 158223 4.32 - 4.90: 260321 Nonbonded interactions: 602816 Sorted by model distance: nonbonded pdb=" OG SER G 4 " pdb=" OD2 ASP H 233 " model vdw 2.021 3.040 nonbonded pdb=" OG SER E 136 " pdb=" OD1 ASP E 139 " model vdw 2.047 3.040 nonbonded pdb=" ND2 ASN d 230 " pdb=" OE1 GLN h 69 " model vdw 2.111 3.120 nonbonded pdb=" O ALA d 256 " pdb=" NE2 GLN h 29 " model vdw 2.137 3.120 nonbonded pdb=" O ALA S 130 " pdb=" OG SER S 136 " model vdw 2.149 3.040 ... (remaining 602811 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: 12.670 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: 0.080 Extract box with map and model: 2.360 Check model and map are aligned: 0.430 Set scattering table: 0.520 Process input model: 121.340 Find NCS groups from input model: 2.810 Set up NCS constraints: 0.590 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:10.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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 0.044 72816 Z= 0.191 Angle : 0.613 10.060 98753 Z= 0.359 Chirality : 0.038 0.298 12802 Planarity : 0.004 0.054 12617 Dihedral : 13.441 89.853 25863 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.10 % Favored : 98.88 % Rotamer: Outliers : 0.04 % Allowed : 0.19 % Favored : 99.77 % 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: 0.00 (0.07), residues: 9916 helix: 0.15 (0.04), residues: 7474 sheet: -3.98 (0.15), residues: 444 loop : 1.17 (0.16), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP Q 48 HIS 0.005 0.001 HIS e 213 PHE 0.021 0.002 PHE f 116 ARG 0.009 0.001 ARG Y 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 1411 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1408 time to evaluate : 6.283 Fit side-chains revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8062 (mt-10) REVERT: B 154 SER cc_start: 0.8324 (t) cc_final: 0.8064 (p) REVERT: C 24 GLU cc_start: 0.8212 (tt0) cc_final: 0.7831 (mm-30) REVERT: D 86 THR cc_start: 0.8223 (m) cc_final: 0.7858 (p) REVERT: E 91 LYS cc_start: 0.8048 (mtpt) cc_final: 0.7691 (mtpp) REVERT: F 86 THR cc_start: 0.8080 (m) cc_final: 0.7636 (p) REVERT: G 24 GLU cc_start: 0.8047 (tt0) cc_final: 0.7820 (mm-30) REVERT: G 151 GLU cc_start: 0.7995 (pp20) cc_final: 0.7726 (pp20) REVERT: H 94 GLU cc_start: 0.8024 (tp30) cc_final: 0.7786 (mt-10) REVERT: H 115 ASP cc_start: 0.7684 (m-30) cc_final: 0.7455 (m-30) REVERT: H 131 LYS cc_start: 0.8214 (ptpt) cc_final: 0.7830 (pttp) REVERT: I 50 MET cc_start: 0.7469 (mtp) cc_final: 0.7266 (mtp) REVERT: I 87 ASP cc_start: 0.8051 (m-30) cc_final: 0.7784 (m-30) REVERT: J 54 GLN cc_start: 0.7265 (mm-40) cc_final: 0.6920 (tt0) REVERT: J 92 MET cc_start: 0.9076 (mtp) cc_final: 0.8740 (mtp) REVERT: J 131 LYS cc_start: 0.8387 (ptpp) cc_final: 0.7937 (pttp) REVERT: K 24 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7598 (tp30) REVERT: K 86 THR cc_start: 0.8084 (m) cc_final: 0.7771 (p) REVERT: K 242 LYS cc_start: 0.7795 (tttp) cc_final: 0.7503 (mtmt) REVERT: L 101 ASP cc_start: 0.5983 (p0) cc_final: 0.5648 (p0) REVERT: L 128 THR cc_start: 0.7983 (m) cc_final: 0.7632 (m) REVERT: L 150 ASN cc_start: 0.8240 (t0) cc_final: 0.7923 (t0) REVERT: L 152 ASP cc_start: 0.7520 (m-30) cc_final: 0.7263 (m-30) REVERT: O 122 GLN cc_start: 0.6909 (tp40) cc_final: 0.6699 (tm130) REVERT: O 133 ASN cc_start: 0.8278 (t0) cc_final: 0.8000 (t160) REVERT: P 31 ARG cc_start: 0.8243 (ttm-80) cc_final: 0.7814 (ttm110) REVERT: P 83 ASP cc_start: 0.7476 (m-30) cc_final: 0.7231 (m-30) REVERT: P 86 THR cc_start: 0.8474 (m) cc_final: 0.8195 (p) REVERT: P 255 GLN cc_start: 0.7461 (tt0) cc_final: 0.7155 (tp-100) REVERT: Q 94 GLU cc_start: 0.7520 (tp30) cc_final: 0.7058 (mp0) REVERT: Q 122 GLN cc_start: 0.8227 (mt0) cc_final: 0.7433 (mm-40) REVERT: Q 258 SER cc_start: 0.8432 (t) cc_final: 0.8194 (m) REVERT: R 117 GLU cc_start: 0.7792 (mt-10) cc_final: 0.6958 (pp20) REVERT: R 125 LYS cc_start: 0.7954 (mttp) cc_final: 0.6785 (tttt) REVERT: S 37 LYS cc_start: 0.8349 (ptmm) cc_final: 0.8110 (pttp) REVERT: S 75 ILE cc_start: 0.8770 (mt) cc_final: 0.8436 (tt) REVERT: S 122 GLN cc_start: 0.8077 (mt0) cc_final: 0.7393 (tp-100) REVERT: T 13 LEU cc_start: 0.8182 (mt) cc_final: 0.7899 (mm) REVERT: T 125 LYS cc_start: 0.6791 (mtmm) cc_final: 0.6225 (pptt) REVERT: U 133 ASN cc_start: 0.8148 (t0) cc_final: 0.7919 (t0) REVERT: U 222 ASP cc_start: 0.8535 (m-30) cc_final: 0.8270 (m-30) REVERT: W 185 MET cc_start: 0.8603 (tpp) cc_final: 0.8157 (tpp) REVERT: W 222 ASP cc_start: 0.7699 (p0) cc_final: 0.7302 (m-30) REVERT: X 37 LYS cc_start: 0.8639 (ttmt) cc_final: 0.8369 (tttt) REVERT: X 150 ASN cc_start: 0.7906 (t0) cc_final: 0.7601 (t0) REVERT: a 83 ASP cc_start: 0.8770 (t70) cc_final: 0.8491 (t0) REVERT: a 87 ASP cc_start: 0.8489 (t0) cc_final: 0.8152 (m-30) REVERT: a 91 LYS cc_start: 0.8104 (mmtt) cc_final: 0.7571 (mppt) REVERT: a 265 GLN cc_start: 0.8183 (mt0) cc_final: 0.7785 (mp10) REVERT: b 152 ASP cc_start: 0.7917 (m-30) cc_final: 0.7534 (p0) REVERT: c 133 ASN cc_start: 0.8702 (t0) cc_final: 0.8255 (t0) REVERT: c 177 THR cc_start: 0.7527 (m) cc_final: 0.7194 (p) REVERT: c 262 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7494 (mm110) REVERT: d 42 LYS cc_start: 0.6079 (tptt) cc_final: 0.5409 (mtmt) REVERT: e 66 ASP cc_start: 0.7718 (m-30) cc_final: 0.7478 (m-30) REVERT: e 125 LYS cc_start: 0.7742 (mtpt) cc_final: 0.7477 (mtpt) REVERT: e 131 LYS cc_start: 0.7551 (ptpt) cc_final: 0.6972 (pptt) REVERT: h 42 LYS cc_start: 0.5877 (tptt) cc_final: 0.5246 (mtmm) REVERT: h 239 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7283 (tp30) REVERT: h 262 GLN cc_start: 0.7966 (tp-100) cc_final: 0.7635 (tp-100) REVERT: i 94 GLU cc_start: 0.6646 (mm-30) cc_final: 0.6271 (mt-10) REVERT: i 267 ILE cc_start: 0.8598 (mt) cc_final: 0.8363 (pp) REVERT: k 53 MET cc_start: 0.8877 (mmm) cc_final: 0.8614 (mmm) REVERT: k 76 ASP cc_start: 0.7916 (m-30) cc_final: 0.7654 (m-30) REVERT: k 242 LYS cc_start: 0.8349 (mtpt) cc_final: 0.8032 (mttm) outliers start: 3 outliers final: 3 residues processed: 1411 average time/residue: 1.3927 time to fit residues: 2626.0844 Evaluate side-chains 929 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 926 time to evaluate : 6.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain X residue 239 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 843 optimal weight: 3.9990 chunk 757 optimal weight: 6.9990 chunk 420 optimal weight: 9.9990 chunk 258 optimal weight: 4.9990 chunk 510 optimal weight: 7.9990 chunk 404 optimal weight: 6.9990 chunk 783 optimal weight: 0.6980 chunk 303 optimal weight: 0.9990 chunk 476 optimal weight: 20.0000 chunk 582 optimal weight: 3.9990 chunk 907 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 198 ASN A 244 GLN B 129 ASN B 251 GLN B 255 GLN C 6 ASN C 40 ASN C 250 GLN C 255 GLN D 69 GLN D 129 ASN D 251 GLN D 262 GLN E 17 ASN E 250 GLN F 40 ASN F 244 GLN F 250 GLN G 6 ASN G 40 ASN G 251 GLN G 255 GLN H 40 ASN H 129 ASN H 255 GLN H 262 GLN I 230 ASN J 29 GLN J 33 ASN J 129 ASN J 230 ASN J 262 GLN K 22 ASN K 110 ASN L 72 GLN L 230 ASN L 262 GLN M 17 ASN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 ASN M 150 ASN N 54 GLN O 22 ASN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 262 GLN P 122 GLN P 150 ASN Q 29 GLN ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 124 GLN Q 129 ASN Q 247 GLN Q 255 GLN R 150 ASN R 261 ASN R 262 GLN R 265 GLN S 72 GLN ** S 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 230 ASN T 3 ASN U 17 ASN U 29 GLN U 265 GLN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 40 ASN V 129 ASN V 150 ASN W 129 ASN W 150 ASN X 40 ASN X 122 GLN X 150 ASN Y 17 ASN Y 19 ASN Y 22 ASN Y 244 GLN Y 250 GLN Z 22 ASN Z 122 GLN Z 150 ASN Z 230 ASN Z 250 GLN Z 265 GLN a 54 GLN a 262 GLN ** b 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 124 GLN b 155 ASN c 29 GLN c 54 GLN c 265 GLN d 40 ASN d 122 GLN e 17 ASN e 54 GLN e 251 GLN f 3 ASN f 6 ASN ** f 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 17 ASN ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 251 GLN f 265 GLN g 17 ASN g 44 ASN g 124 GLN g 133 ASN h 29 GLN i 17 ASN i 250 GLN j 17 ASN j 29 GLN j 40 ASN j 133 ASN j 250 GLN k 19 ASN k 244 GLN Total number of N/Q/H flips: 111 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.119429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.105314 restraints weight = 99230.385| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.41 r_work: 0.3301 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 72816 Z= 0.290 Angle : 0.577 14.085 98753 Z= 0.318 Chirality : 0.040 0.219 12802 Planarity : 0.004 0.056 12617 Dihedral : 4.233 62.732 10071 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 2.79 % Allowed : 7.13 % Favored : 90.08 % 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: 2.98 (0.08), residues: 9916 helix: 2.70 (0.06), residues: 7474 sheet: -3.62 (0.15), residues: 444 loop : 0.57 (0.15), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP Q 48 HIS 0.006 0.002 HIS f 213 PHE 0.022 0.002 PHE D 147 ARG 0.006 0.001 ARG U 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 1132 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 909 time to evaluate : 6.432 Fit side-chains revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8086 (mt-10) REVERT: C 91 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8395 (mtmp) REVERT: D 24 GLU cc_start: 0.7909 (mp0) cc_final: 0.7591 (mt-10) REVERT: D 86 THR cc_start: 0.8519 (m) cc_final: 0.8129 (p) REVERT: D 117 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8748 (mt-10) REVERT: E 91 LYS cc_start: 0.7946 (mtpt) cc_final: 0.7718 (mtpm) REVERT: F 86 THR cc_start: 0.8177 (m) cc_final: 0.7846 (p) REVERT: F 148 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8562 (mp) REVERT: F 151 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7749 (pp20) REVERT: G 24 GLU cc_start: 0.8214 (tt0) cc_final: 0.7862 (mm-30) REVERT: G 255 GLN cc_start: 0.8194 (tt0) cc_final: 0.7975 (mt0) REVERT: H 131 LYS cc_start: 0.8427 (ptpt) cc_final: 0.8112 (pttp) REVERT: I 52 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7409 (tttp) REVERT: I 87 ASP cc_start: 0.8052 (m-30) cc_final: 0.7750 (m-30) REVERT: J 92 MET cc_start: 0.9049 (mtp) cc_final: 0.8770 (mtp) REVERT: J 131 LYS cc_start: 0.8561 (ptpp) cc_final: 0.8030 (pttp) REVERT: J 255 GLN cc_start: 0.8169 (tt0) cc_final: 0.7800 (mt0) REVERT: K 86 THR cc_start: 0.8296 (m) cc_final: 0.7974 (p) REVERT: K 92 MET cc_start: 0.9018 (mtp) cc_final: 0.8779 (mtp) REVERT: K 117 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8383 (mt-10) REVERT: K 255 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7860 (mm-40) REVERT: L 8 ASN cc_start: 0.8804 (p0) cc_final: 0.8564 (p0) REVERT: L 128 THR cc_start: 0.8018 (m) cc_final: 0.7717 (m) REVERT: L 150 ASN cc_start: 0.8166 (t0) cc_final: 0.7744 (t0) REVERT: O 91 LYS cc_start: 0.7746 (mtpt) cc_final: 0.7490 (mttm) REVERT: O 150 ASN cc_start: 0.8583 (t0) cc_final: 0.8325 (t0) REVERT: P 31 ARG cc_start: 0.7969 (ttm-80) cc_final: 0.7507 (mtm110) REVERT: P 83 ASP cc_start: 0.7541 (m-30) cc_final: 0.7256 (m-30) REVERT: P 86 THR cc_start: 0.8519 (m) cc_final: 0.8062 (p) REVERT: P 255 GLN cc_start: 0.7301 (tt0) cc_final: 0.6952 (tp-100) REVERT: Q 83 ASP cc_start: 0.6911 (m-30) cc_final: 0.6662 (m-30) REVERT: Q 91 LYS cc_start: 0.7774 (tttt) cc_final: 0.7509 (mttt) REVERT: Q 94 GLU cc_start: 0.7277 (tp30) cc_final: 0.6658 (mp0) REVERT: R 125 LYS cc_start: 0.7928 (mttp) cc_final: 0.6521 (pttt) REVERT: R 235 ASP cc_start: 0.7678 (p0) cc_final: 0.7469 (p0) REVERT: R 242 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7562 (ttpp) REVERT: R 252 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7358 (tm) REVERT: S 24 GLU cc_start: 0.7873 (tp30) cc_final: 0.7618 (tp30) REVERT: S 37 LYS cc_start: 0.8221 (ptmm) cc_final: 0.7863 (pttp) REVERT: S 122 GLN cc_start: 0.7875 (mt0) cc_final: 0.7190 (tp40) REVERT: T 13 LEU cc_start: 0.8312 (mt) cc_final: 0.7931 (mm) REVERT: U 93 LYS cc_start: 0.8312 (ttpt) cc_final: 0.7913 (tttm) REVERT: U 239 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8051 (mm-30) REVERT: U 244 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8078 (mm-40) REVERT: W 222 ASP cc_start: 0.7850 (p0) cc_final: 0.7522 (m-30) REVERT: X 94 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: X 242 LYS cc_start: 0.8081 (ttmt) cc_final: 0.7499 (tptm) REVERT: Y 117 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: a 87 ASP cc_start: 0.8388 (t0) cc_final: 0.7987 (m-30) REVERT: a 91 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7720 (mppt) REVERT: a 265 GLN cc_start: 0.8114 (mt0) cc_final: 0.7818 (mp10) REVERT: b 29 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: b 66 ASP cc_start: 0.7515 (m-30) cc_final: 0.7100 (m-30) REVERT: b 177 THR cc_start: 0.7514 (m) cc_final: 0.7049 (p) REVERT: c 133 ASN cc_start: 0.8679 (t0) cc_final: 0.8245 (t0) REVERT: c 177 THR cc_start: 0.7484 (m) cc_final: 0.7002 (p) REVERT: c 262 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7662 (mt0) REVERT: d 42 LYS cc_start: 0.6041 (tptt) cc_final: 0.5248 (mtmt) REVERT: e 24 GLU cc_start: 0.8534 (tp30) cc_final: 0.7840 (mt-10) REVERT: e 66 ASP cc_start: 0.7764 (m-30) cc_final: 0.7327 (m-30) REVERT: e 131 LYS cc_start: 0.7904 (ptpt) cc_final: 0.7421 (pttp) REVERT: e 154 SER cc_start: 0.8699 (OUTLIER) cc_final: 0.7971 (p) REVERT: f 24 GLU cc_start: 0.8051 (tp30) cc_final: 0.7830 (tt0) REVERT: f 151 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7853 (pp20) REVERT: f 267 ILE cc_start: 0.8851 (tp) cc_final: 0.8643 (tp) REVERT: g 151 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8008 (pp20) REVERT: h 42 LYS cc_start: 0.5781 (tptt) cc_final: 0.5030 (mtmm) REVERT: h 262 GLN cc_start: 0.7881 (tp-100) cc_final: 0.7477 (tp-100) REVERT: h 265 GLN cc_start: 0.6796 (OUTLIER) cc_final: 0.6362 (mm110) REVERT: i 94 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6883 (mt-10) REVERT: j 83 ASP cc_start: 0.8177 (m-30) cc_final: 0.7952 (m-30) REVERT: j 92 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8179 (mtt) REVERT: k 76 ASP cc_start: 0.8161 (m-30) cc_final: 0.7902 (m-30) REVERT: k 117 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.7575 (mm-30) REVERT: k 242 LYS cc_start: 0.8544 (mtpt) cc_final: 0.8210 (mttm) outliers start: 223 outliers final: 104 residues processed: 1046 average time/residue: 1.3571 time to fit residues: 1925.0284 Evaluate side-chains 956 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 836 time to evaluate : 6.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 250 GLN Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain I residue 52 LYS Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 269 SER Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain K residue 248 THR Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 255 GLN Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 91 LYS Chi-restraints excluded: chain L residue 95 LYS Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 34 THR Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain N residue 94 GLU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain P residue 258 SER Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 73 SER Chi-restraints excluded: chain Q residue 252 LEU Chi-restraints excluded: chain R residue 8 ASN Chi-restraints excluded: chain R residue 242 LYS Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain T residue 55 SER Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain T residue 152 ASP Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain T residue 263 THR Chi-restraints excluded: chain U residue 154 SER Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 232 VAL Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain V residue 13 LEU Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain V residue 222 ASP Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 244 GLN Chi-restraints excluded: chain W residue 252 LEU Chi-restraints excluded: chain W residue 263 THR Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain X residue 94 GLU Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 117 GLU Chi-restraints excluded: chain Z residue 13 LEU Chi-restraints excluded: chain Z residue 91 LYS Chi-restraints excluded: chain a residue 67 SER Chi-restraints excluded: chain a residue 84 THR Chi-restraints excluded: chain a residue 207 SER Chi-restraints excluded: chain a residue 210 LEU Chi-restraints excluded: chain b residue 2 LEU Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 29 GLN Chi-restraints excluded: chain b residue 168 ILE Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 2 LEU Chi-restraints excluded: chain c residue 15 LEU Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain d residue 5 ILE Chi-restraints excluded: chain d residue 108 SER Chi-restraints excluded: chain d residue 184 THR Chi-restraints excluded: chain d residue 239 GLU Chi-restraints excluded: chain e residue 85 ILE Chi-restraints excluded: chain e residue 154 SER Chi-restraints excluded: chain e residue 168 ILE Chi-restraints excluded: chain e residue 184 THR Chi-restraints excluded: chain e residue 232 VAL Chi-restraints excluded: chain e residue 267 ILE Chi-restraints excluded: chain f residue 52 LYS Chi-restraints excluded: chain f residue 128 THR Chi-restraints excluded: chain f residue 151 GLU Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 151 GLU Chi-restraints excluded: chain h residue 131 LYS Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 265 GLN Chi-restraints excluded: chain i residue 7 THR Chi-restraints excluded: chain i residue 86 THR Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 250 GLN Chi-restraints excluded: chain i residue 267 ILE Chi-restraints excluded: chain j residue 92 MET Chi-restraints excluded: chain j residue 157 THR Chi-restraints excluded: chain j residue 267 ILE Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 117 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 442 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 877 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 403 optimal weight: 0.8980 chunk 912 optimal weight: 0.9980 chunk 191 optimal weight: 7.9990 chunk 873 optimal weight: 8.9990 chunk 174 optimal weight: 0.9990 chunk 283 optimal weight: 7.9990 chunk 687 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 ASN B 251 GLN B 255 GLN C 29 GLN C 133 ASN C 250 GLN C 255 GLN C 265 GLN D 262 GLN E 250 GLN H 29 GLN H 262 GLN I 69 GLN J 261 ASN L 72 GLN L 262 GLN M 133 ASN M 150 ASN N 54 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 133 ASN O 262 GLN R 54 GLN S 133 ASN S 150 ASN S 262 GLN T 150 ASN U 3 ASN U 17 ASN U 19 ASN U 124 GLN U 251 GLN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 40 ASN W 40 ASN W 129 ASN X 40 ASN X 129 ASN Y 19 ASN Y 129 ASN Y 244 GLN Z 150 ASN Z 230 ASN Z 250 GLN a 17 ASN a 54 GLN a 122 GLN ** b 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 122 GLN c 265 GLN d 40 ASN d 122 GLN d 230 ASN e 3 ASN f 8 ASN ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 133 ASN h 69 GLN ** i 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 110 ASN i 133 ASN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.124094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.109951 restraints weight = 98886.441| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.42 r_work: 0.3373 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 72816 Z= 0.152 Angle : 0.435 11.035 98753 Z= 0.245 Chirality : 0.033 0.197 12802 Planarity : 0.003 0.049 12617 Dihedral : 3.823 52.600 10066 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.21 % Allowed : 8.85 % Favored : 88.94 % 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: 3.95 (0.09), residues: 9916 helix: 3.53 (0.06), residues: 7511 sheet: -3.23 (0.16), residues: 444 loop : 0.18 (0.15), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP d 48 HIS 0.003 0.001 HIS e 213 PHE 0.016 0.001 PHE R 109 ARG 0.003 0.000 ARG N 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 1142 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 965 time to evaluate : 6.475 Fit side-chains REVERT: D 86 THR cc_start: 0.8534 (m) cc_final: 0.8061 (p) REVERT: D 265 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7949 (mm-40) REVERT: E 87 ASP cc_start: 0.8050 (m-30) cc_final: 0.7842 (m-30) REVERT: E 91 LYS cc_start: 0.7876 (mtpt) cc_final: 0.7463 (mtpp) REVERT: E 239 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7827 (mm-30) REVERT: F 86 THR cc_start: 0.8082 (m) cc_final: 0.7715 (p) REVERT: F 151 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7702 (pp20) REVERT: F 242 LYS cc_start: 0.8306 (mtpt) cc_final: 0.8059 (mtpp) REVERT: G 24 GLU cc_start: 0.8184 (tt0) cc_final: 0.7807 (mm-30) REVERT: G 255 GLN cc_start: 0.8152 (tt0) cc_final: 0.7926 (mt0) REVERT: H 131 LYS cc_start: 0.8267 (ptpt) cc_final: 0.7911 (pttp) REVERT: I 52 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7405 (tttp) REVERT: I 87 ASP cc_start: 0.7982 (m-30) cc_final: 0.7632 (m-30) REVERT: I 255 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6875 (mm110) REVERT: J 54 GLN cc_start: 0.7352 (mm-40) cc_final: 0.6692 (tt0) REVERT: J 92 MET cc_start: 0.9055 (mtp) cc_final: 0.8710 (mtp) REVERT: J 131 LYS cc_start: 0.8439 (ptpp) cc_final: 0.7974 (pttp) REVERT: K 86 THR cc_start: 0.8125 (m) cc_final: 0.7784 (p) REVERT: K 92 MET cc_start: 0.8987 (mtp) cc_final: 0.8500 (mtp) REVERT: K 251 GLN cc_start: 0.7262 (tp-100) cc_final: 0.7016 (tp-100) REVERT: L 8 ASN cc_start: 0.8563 (p0) cc_final: 0.8342 (p0) REVERT: L 24 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7653 (mt-10) REVERT: L 92 MET cc_start: 0.7350 (mtp) cc_final: 0.6958 (mtp) REVERT: L 128 THR cc_start: 0.7892 (m) cc_final: 0.7596 (m) REVERT: L 150 ASN cc_start: 0.8009 (t0) cc_final: 0.7589 (t0) REVERT: L 231 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8120 (mp) REVERT: M 250 GLN cc_start: 0.8537 (tt0) cc_final: 0.8297 (tt0) REVERT: O 150 ASN cc_start: 0.8346 (t0) cc_final: 0.7965 (t0) REVERT: P 31 ARG cc_start: 0.7794 (ttm-80) cc_final: 0.7384 (ttm110) REVERT: P 83 ASP cc_start: 0.7445 (m-30) cc_final: 0.7059 (m-30) REVERT: P 86 THR cc_start: 0.8325 (m) cc_final: 0.7785 (p) REVERT: P 255 GLN cc_start: 0.7355 (tt0) cc_final: 0.7005 (tp-100) REVERT: Q 83 ASP cc_start: 0.6988 (m-30) cc_final: 0.6755 (m-30) REVERT: Q 91 LYS cc_start: 0.7605 (tttt) cc_final: 0.7366 (mttt) REVERT: Q 94 GLU cc_start: 0.7299 (tp30) cc_final: 0.6533 (mp0) REVERT: Q 122 GLN cc_start: 0.8129 (mt0) cc_final: 0.7118 (mm-40) REVERT: R 125 LYS cc_start: 0.7760 (mttp) cc_final: 0.6536 (tttt) REVERT: S 24 GLU cc_start: 0.7776 (tp30) cc_final: 0.7510 (tp30) REVERT: S 37 LYS cc_start: 0.8171 (ptmm) cc_final: 0.7728 (pttp) REVERT: S 75 ILE cc_start: 0.8579 (mt) cc_final: 0.8272 (tt) REVERT: S 122 GLN cc_start: 0.7789 (mt0) cc_final: 0.7132 (tp40) REVERT: T 13 LEU cc_start: 0.8170 (mt) cc_final: 0.7804 (mm) REVERT: T 76 ASP cc_start: 0.8168 (t70) cc_final: 0.7689 (t70) REVERT: T 83 ASP cc_start: 0.8378 (t70) cc_final: 0.8013 (t70) REVERT: T 122 GLN cc_start: 0.8267 (mt0) cc_final: 0.7201 (tp40) REVERT: U 244 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8064 (mm-40) REVERT: V 13 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7807 (mm) REVERT: W 222 ASP cc_start: 0.7763 (p0) cc_final: 0.7467 (m-30) REVERT: X 94 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7552 (tm-30) REVERT: X 222 ASP cc_start: 0.7684 (p0) cc_final: 0.6912 (m-30) REVERT: X 242 LYS cc_start: 0.7854 (ttmt) cc_final: 0.7181 (tptm) REVERT: a 87 ASP cc_start: 0.8328 (t0) cc_final: 0.7906 (m-30) REVERT: a 91 LYS cc_start: 0.8264 (mmtt) cc_final: 0.7657 (mppt) REVERT: a 94 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7555 (mm-30) REVERT: a 117 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8251 (mm-30) REVERT: a 265 GLN cc_start: 0.8105 (mt0) cc_final: 0.7760 (mp10) REVERT: b 177 THR cc_start: 0.7531 (m) cc_final: 0.7040 (p) REVERT: c 36 LYS cc_start: 0.8786 (mttt) cc_final: 0.8426 (mttp) REVERT: c 133 ASN cc_start: 0.8553 (t0) cc_final: 0.8116 (t0) REVERT: c 151 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7569 (pp20) REVERT: c 177 THR cc_start: 0.7361 (m) cc_final: 0.6856 (p) REVERT: c 262 GLN cc_start: 0.7706 (mm-40) cc_final: 0.7455 (mm-40) REVERT: d 42 LYS cc_start: 0.6076 (tptt) cc_final: 0.5433 (mtmt) REVERT: d 60 SER cc_start: 0.7841 (t) cc_final: 0.7628 (m) REVERT: d 120 ARG cc_start: 0.6876 (tmm160) cc_final: 0.6614 (tmm160) REVERT: d 251 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8276 (mp10) REVERT: e 24 GLU cc_start: 0.8485 (tp30) cc_final: 0.7777 (mt-10) REVERT: e 66 ASP cc_start: 0.7542 (m-30) cc_final: 0.7097 (m-30) REVERT: e 110 ASN cc_start: 0.7622 (m-40) cc_final: 0.7402 (m110) REVERT: e 131 LYS cc_start: 0.7847 (ptpt) cc_final: 0.7275 (mtmt) REVERT: e 154 SER cc_start: 0.8642 (OUTLIER) cc_final: 0.7920 (p) REVERT: f 24 GLU cc_start: 0.8120 (tp30) cc_final: 0.7814 (tt0) REVERT: f 151 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7738 (pp20) REVERT: f 267 ILE cc_start: 0.8814 (tp) cc_final: 0.8593 (tp) REVERT: h 42 LYS cc_start: 0.5723 (tptt) cc_final: 0.4956 (mtmm) REVERT: h 151 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7913 (pt0) REVERT: h 262 GLN cc_start: 0.7789 (tp-100) cc_final: 0.7380 (tp-100) REVERT: h 265 GLN cc_start: 0.6729 (mm110) cc_final: 0.6336 (mm-40) REVERT: i 94 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6780 (mt-10) REVERT: i 123 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8773 (tt) REVERT: j 151 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8040 (pp20) REVERT: k 76 ASP cc_start: 0.8057 (m-30) cc_final: 0.7788 (m-30) REVERT: k 242 LYS cc_start: 0.8491 (mtpt) cc_final: 0.8142 (mttm) outliers start: 177 outliers final: 68 residues processed: 1070 average time/residue: 1.3527 time to fit residues: 1969.4106 Evaluate side-chains 959 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 876 time to evaluate : 6.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 250 GLN Chi-restraints excluded: chain I residue 52 LYS Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 255 GLN Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain K residue 248 THR Chi-restraints excluded: chain L residue 3 ASN Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 91 LYS Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain N residue 115 ASP Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 73 SER Chi-restraints excluded: chain Q residue 252 LEU Chi-restraints excluded: chain R residue 8 ASN Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain T residue 55 SER Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain U residue 154 SER Chi-restraints excluded: chain U residue 232 VAL Chi-restraints excluded: chain V residue 13 LEU Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 231 LEU Chi-restraints excluded: chain W residue 252 LEU Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain X residue 94 GLU Chi-restraints excluded: chain X residue 239 GLU Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 207 SER Chi-restraints excluded: chain a residue 255 GLN Chi-restraints excluded: chain b residue 2 LEU Chi-restraints excluded: chain b residue 135 VAL Chi-restraints excluded: chain b residue 168 ILE Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 15 LEU Chi-restraints excluded: chain c residue 52 LYS Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain d residue 108 SER Chi-restraints excluded: chain d residue 239 GLU Chi-restraints excluded: chain d residue 251 GLN Chi-restraints excluded: chain e residue 154 SER Chi-restraints excluded: chain e residue 168 ILE Chi-restraints excluded: chain e residue 232 VAL Chi-restraints excluded: chain e residue 267 ILE Chi-restraints excluded: chain f residue 151 GLU Chi-restraints excluded: chain h residue 128 THR Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 131 LYS Chi-restraints excluded: chain h residue 151 GLU Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain i residue 123 LEU Chi-restraints excluded: chain i residue 267 ILE Chi-restraints excluded: chain j residue 151 GLU Chi-restraints excluded: chain j residue 157 THR Chi-restraints excluded: chain j residue 267 ILE Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 150 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 923 optimal weight: 4.9990 chunk 739 optimal weight: 1.9990 chunk 887 optimal weight: 0.9990 chunk 962 optimal weight: 9.9990 chunk 395 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 790 optimal weight: 6.9990 chunk 404 optimal weight: 0.8980 chunk 605 optimal weight: 4.9990 chunk 737 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 GLN B 255 GLN C 250 GLN C 255 GLN D 251 GLN D 262 GLN E 250 GLN E 262 GLN H 262 GLN L 3 ASN L 72 GLN L 262 GLN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 230 ASN N 54 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 250 GLN O 262 GLN Q 250 GLN R 54 GLN S 230 ASN T 255 GLN U 40 ASN U 250 GLN V 29 GLN V 150 ASN W 150 ASN X 40 ASN X 122 GLN Y 250 GLN Z 150 ASN Z 230 ASN Z 250 GLN a 54 GLN a 122 GLN a 262 GLN ** b 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 265 GLN d 122 GLN d 133 ASN d 230 ASN f 8 ASN ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 29 GLN ** i 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 110 ASN i 250 GLN j 29 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.121191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.107028 restraints weight = 99071.220| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.41 r_work: 0.3333 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 72816 Z= 0.194 Angle : 0.463 12.782 98753 Z= 0.258 Chirality : 0.035 0.198 12802 Planarity : 0.003 0.065 12617 Dihedral : 3.828 18.022 10064 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.58 % Allowed : 9.66 % Favored : 87.76 % 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: 4.10 (0.09), residues: 9916 helix: 3.66 (0.06), residues: 7474 sheet: -2.93 (0.16), residues: 444 loop : 0.15 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP d 48 HIS 0.004 0.001 HIS f 213 PHE 0.017 0.002 PHE R 109 ARG 0.003 0.000 ARG U 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 1109 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 903 time to evaluate : 6.487 Fit side-chains revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8604 (pm20) cc_final: 0.8356 (pp20) REVERT: C 94 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7933 (mt-10) REVERT: D 86 THR cc_start: 0.8555 (m) cc_final: 0.8079 (p) REVERT: D 265 GLN cc_start: 0.8299 (mm-40) cc_final: 0.8057 (mm-40) REVERT: E 87 ASP cc_start: 0.8134 (m-30) cc_final: 0.7917 (m-30) REVERT: E 91 LYS cc_start: 0.7894 (mtpt) cc_final: 0.7547 (mtpp) REVERT: E 239 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7828 (mm-30) REVERT: F 86 THR cc_start: 0.8155 (m) cc_final: 0.7768 (p) REVERT: F 151 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7684 (pp20) REVERT: G 24 GLU cc_start: 0.8232 (tt0) cc_final: 0.7825 (mm-30) REVERT: G 151 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7695 (pp20) REVERT: G 255 GLN cc_start: 0.8165 (tt0) cc_final: 0.7951 (mt0) REVERT: H 131 LYS cc_start: 0.8290 (ptpt) cc_final: 0.8021 (pttp) REVERT: I 52 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7425 (tttp) REVERT: I 87 ASP cc_start: 0.8035 (m-30) cc_final: 0.7719 (m-30) REVERT: I 117 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6584 (mm-30) REVERT: I 255 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6775 (mm110) REVERT: J 54 GLN cc_start: 0.7348 (mm-40) cc_final: 0.6707 (tt0) REVERT: J 92 MET cc_start: 0.9045 (mtp) cc_final: 0.8780 (mtp) REVERT: K 86 THR cc_start: 0.8197 (m) cc_final: 0.7858 (p) REVERT: K 117 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8371 (mt-10) REVERT: K 251 GLN cc_start: 0.7285 (tp-100) cc_final: 0.7055 (tp-100) REVERT: K 255 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7785 (mm-40) REVERT: L 8 ASN cc_start: 0.8618 (p0) cc_final: 0.8372 (p0) REVERT: L 24 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7694 (mt-10) REVERT: L 92 MET cc_start: 0.7352 (mtp) cc_final: 0.6953 (mtp) REVERT: L 128 THR cc_start: 0.7913 (m) cc_final: 0.7628 (m) REVERT: L 150 ASN cc_start: 0.8082 (t0) cc_final: 0.7652 (t0) REVERT: L 152 ASP cc_start: 0.7482 (m-30) cc_final: 0.7277 (m-30) REVERT: L 231 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8116 (mp) REVERT: M 76 ASP cc_start: 0.8128 (m-30) cc_final: 0.7914 (m-30) REVERT: N 120 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7281 (ptt90) REVERT: P 5 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7350 (pp) REVERT: P 31 ARG cc_start: 0.7786 (ttm-80) cc_final: 0.7386 (ttm110) REVERT: P 83 ASP cc_start: 0.7397 (m-30) cc_final: 0.7062 (m-30) REVERT: P 86 THR cc_start: 0.8334 (m) cc_final: 0.7813 (p) REVERT: P 122 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6539 (tm-30) REVERT: P 163 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8288 (mp) REVERT: P 255 GLN cc_start: 0.7362 (tt0) cc_final: 0.6968 (tp-100) REVERT: Q 91 LYS cc_start: 0.7643 (tttt) cc_final: 0.7383 (mttt) REVERT: Q 94 GLU cc_start: 0.7413 (tp30) cc_final: 0.6657 (mp0) REVERT: Q 122 GLN cc_start: 0.8154 (mt0) cc_final: 0.7128 (mm-40) REVERT: R 125 LYS cc_start: 0.7794 (mttp) cc_final: 0.6538 (tttt) REVERT: S 24 GLU cc_start: 0.7786 (tp30) cc_final: 0.7510 (tp30) REVERT: S 37 LYS cc_start: 0.8189 (ptmm) cc_final: 0.7781 (pttp) REVERT: S 75 ILE cc_start: 0.8653 (mt) cc_final: 0.8335 (tt) REVERT: S 122 GLN cc_start: 0.7763 (mt0) cc_final: 0.7125 (tp40) REVERT: T 13 LEU cc_start: 0.8197 (mt) cc_final: 0.7816 (mm) REVERT: T 76 ASP cc_start: 0.8186 (t70) cc_final: 0.7727 (t70) REVERT: T 83 ASP cc_start: 0.8347 (t70) cc_final: 0.7978 (t70) REVERT: T 122 GLN cc_start: 0.8240 (mt0) cc_final: 0.7198 (tp40) REVERT: T 252 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7952 (tt) REVERT: U 83 ASP cc_start: 0.8152 (t70) cc_final: 0.7838 (t0) REVERT: U 244 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8153 (mm-40) REVERT: V 13 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7873 (mm) REVERT: V 231 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7718 (mp) REVERT: X 94 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: X 222 ASP cc_start: 0.7663 (p0) cc_final: 0.7195 (m-30) REVERT: X 231 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8372 (mp) REVERT: X 242 LYS cc_start: 0.7874 (ttmt) cc_final: 0.7223 (tptm) REVERT: Z 242 LYS cc_start: 0.8349 (mttt) cc_final: 0.7764 (mmtt) REVERT: a 87 ASP cc_start: 0.8349 (t0) cc_final: 0.7926 (m-30) REVERT: a 91 LYS cc_start: 0.8321 (mmtt) cc_final: 0.7721 (mppt) REVERT: a 94 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7674 (mm-30) REVERT: a 255 GLN cc_start: 0.6699 (OUTLIER) cc_final: 0.6496 (mm110) REVERT: a 265 GLN cc_start: 0.8075 (mt0) cc_final: 0.7727 (mp10) REVERT: b 7 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8091 (t) REVERT: b 177 THR cc_start: 0.7547 (m) cc_final: 0.7073 (p) REVERT: c 133 ASN cc_start: 0.8611 (t0) cc_final: 0.8162 (t0) REVERT: c 151 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7574 (pp20) REVERT: c 262 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7524 (mm-40) REVERT: d 42 LYS cc_start: 0.6301 (tptt) cc_final: 0.5567 (mtmt) REVERT: d 60 SER cc_start: 0.7896 (t) cc_final: 0.7675 (m) REVERT: d 251 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8284 (mp10) REVERT: e 24 GLU cc_start: 0.8462 (tp30) cc_final: 0.8130 (tp30) REVERT: e 66 ASP cc_start: 0.7609 (m-30) cc_final: 0.7141 (m-30) REVERT: e 131 LYS cc_start: 0.7866 (ptpt) cc_final: 0.7337 (mtmt) REVERT: f 24 GLU cc_start: 0.8142 (tp30) cc_final: 0.7825 (tt0) REVERT: f 65 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.7980 (mttt) REVERT: f 151 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7755 (pp20) REVERT: f 267 ILE cc_start: 0.8871 (tp) cc_final: 0.8628 (tp) REVERT: g 151 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8029 (pp20) REVERT: h 42 LYS cc_start: 0.5852 (tptt) cc_final: 0.5067 (mtmm) REVERT: h 84 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8605 (p) REVERT: h 265 GLN cc_start: 0.6700 (OUTLIER) cc_final: 0.6384 (mm-40) REVERT: i 94 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6768 (mt-10) REVERT: i 123 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8771 (tt) REVERT: i 186 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8048 (mt) REVERT: j 117 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8384 (mt-10) REVERT: j 151 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8047 (pp20) REVERT: k 76 ASP cc_start: 0.8064 (m-30) cc_final: 0.7788 (m-30) REVERT: k 117 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.7582 (mm-30) REVERT: k 242 LYS cc_start: 0.8484 (mtpt) cc_final: 0.8149 (mttm) outliers start: 206 outliers final: 103 residues processed: 1027 average time/residue: 1.3536 time to fit residues: 1872.8184 Evaluate side-chains 989 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 853 time to evaluate : 6.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 255 GLN Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 250 GLN Chi-restraints excluded: chain I residue 52 LYS Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 255 GLN Chi-restraints excluded: chain I residue 269 SER Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain K residue 248 THR Chi-restraints excluded: chain K residue 255 GLN Chi-restraints excluded: chain L residue 3 ASN Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 91 LYS Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain N residue 115 ASP Chi-restraints excluded: chain N residue 120 ARG Chi-restraints excluded: chain N residue 128 THR Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 258 SER Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain O residue 83 ASP Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 115 ASP Chi-restraints excluded: chain P residue 122 GLN Chi-restraints excluded: chain P residue 163 LEU Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 73 SER Chi-restraints excluded: chain Q residue 252 LEU Chi-restraints excluded: chain R residue 8 ASN Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain S residue 231 LEU Chi-restraints excluded: chain T residue 55 SER Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain T residue 152 ASP Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain T residue 252 LEU Chi-restraints excluded: chain U residue 91 LYS Chi-restraints excluded: chain U residue 154 SER Chi-restraints excluded: chain U residue 232 VAL Chi-restraints excluded: chain V residue 8 ASN Chi-restraints excluded: chain V residue 13 LEU Chi-restraints excluded: chain V residue 24 GLU Chi-restraints excluded: chain V residue 40 ASN Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain V residue 231 LEU Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 231 LEU Chi-restraints excluded: chain W residue 244 GLN Chi-restraints excluded: chain W residue 252 LEU Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain X residue 94 GLU Chi-restraints excluded: chain X residue 231 LEU Chi-restraints excluded: chain X residue 239 GLU Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 263 THR Chi-restraints excluded: chain Z residue 91 LYS Chi-restraints excluded: chain Z residue 258 SER Chi-restraints excluded: chain a residue 84 THR Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 122 GLN Chi-restraints excluded: chain a residue 207 SER Chi-restraints excluded: chain a residue 210 LEU Chi-restraints excluded: chain a residue 255 GLN Chi-restraints excluded: chain b residue 2 LEU Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 135 VAL Chi-restraints excluded: chain b residue 168 ILE Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 15 LEU Chi-restraints excluded: chain c residue 52 LYS Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain d residue 108 SER Chi-restraints excluded: chain d residue 184 THR Chi-restraints excluded: chain d residue 239 GLU Chi-restraints excluded: chain d residue 251 GLN Chi-restraints excluded: chain e residue 85 ILE Chi-restraints excluded: chain e residue 154 SER Chi-restraints excluded: chain e residue 168 ILE Chi-restraints excluded: chain e residue 232 VAL Chi-restraints excluded: chain e residue 267 ILE Chi-restraints excluded: chain f residue 52 LYS Chi-restraints excluded: chain f residue 65 LYS Chi-restraints excluded: chain f residue 151 GLU Chi-restraints excluded: chain g residue 151 GLU Chi-restraints excluded: chain h residue 69 GLN Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain h residue 128 THR Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 131 LYS Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 265 GLN Chi-restraints excluded: chain i residue 89 LEU Chi-restraints excluded: chain i residue 123 LEU Chi-restraints excluded: chain i residue 186 ILE Chi-restraints excluded: chain i residue 267 ILE Chi-restraints excluded: chain j residue 92 MET Chi-restraints excluded: chain j residue 117 GLU Chi-restraints excluded: chain j residue 151 GLU Chi-restraints excluded: chain j residue 157 THR Chi-restraints excluded: chain j residue 267 ILE Chi-restraints excluded: chain j residue 268 LEU Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 117 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 93 optimal weight: 9.9990 chunk 358 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 659 optimal weight: 5.9990 chunk 442 optimal weight: 7.9990 chunk 943 optimal weight: 0.7980 chunk 509 optimal weight: 2.9990 chunk 424 optimal weight: 2.9990 chunk 922 optimal weight: 4.9990 chunk 891 optimal weight: 10.0000 chunk 567 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 GLN B 255 GLN C 250 GLN C 255 GLN D 251 GLN D 262 GLN E 250 GLN H 262 GLN I 261 ASN L 3 ASN L 72 GLN L 262 GLN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 ASN N 54 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN ** U 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 150 ASN W 150 ASN X 40 ASN Z 150 ASN Z 230 ASN Z 250 GLN Z 265 GLN a 17 ASN a 54 GLN ** a 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 265 GLN c 122 GLN d 122 GLN d 133 ASN f 8 ASN f 265 GLN g 44 ASN g 133 ASN h 29 GLN i 110 ASN i 250 GLN i 251 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.121104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.106912 restraints weight = 98828.295| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.41 r_work: 0.3333 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 72816 Z= 0.195 Angle : 0.458 11.869 98753 Z= 0.256 Chirality : 0.034 0.199 12802 Planarity : 0.003 0.058 12617 Dihedral : 3.812 17.871 10064 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 2.70 % Allowed : 9.98 % Favored : 87.31 % 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: 4.14 (0.08), residues: 9916 helix: 3.71 (0.06), residues: 7474 sheet: -2.67 (0.17), residues: 444 loop : -0.01 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP d 48 HIS 0.004 0.001 HIS f 213 PHE 0.018 0.002 PHE R 109 ARG 0.004 0.000 ARG Q 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 1108 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 892 time to evaluate : 6.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7735 (mp) REVERT: A 151 GLU cc_start: 0.8607 (pm20) cc_final: 0.8356 (pp20) REVERT: D 265 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7966 (mm-40) REVERT: E 87 ASP cc_start: 0.8119 (m-30) cc_final: 0.7892 (m-30) REVERT: E 91 LYS cc_start: 0.7872 (mtpt) cc_final: 0.7490 (mtpp) REVERT: E 239 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7848 (mm-30) REVERT: F 86 THR cc_start: 0.8108 (m) cc_final: 0.7730 (p) REVERT: F 151 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7676 (pp20) REVERT: G 24 GLU cc_start: 0.8210 (tt0) cc_final: 0.7812 (mm-30) REVERT: G 151 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7710 (pp20) REVERT: G 255 GLN cc_start: 0.8147 (tt0) cc_final: 0.7929 (mt0) REVERT: H 2 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6048 (tm) REVERT: H 131 LYS cc_start: 0.8272 (ptpt) cc_final: 0.7989 (pttp) REVERT: I 52 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7398 (tttp) REVERT: I 87 ASP cc_start: 0.8026 (m-30) cc_final: 0.7706 (m-30) REVERT: I 117 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.6566 (mm-30) REVERT: I 255 GLN cc_start: 0.7062 (OUTLIER) cc_final: 0.6751 (mm110) REVERT: J 54 GLN cc_start: 0.7392 (mm-40) cc_final: 0.6721 (tt0) REVERT: J 92 MET cc_start: 0.9028 (mtp) cc_final: 0.8773 (mtp) REVERT: K 86 THR cc_start: 0.8216 (m) cc_final: 0.7850 (p) REVERT: K 117 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8354 (mt-10) REVERT: K 251 GLN cc_start: 0.7276 (tp-100) cc_final: 0.7003 (tp-100) REVERT: L 8 ASN cc_start: 0.8612 (p0) cc_final: 0.8360 (p0) REVERT: L 24 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: L 92 MET cc_start: 0.7335 (mtp) cc_final: 0.6922 (mtp) REVERT: L 150 ASN cc_start: 0.8077 (t0) cc_final: 0.7629 (t0) REVERT: L 231 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8142 (mp) REVERT: M 76 ASP cc_start: 0.8119 (m-30) cc_final: 0.7913 (m-30) REVERT: N 120 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7385 (ptt90) REVERT: O 251 GLN cc_start: 0.8266 (mt0) cc_final: 0.7966 (mt0) REVERT: P 5 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7182 (pp) REVERT: P 31 ARG cc_start: 0.7815 (ttm-80) cc_final: 0.7396 (ttm110) REVERT: P 86 THR cc_start: 0.8294 (m) cc_final: 0.7763 (p) REVERT: P 122 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6608 (tm-30) REVERT: P 163 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8292 (mp) REVERT: P 255 GLN cc_start: 0.7410 (tt0) cc_final: 0.6930 (tp-100) REVERT: Q 83 ASP cc_start: 0.6854 (m-30) cc_final: 0.6596 (m-30) REVERT: Q 91 LYS cc_start: 0.7635 (tttt) cc_final: 0.7374 (mttt) REVERT: Q 94 GLU cc_start: 0.7416 (tp30) cc_final: 0.6647 (mp0) REVERT: Q 122 GLN cc_start: 0.8126 (mt0) cc_final: 0.7119 (mm-40) REVERT: R 125 LYS cc_start: 0.7781 (mttp) cc_final: 0.6536 (tttt) REVERT: R 252 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7479 (tm) REVERT: S 24 GLU cc_start: 0.7763 (tp30) cc_final: 0.7491 (tp30) REVERT: S 37 LYS cc_start: 0.8176 (ptmm) cc_final: 0.7767 (pttp) REVERT: S 75 ILE cc_start: 0.8643 (mt) cc_final: 0.8336 (tt) REVERT: S 122 GLN cc_start: 0.7754 (mt0) cc_final: 0.7108 (tp40) REVERT: T 13 LEU cc_start: 0.8182 (mt) cc_final: 0.7793 (mm) REVERT: T 76 ASP cc_start: 0.8172 (t70) cc_final: 0.7692 (t70) REVERT: T 83 ASP cc_start: 0.8339 (t70) cc_final: 0.7966 (t70) REVERT: T 122 GLN cc_start: 0.8214 (mt0) cc_final: 0.7173 (tp40) REVERT: T 252 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7955 (tt) REVERT: U 83 ASP cc_start: 0.8159 (t70) cc_final: 0.7833 (t0) REVERT: U 91 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7950 (mtpt) REVERT: U 244 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8154 (mm-40) REVERT: V 13 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7852 (mm) REVERT: V 94 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7637 (tm-30) REVERT: V 231 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7705 (mp) REVERT: X 94 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: X 211 ASP cc_start: 0.8095 (p0) cc_final: 0.7887 (p0) REVERT: X 231 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8310 (mp) REVERT: X 242 LYS cc_start: 0.7877 (ttmt) cc_final: 0.7221 (tptm) REVERT: Y 117 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.8015 (mp0) REVERT: a 87 ASP cc_start: 0.8355 (t0) cc_final: 0.7915 (m-30) REVERT: a 91 LYS cc_start: 0.8305 (mmtt) cc_final: 0.7711 (mppt) REVERT: a 265 GLN cc_start: 0.8076 (mt0) cc_final: 0.7779 (mp10) REVERT: b 7 THR cc_start: 0.8456 (p) cc_final: 0.8128 (t) REVERT: b 177 THR cc_start: 0.7529 (m) cc_final: 0.7056 (p) REVERT: c 133 ASN cc_start: 0.8612 (t0) cc_final: 0.8150 (t0) REVERT: c 151 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7566 (pp20) REVERT: c 185 MET cc_start: 0.8278 (tpt) cc_final: 0.8075 (mmt) REVERT: c 262 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7512 (mm-40) REVERT: d 42 LYS cc_start: 0.6323 (tptt) cc_final: 0.5550 (mtmt) REVERT: d 52 LYS cc_start: 0.7068 (mttp) cc_final: 0.6848 (tppt) REVERT: d 60 SER cc_start: 0.7920 (t) cc_final: 0.7651 (m) REVERT: d 251 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8272 (mp10) REVERT: e 24 GLU cc_start: 0.8424 (tp30) cc_final: 0.8087 (tp30) REVERT: e 66 ASP cc_start: 0.7599 (m-30) cc_final: 0.7097 (m-30) REVERT: e 131 LYS cc_start: 0.7877 (ptpt) cc_final: 0.7394 (mtmt) REVERT: f 24 GLU cc_start: 0.8141 (tp30) cc_final: 0.7811 (tt0) REVERT: f 65 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.7951 (mttt) REVERT: f 151 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7728 (pp20) REVERT: f 267 ILE cc_start: 0.8911 (tp) cc_final: 0.8647 (tp) REVERT: g 129 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.8437 (m-40) REVERT: g 151 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8034 (pp20) REVERT: h 42 LYS cc_start: 0.5849 (tptt) cc_final: 0.5062 (mtmm) REVERT: h 84 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8642 (p) REVERT: h 265 GLN cc_start: 0.6718 (OUTLIER) cc_final: 0.6375 (mm-40) REVERT: i 94 GLU cc_start: 0.7359 (mm-30) cc_final: 0.6807 (mt-10) REVERT: i 123 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8774 (tt) REVERT: j 83 ASP cc_start: 0.8022 (m-30) cc_final: 0.7696 (m-30) REVERT: j 117 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8375 (mt-10) REVERT: j 151 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8003 (pp20) REVERT: k 76 ASP cc_start: 0.8055 (m-30) cc_final: 0.7770 (m-30) REVERT: k 117 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.7561 (mm-30) REVERT: k 242 LYS cc_start: 0.8441 (mtpt) cc_final: 0.8079 (mttm) outliers start: 216 outliers final: 112 residues processed: 1030 average time/residue: 1.3327 time to fit residues: 1852.9192 Evaluate side-chains 1007 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 861 time to evaluate : 6.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 255 GLN Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 250 GLN Chi-restraints excluded: chain I residue 52 LYS Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 255 GLN Chi-restraints excluded: chain I residue 269 SER Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain K residue 248 THR Chi-restraints excluded: chain L residue 3 ASN Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 91 LYS Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain N residue 115 ASP Chi-restraints excluded: chain N residue 120 ARG Chi-restraints excluded: chain N residue 128 THR Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 258 SER Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain O residue 83 ASP Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 115 ASP Chi-restraints excluded: chain P residue 122 GLN Chi-restraints excluded: chain P residue 163 LEU Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 73 SER Chi-restraints excluded: chain Q residue 252 LEU Chi-restraints excluded: chain R residue 8 ASN Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain S residue 231 LEU Chi-restraints excluded: chain T residue 55 SER Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain T residue 150 ASN Chi-restraints excluded: chain T residue 152 ASP Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain T residue 252 LEU Chi-restraints excluded: chain U residue 91 LYS Chi-restraints excluded: chain U residue 154 SER Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 232 VAL Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain V residue 13 LEU Chi-restraints excluded: chain V residue 24 GLU Chi-restraints excluded: chain V residue 40 ASN Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain V residue 231 LEU Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 231 LEU Chi-restraints excluded: chain W residue 244 GLN Chi-restraints excluded: chain W residue 252 LEU Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain X residue 94 GLU Chi-restraints excluded: chain X residue 231 LEU Chi-restraints excluded: chain X residue 239 GLU Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 117 GLU Chi-restraints excluded: chain Y residue 263 THR Chi-restraints excluded: chain Z residue 91 LYS Chi-restraints excluded: chain a residue 84 THR Chi-restraints excluded: chain a residue 210 LEU Chi-restraints excluded: chain b residue 2 LEU Chi-restraints excluded: chain b residue 135 VAL Chi-restraints excluded: chain b residue 168 ILE Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 15 LEU Chi-restraints excluded: chain c residue 52 LYS Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain d residue 108 SER Chi-restraints excluded: chain d residue 175 THR Chi-restraints excluded: chain d residue 184 THR Chi-restraints excluded: chain d residue 239 GLU Chi-restraints excluded: chain d residue 251 GLN Chi-restraints excluded: chain e residue 85 ILE Chi-restraints excluded: chain e residue 154 SER Chi-restraints excluded: chain e residue 168 ILE Chi-restraints excluded: chain e residue 232 VAL Chi-restraints excluded: chain e residue 267 ILE Chi-restraints excluded: chain f residue 52 LYS Chi-restraints excluded: chain f residue 65 LYS Chi-restraints excluded: chain f residue 151 GLU Chi-restraints excluded: chain g residue 129 ASN Chi-restraints excluded: chain g residue 131 LYS Chi-restraints excluded: chain g residue 151 GLU Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain h residue 128 THR Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 131 LYS Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 265 GLN Chi-restraints excluded: chain i residue 86 THR Chi-restraints excluded: chain i residue 89 LEU Chi-restraints excluded: chain i residue 123 LEU Chi-restraints excluded: chain i residue 250 GLN Chi-restraints excluded: chain i residue 267 ILE Chi-restraints excluded: chain j residue 92 MET Chi-restraints excluded: chain j residue 117 GLU Chi-restraints excluded: chain j residue 151 GLU Chi-restraints excluded: chain j residue 157 THR Chi-restraints excluded: chain j residue 267 ILE Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 117 GLU Chi-restraints excluded: chain k residue 150 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 699 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 730 optimal weight: 0.7980 chunk 646 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 933 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 662 optimal weight: 9.9990 chunk 358 optimal weight: 0.9990 chunk 841 optimal weight: 0.6980 chunk 169 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 GLN B 255 GLN C 250 GLN C 255 GLN D 262 GLN E 155 ASN E 250 GLN E 262 GLN H 262 GLN L 3 ASN L 72 GLN L 262 GLN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 ASN N 54 GLN N 133 ASN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 262 GLN Q 44 ASN Q 250 GLN R 54 GLN S 230 ASN ** U 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 150 ASN W 150 ASN W 198 ASN Z 150 ASN Z 230 ASN Z 250 GLN Z 265 GLN a 54 GLN a 122 GLN a 262 GLN ** b 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 265 GLN c 265 GLN d 122 GLN d 133 ASN d 230 ASN e 72 GLN f 8 ASN h 29 GLN h 262 GLN i 110 ASN i 251 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.123291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.109131 restraints weight = 98725.622| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.42 r_work: 0.3364 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 72816 Z= 0.154 Angle : 0.425 12.858 98753 Z= 0.239 Chirality : 0.033 0.196 12802 Planarity : 0.003 0.058 12617 Dihedral : 3.679 16.739 10064 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.39 % Allowed : 10.67 % Favored : 86.94 % 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: 4.28 (0.09), residues: 9916 helix: 3.85 (0.06), residues: 7511 sheet: -2.42 (0.18), residues: 444 loop : -0.29 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 48 HIS 0.003 0.001 HIS f 213 PHE 0.019 0.001 PHE R 109 ARG 0.004 0.000 ARG d 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 1120 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 929 time to evaluate : 6.550 Fit side-chains revert: symmetry clash REVERT: A 148 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7672 (mp) REVERT: A 151 GLU cc_start: 0.8601 (pm20) cc_final: 0.8346 (pp20) REVERT: D 251 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7867 (mm-40) REVERT: D 265 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7777 (mm-40) REVERT: E 87 ASP cc_start: 0.8110 (m-30) cc_final: 0.7862 (m-30) REVERT: E 91 LYS cc_start: 0.7871 (mtpt) cc_final: 0.7517 (mtpp) REVERT: E 239 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7826 (mm-30) REVERT: F 86 THR cc_start: 0.8112 (m) cc_final: 0.7743 (p) REVERT: F 242 LYS cc_start: 0.8278 (mtpt) cc_final: 0.8056 (mtpp) REVERT: G 24 GLU cc_start: 0.8226 (tt0) cc_final: 0.7816 (mm-30) REVERT: G 151 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7710 (pp20) REVERT: G 255 GLN cc_start: 0.8163 (tt0) cc_final: 0.7943 (mt0) REVERT: H 2 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6092 (tm) REVERT: H 131 LYS cc_start: 0.8212 (ptpt) cc_final: 0.7899 (pttp) REVERT: I 24 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6965 (mm-30) REVERT: I 87 ASP cc_start: 0.8024 (m-30) cc_final: 0.7705 (m-30) REVERT: I 247 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7696 (mt0) REVERT: I 255 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6895 (mm110) REVERT: J 92 MET cc_start: 0.9032 (mtp) cc_final: 0.8716 (mtp) REVERT: K 86 THR cc_start: 0.8178 (m) cc_final: 0.7818 (p) REVERT: K 117 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8393 (mt-10) REVERT: K 251 GLN cc_start: 0.7347 (tp-100) cc_final: 0.7081 (tp-100) REVERT: L 8 ASN cc_start: 0.8487 (p0) cc_final: 0.8222 (p0) REVERT: L 24 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7631 (mt-10) REVERT: L 92 MET cc_start: 0.7397 (mtp) cc_final: 0.7010 (mtp) REVERT: L 101 ASP cc_start: 0.5813 (p0) cc_final: 0.5255 (p0) REVERT: L 173 THR cc_start: 0.8215 (m) cc_final: 0.8012 (p) REVERT: L 231 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8108 (mp) REVERT: M 76 ASP cc_start: 0.8137 (m-30) cc_final: 0.7912 (m-30) REVERT: M 250 GLN cc_start: 0.8597 (tt0) cc_final: 0.8332 (tt0) REVERT: N 267 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8537 (mm) REVERT: O 83 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7224 (m-30) REVERT: O 125 LYS cc_start: 0.7690 (ttmm) cc_final: 0.7476 (ttmm) REVERT: O 251 GLN cc_start: 0.8257 (mt0) cc_final: 0.8019 (mt0) REVERT: P 5 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7097 (pp) REVERT: P 31 ARG cc_start: 0.7828 (ttm-80) cc_final: 0.7400 (ttm110) REVERT: P 36 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7968 (mttp) REVERT: P 86 THR cc_start: 0.8120 (m) cc_final: 0.7447 (p) REVERT: P 255 GLN cc_start: 0.7447 (tt0) cc_final: 0.6959 (tp-100) REVERT: Q 44 ASN cc_start: 0.7064 (t0) cc_final: 0.6834 (t0) REVERT: Q 83 ASP cc_start: 0.6948 (m-30) cc_final: 0.6710 (m-30) REVERT: Q 91 LYS cc_start: 0.7636 (tttt) cc_final: 0.7428 (mttt) REVERT: Q 94 GLU cc_start: 0.7347 (tp30) cc_final: 0.6559 (mp0) REVERT: Q 122 GLN cc_start: 0.8040 (mt0) cc_final: 0.7150 (mm-40) REVERT: R 125 LYS cc_start: 0.7797 (mttp) cc_final: 0.6631 (tttt) REVERT: S 24 GLU cc_start: 0.7741 (tp30) cc_final: 0.7486 (tp30) REVERT: S 37 LYS cc_start: 0.8151 (ptmm) cc_final: 0.7711 (pttp) REVERT: S 75 ILE cc_start: 0.8622 (mt) cc_final: 0.8286 (tt) REVERT: S 122 GLN cc_start: 0.7744 (mt0) cc_final: 0.7142 (tp40) REVERT: S 185 MET cc_start: 0.8528 (tpt) cc_final: 0.7908 (tpt) REVERT: T 13 LEU cc_start: 0.8143 (mt) cc_final: 0.7771 (mm) REVERT: T 76 ASP cc_start: 0.8165 (t70) cc_final: 0.7705 (t70) REVERT: T 83 ASP cc_start: 0.8322 (t70) cc_final: 0.7963 (t70) REVERT: T 122 GLN cc_start: 0.8206 (mt0) cc_final: 0.7269 (tp40) REVERT: U 83 ASP cc_start: 0.8133 (t70) cc_final: 0.7789 (t0) REVERT: U 91 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7869 (mtpt) REVERT: U 244 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8158 (mm-40) REVERT: V 94 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: V 231 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7786 (mp) REVERT: X 94 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: X 242 LYS cc_start: 0.7871 (ttmt) cc_final: 0.7233 (tptm) REVERT: Y 117 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: a 87 ASP cc_start: 0.8372 (t0) cc_final: 0.7954 (m-30) REVERT: a 265 GLN cc_start: 0.8052 (mt0) cc_final: 0.7758 (mp10) REVERT: b 7 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8105 (t) REVERT: b 69 GLN cc_start: 0.7294 (mt0) cc_final: 0.6938 (mt0) REVERT: b 177 THR cc_start: 0.7500 (m) cc_final: 0.7030 (p) REVERT: c 133 ASN cc_start: 0.8563 (t0) cc_final: 0.8120 (t0) REVERT: c 151 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7554 (pp20) REVERT: c 262 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7500 (mm110) REVERT: d 40 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7649 (p0) REVERT: d 42 LYS cc_start: 0.6314 (tptt) cc_final: 0.5361 (mtmt) REVERT: d 60 SER cc_start: 0.7909 (t) cc_final: 0.7662 (m) REVERT: d 230 ASN cc_start: 0.8183 (m-40) cc_final: 0.7952 (m110) REVERT: d 262 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7285 (tt0) REVERT: e 24 GLU cc_start: 0.8416 (tp30) cc_final: 0.8111 (tp30) REVERT: e 66 ASP cc_start: 0.7564 (m-30) cc_final: 0.7089 (m-30) REVERT: e 131 LYS cc_start: 0.7826 (ptpt) cc_final: 0.7410 (mtmt) REVERT: f 24 GLU cc_start: 0.8153 (tp30) cc_final: 0.7820 (tt0) REVERT: f 151 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7730 (pp20) REVERT: f 267 ILE cc_start: 0.8939 (tp) cc_final: 0.8621 (tp) REVERT: g 131 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7894 (mtmm) REVERT: h 42 LYS cc_start: 0.5898 (tptt) cc_final: 0.5093 (mtmm) REVERT: h 84 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8607 (p) REVERT: h 131 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7711 (mtpp) REVERT: h 265 GLN cc_start: 0.6474 (mm110) cc_final: 0.6120 (mm-40) REVERT: i 94 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6780 (mt-10) REVERT: i 123 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8789 (tt) REVERT: j 117 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8348 (mt-10) REVERT: j 151 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8007 (pp20) REVERT: k 76 ASP cc_start: 0.8030 (m-30) cc_final: 0.7746 (m-30) REVERT: k 242 LYS cc_start: 0.8467 (mtpt) cc_final: 0.8125 (mttm) outliers start: 191 outliers final: 91 residues processed: 1045 average time/residue: 1.3202 time to fit residues: 1865.3072 Evaluate side-chains 990 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 872 time to evaluate : 6.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 255 GLN Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 247 GLN Chi-restraints excluded: chain I residue 255 GLN Chi-restraints excluded: chain I residue 269 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain K residue 248 THR Chi-restraints excluded: chain L residue 3 ASN Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 91 LYS Chi-restraints excluded: chain L residue 95 LYS Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain N residue 115 ASP Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain O residue 83 ASP Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 36 LYS Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 115 ASP Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 73 SER Chi-restraints excluded: chain Q residue 252 LEU Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain S residue 150 ASN Chi-restraints excluded: chain T residue 55 SER Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain T residue 152 ASP Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain U residue 91 LYS Chi-restraints excluded: chain U residue 154 SER Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 232 VAL Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain V residue 13 LEU Chi-restraints excluded: chain V residue 40 ASN Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain V residue 231 LEU Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 244 GLN Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain X residue 94 GLU Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 117 GLU Chi-restraints excluded: chain Y residue 263 THR Chi-restraints excluded: chain Z residue 91 LYS Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 258 SER Chi-restraints excluded: chain a residue 84 THR Chi-restraints excluded: chain a residue 210 LEU Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 135 VAL Chi-restraints excluded: chain b residue 168 ILE Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 15 LEU Chi-restraints excluded: chain c residue 52 LYS Chi-restraints excluded: chain c residue 125 LYS Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain d residue 40 ASN Chi-restraints excluded: chain d residue 108 SER Chi-restraints excluded: chain d residue 168 ILE Chi-restraints excluded: chain d residue 175 THR Chi-restraints excluded: chain d residue 239 GLU Chi-restraints excluded: chain e residue 168 ILE Chi-restraints excluded: chain e residue 232 VAL Chi-restraints excluded: chain e residue 267 ILE Chi-restraints excluded: chain f residue 151 GLU Chi-restraints excluded: chain g residue 131 LYS Chi-restraints excluded: chain h residue 29 GLN Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 131 LYS Chi-restraints excluded: chain h residue 151 GLU Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain i residue 89 LEU Chi-restraints excluded: chain i residue 123 LEU Chi-restraints excluded: chain i residue 267 ILE Chi-restraints excluded: chain j residue 92 MET Chi-restraints excluded: chain j residue 117 GLU Chi-restraints excluded: chain j residue 151 GLU Chi-restraints excluded: chain j residue 157 THR Chi-restraints excluded: chain j residue 267 ILE Chi-restraints excluded: chain k residue 55 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 103 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 417 optimal weight: 6.9990 chunk 691 optimal weight: 0.0670 chunk 931 optimal weight: 4.9990 chunk 637 optimal weight: 5.9990 chunk 438 optimal weight: 5.9990 chunk 842 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 993 optimal weight: 0.9990 chunk 330 optimal weight: 0.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 GLN C 250 GLN C 255 GLN D 262 GLN E 250 GLN E 262 GLN H 262 GLN J 33 ASN ** K 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 ASN L 72 GLN L 262 GLN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 ASN M 262 GLN N 54 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN S 230 ASN S 262 GLN T 54 GLN T 150 ASN U 247 GLN ** U 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 150 ASN X 255 GLN Z 150 ASN Z 230 ASN Z 250 GLN Z 265 GLN a 17 ASN a 54 GLN a 122 GLN a 150 ASN a 262 GLN ** b 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 265 GLN c 122 GLN d 122 GLN d 133 ASN f 8 ASN h 29 GLN h 262 GLN i 110 ASN i 251 GLN j 29 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.121628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.107424 restraints weight = 98895.737| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.41 r_work: 0.3344 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 72816 Z= 0.183 Angle : 0.451 12.298 98753 Z= 0.252 Chirality : 0.034 0.203 12802 Planarity : 0.003 0.062 12617 Dihedral : 3.739 17.535 10064 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 2.44 % Allowed : 10.99 % Favored : 86.57 % 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: 4.24 (0.08), residues: 9916 helix: 3.81 (0.06), residues: 7474 sheet: -2.32 (0.19), residues: 444 loop : -0.16 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 48 HIS 0.004 0.001 HIS f 213 PHE 0.020 0.002 PHE R 109 ARG 0.005 0.000 ARG d 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 1079 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 884 time to evaluate : 6.475 Fit side-chains revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8605 (pm20) cc_final: 0.8361 (pp20) REVERT: C 94 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: D 265 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7790 (mm-40) REVERT: E 87 ASP cc_start: 0.8090 (m-30) cc_final: 0.7854 (m-30) REVERT: E 91 LYS cc_start: 0.7863 (mtpt) cc_final: 0.7508 (mtpp) REVERT: E 239 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7819 (mm-30) REVERT: F 86 THR cc_start: 0.8122 (m) cc_final: 0.7746 (p) REVERT: F 92 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8663 (mtp) REVERT: F 151 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7709 (pp20) REVERT: G 24 GLU cc_start: 0.8240 (tt0) cc_final: 0.7793 (mm-30) REVERT: G 151 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7724 (pp20) REVERT: G 255 GLN cc_start: 0.8138 (tt0) cc_final: 0.7910 (mt0) REVERT: H 2 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6027 (tm) REVERT: H 131 LYS cc_start: 0.8192 (ptpt) cc_final: 0.7926 (pttp) REVERT: I 87 ASP cc_start: 0.8031 (m-30) cc_final: 0.7718 (m-30) REVERT: I 117 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.6588 (mm-30) REVERT: I 247 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7791 (mt0) REVERT: I 255 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6795 (mm110) REVERT: J 92 MET cc_start: 0.9039 (mtp) cc_final: 0.8793 (mtp) REVERT: K 86 THR cc_start: 0.8201 (m) cc_final: 0.7834 (p) REVERT: K 92 MET cc_start: 0.8957 (mtp) cc_final: 0.8536 (mtp) REVERT: K 117 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8364 (mt-10) REVERT: K 251 GLN cc_start: 0.7361 (tp-100) cc_final: 0.7080 (tp-100) REVERT: L 8 ASN cc_start: 0.8541 (p0) cc_final: 0.8269 (p0) REVERT: L 24 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7618 (mt-10) REVERT: L 92 MET cc_start: 0.7310 (mtp) cc_final: 0.6898 (mtp) REVERT: L 150 ASN cc_start: 0.8083 (t0) cc_final: 0.7614 (t0) REVERT: L 231 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8106 (mp) REVERT: M 76 ASP cc_start: 0.8111 (m-30) cc_final: 0.7899 (m-30) REVERT: N 267 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8552 (mm) REVERT: O 83 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7213 (m-30) REVERT: O 125 LYS cc_start: 0.7680 (ttmm) cc_final: 0.7450 (ttmm) REVERT: O 251 GLN cc_start: 0.8251 (mt0) cc_final: 0.7960 (mt0) REVERT: P 5 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7007 (pp) REVERT: P 31 ARG cc_start: 0.7764 (ttm-80) cc_final: 0.7378 (ttm110) REVERT: P 36 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7966 (mttp) REVERT: P 86 THR cc_start: 0.8113 (m) cc_final: 0.7430 (p) REVERT: P 122 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6649 (tm-30) REVERT: Q 91 LYS cc_start: 0.7629 (tttt) cc_final: 0.7371 (mttt) REVERT: Q 94 GLU cc_start: 0.7397 (tp30) cc_final: 0.6620 (mp0) REVERT: Q 122 GLN cc_start: 0.8115 (mt0) cc_final: 0.7176 (mm-40) REVERT: R 125 LYS cc_start: 0.7817 (mttp) cc_final: 0.6613 (tttt) REVERT: R 235 ASP cc_start: 0.7635 (p0) cc_final: 0.7300 (p0) REVERT: S 24 GLU cc_start: 0.7736 (tp30) cc_final: 0.7466 (tp30) REVERT: S 37 LYS cc_start: 0.8148 (ptmm) cc_final: 0.7719 (pttp) REVERT: S 75 ILE cc_start: 0.8642 (mt) cc_final: 0.8305 (tt) REVERT: S 122 GLN cc_start: 0.7720 (mt0) cc_final: 0.7099 (tp40) REVERT: T 13 LEU cc_start: 0.8178 (mt) cc_final: 0.7800 (mm) REVERT: T 76 ASP cc_start: 0.8166 (t70) cc_final: 0.7694 (t70) REVERT: T 83 ASP cc_start: 0.8344 (t70) cc_final: 0.7977 (t70) REVERT: T 122 GLN cc_start: 0.8188 (mt0) cc_final: 0.7239 (tp40) REVERT: T 139 ASP cc_start: 0.8096 (p0) cc_final: 0.7895 (p0) REVERT: U 83 ASP cc_start: 0.8116 (t70) cc_final: 0.7780 (t0) REVERT: U 91 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7875 (mtpt) REVERT: V 94 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7626 (tm-30) REVERT: V 231 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7685 (mp) REVERT: X 94 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7529 (tm-30) REVERT: X 211 ASP cc_start: 0.8134 (p0) cc_final: 0.7896 (p0) REVERT: X 231 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8145 (mp) REVERT: X 242 LYS cc_start: 0.7884 (ttmt) cc_final: 0.7241 (tptm) REVERT: Y 117 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.8005 (mp0) REVERT: a 87 ASP cc_start: 0.8347 (t0) cc_final: 0.7919 (m-30) REVERT: a 265 GLN cc_start: 0.8048 (mt0) cc_final: 0.7744 (mp10) REVERT: b 7 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8117 (t) REVERT: b 69 GLN cc_start: 0.7366 (mt0) cc_final: 0.7032 (mt0) REVERT: b 106 THR cc_start: 0.6367 (p) cc_final: 0.6074 (m) REVERT: b 177 THR cc_start: 0.7400 (m) cc_final: 0.6972 (p) REVERT: c 133 ASN cc_start: 0.8600 (t0) cc_final: 0.8136 (t0) REVERT: c 151 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7568 (pp20) REVERT: c 262 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7522 (mm110) REVERT: d 40 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7659 (p0) REVERT: d 42 LYS cc_start: 0.6291 (tptt) cc_final: 0.5330 (mtmt) REVERT: d 60 SER cc_start: 0.7927 (t) cc_final: 0.7663 (m) REVERT: e 24 GLU cc_start: 0.8418 (tp30) cc_final: 0.8109 (tp30) REVERT: e 66 ASP cc_start: 0.7619 (m-30) cc_final: 0.7111 (m-30) REVERT: e 131 LYS cc_start: 0.7851 (ptpt) cc_final: 0.7463 (mtmt) REVERT: f 24 GLU cc_start: 0.8144 (tp30) cc_final: 0.7808 (tt0) REVERT: f 151 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7689 (pp20) REVERT: f 267 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8627 (tp) REVERT: g 131 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7933 (mtmm) REVERT: h 42 LYS cc_start: 0.5935 (tptt) cc_final: 0.5119 (mtmm) REVERT: h 84 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8637 (p) REVERT: h 131 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7442 (ptpt) REVERT: h 265 GLN cc_start: 0.6493 (OUTLIER) cc_final: 0.6138 (mm-40) REVERT: i 92 MET cc_start: 0.8348 (mtp) cc_final: 0.8122 (mtp) REVERT: i 94 GLU cc_start: 0.7350 (mm-30) cc_final: 0.6812 (mt-10) REVERT: i 123 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8782 (tt) REVERT: j 117 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8422 (mt-10) REVERT: j 151 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8023 (pp20) REVERT: k 76 ASP cc_start: 0.8029 (m-30) cc_final: 0.7753 (m-30) REVERT: k 242 LYS cc_start: 0.8425 (mtpt) cc_final: 0.8052 (mttm) outliers start: 195 outliers final: 110 residues processed: 1003 average time/residue: 1.3440 time to fit residues: 1830.8189 Evaluate side-chains 998 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 855 time to evaluate : 6.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 255 GLN Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain F residue 92 MET Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 250 GLN Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 247 GLN Chi-restraints excluded: chain I residue 255 GLN Chi-restraints excluded: chain I residue 269 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain K residue 248 THR Chi-restraints excluded: chain L residue 3 ASN Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 91 LYS Chi-restraints excluded: chain L residue 95 LYS Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 159 THR Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain N residue 115 ASP Chi-restraints excluded: chain N residue 128 THR Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 258 SER Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain O residue 83 ASP Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 36 LYS Chi-restraints excluded: chain P residue 115 ASP Chi-restraints excluded: chain P residue 122 GLN Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 73 SER Chi-restraints excluded: chain Q residue 252 LEU Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain S residue 150 ASN Chi-restraints excluded: chain T residue 55 SER Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain T residue 152 ASP Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain U residue 75 ILE Chi-restraints excluded: chain U residue 91 LYS Chi-restraints excluded: chain U residue 154 SER Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 232 VAL Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain V residue 13 LEU Chi-restraints excluded: chain V residue 24 GLU Chi-restraints excluded: chain V residue 40 ASN Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain V residue 231 LEU Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 244 GLN Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain X residue 40 ASN Chi-restraints excluded: chain X residue 94 GLU Chi-restraints excluded: chain X residue 231 LEU Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 117 GLU Chi-restraints excluded: chain Y residue 210 LEU Chi-restraints excluded: chain Y residue 263 THR Chi-restraints excluded: chain Z residue 91 LYS Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain a residue 84 THR Chi-restraints excluded: chain a residue 210 LEU Chi-restraints excluded: chain b residue 2 LEU Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 135 VAL Chi-restraints excluded: chain b residue 168 ILE Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 15 LEU Chi-restraints excluded: chain c residue 52 LYS Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain d residue 40 ASN Chi-restraints excluded: chain d residue 108 SER Chi-restraints excluded: chain d residue 168 ILE Chi-restraints excluded: chain d residue 175 THR Chi-restraints excluded: chain d residue 184 THR Chi-restraints excluded: chain d residue 239 GLU Chi-restraints excluded: chain e residue 168 ILE Chi-restraints excluded: chain e residue 232 VAL Chi-restraints excluded: chain e residue 267 ILE Chi-restraints excluded: chain f residue 151 GLU Chi-restraints excluded: chain f residue 267 ILE Chi-restraints excluded: chain g residue 131 LYS Chi-restraints excluded: chain h residue 24 GLU Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain h residue 128 THR Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 131 LYS Chi-restraints excluded: chain h residue 151 GLU Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 265 GLN Chi-restraints excluded: chain i residue 89 LEU Chi-restraints excluded: chain i residue 123 LEU Chi-restraints excluded: chain i residue 267 ILE Chi-restraints excluded: chain j residue 92 MET Chi-restraints excluded: chain j residue 117 GLU Chi-restraints excluded: chain j residue 151 GLU Chi-restraints excluded: chain j residue 157 THR Chi-restraints excluded: chain j residue 267 ILE Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 150 ASN 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: 2.9990 chunk 104 optimal weight: 10.0000 chunk 810 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 295 optimal weight: 0.9990 chunk 429 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 268 optimal weight: 5.9990 chunk 841 optimal weight: 5.9990 chunk 566 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 GLN C 250 GLN C 255 GLN D 262 GLN E 250 GLN E 262 GLN H 262 GLN ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 ASN K 8 ASN L 3 ASN L 17 ASN L 72 GLN L 262 GLN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 ASN N 54 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 262 GLN P 255 GLN R 54 GLN S 262 GLN T 150 ASN ** U 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 150 ASN W 150 ASN X 255 GLN Z 150 ASN Z 230 ASN Z 250 GLN Z 265 GLN a 54 GLN a 122 GLN a 150 ASN a 262 GLN ** b 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 265 GLN c 122 GLN d 122 GLN d 133 ASN d 230 ASN f 8 ASN h 29 GLN h 262 GLN i 251 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.122718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.108499 restraints weight = 98533.119| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.41 r_work: 0.3354 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 72816 Z= 0.169 Angle : 0.439 11.765 98753 Z= 0.246 Chirality : 0.033 0.200 12802 Planarity : 0.003 0.081 12617 Dihedral : 3.700 17.277 10064 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 2.35 % Allowed : 11.27 % Favored : 86.37 % 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: 4.31 (0.09), residues: 9916 helix: 3.86 (0.06), residues: 7474 sheet: -2.23 (0.19), residues: 444 loop : -0.19 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 48 HIS 0.003 0.001 HIS f 213 PHE 0.021 0.001 PHE R 109 ARG 0.005 0.000 ARG Q 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 1077 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 889 time to evaluate : 6.388 Fit side-chains revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8610 (pm20) cc_final: 0.8364 (pp20) REVERT: C 94 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: D 251 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7864 (mm-40) REVERT: D 265 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7794 (mm-40) REVERT: E 87 ASP cc_start: 0.8104 (m-30) cc_final: 0.7864 (m-30) REVERT: E 91 LYS cc_start: 0.7875 (mtpt) cc_final: 0.7518 (mtpp) REVERT: E 239 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7792 (mm-30) REVERT: F 86 THR cc_start: 0.8094 (m) cc_final: 0.7720 (p) REVERT: F 151 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7709 (pp20) REVERT: G 24 GLU cc_start: 0.8200 (tt0) cc_final: 0.7774 (mm-30) REVERT: G 151 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7758 (pp20) REVERT: G 255 GLN cc_start: 0.8132 (tt0) cc_final: 0.7925 (mt0) REVERT: H 2 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6050 (tm) REVERT: H 36 LYS cc_start: 0.8601 (mtmt) cc_final: 0.8237 (mttm) REVERT: H 131 LYS cc_start: 0.8108 (ptpt) cc_final: 0.7819 (pttp) REVERT: I 87 ASP cc_start: 0.7997 (m-30) cc_final: 0.7681 (m-30) REVERT: I 117 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.6628 (mm-30) REVERT: I 247 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7754 (mt0) REVERT: I 255 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6809 (mm110) REVERT: J 92 MET cc_start: 0.9040 (mtp) cc_final: 0.8808 (mtp) REVERT: K 92 MET cc_start: 0.8962 (mtp) cc_final: 0.8659 (mtp) REVERT: K 117 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8367 (mt-10) REVERT: K 251 GLN cc_start: 0.7344 (tp-100) cc_final: 0.7087 (tp-100) REVERT: L 8 ASN cc_start: 0.8516 (p0) cc_final: 0.8240 (p0) REVERT: L 24 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7614 (mt-10) REVERT: L 92 MET cc_start: 0.7311 (mtp) cc_final: 0.6897 (mtp) REVERT: L 101 ASP cc_start: 0.5670 (p0) cc_final: 0.5230 (p0) REVERT: L 150 ASN cc_start: 0.8039 (t0) cc_final: 0.7572 (t0) REVERT: L 231 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8115 (mp) REVERT: M 76 ASP cc_start: 0.8099 (m-30) cc_final: 0.7878 (m-30) REVERT: M 250 GLN cc_start: 0.8502 (tt0) cc_final: 0.8250 (tt0) REVERT: N 267 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8529 (mm) REVERT: O 83 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7168 (m-30) REVERT: O 125 LYS cc_start: 0.7685 (ttmm) cc_final: 0.7466 (ttmm) REVERT: O 251 GLN cc_start: 0.8235 (mt0) cc_final: 0.7948 (mt0) REVERT: P 5 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7016 (pp) REVERT: P 31 ARG cc_start: 0.7705 (ttm-80) cc_final: 0.7351 (ttm110) REVERT: P 36 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7968 (mttp) REVERT: P 86 THR cc_start: 0.7943 (m) cc_final: 0.7242 (p) REVERT: P 122 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6599 (tm-30) REVERT: Q 91 LYS cc_start: 0.7627 (tttt) cc_final: 0.7392 (mttt) REVERT: Q 94 GLU cc_start: 0.7381 (tp30) cc_final: 0.6558 (mp0) REVERT: Q 122 GLN cc_start: 0.8067 (mt0) cc_final: 0.7152 (mm-40) REVERT: R 24 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8056 (tp30) REVERT: R 125 LYS cc_start: 0.7817 (mttp) cc_final: 0.6622 (tttt) REVERT: R 235 ASP cc_start: 0.7593 (p0) cc_final: 0.7237 (p0) REVERT: R 242 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7473 (ttpp) REVERT: S 24 GLU cc_start: 0.7741 (tp30) cc_final: 0.7471 (tp30) REVERT: S 37 LYS cc_start: 0.8153 (ptmm) cc_final: 0.7734 (pttp) REVERT: S 75 ILE cc_start: 0.8645 (mt) cc_final: 0.8308 (tt) REVERT: S 122 GLN cc_start: 0.7712 (mt0) cc_final: 0.7110 (tp40) REVERT: T 13 LEU cc_start: 0.8163 (mt) cc_final: 0.7791 (mm) REVERT: T 76 ASP cc_start: 0.8161 (t70) cc_final: 0.7690 (t70) REVERT: T 83 ASP cc_start: 0.8368 (t70) cc_final: 0.8018 (t70) REVERT: T 122 GLN cc_start: 0.8178 (mt0) cc_final: 0.7236 (tp40) REVERT: T 139 ASP cc_start: 0.8089 (p0) cc_final: 0.7884 (p0) REVERT: T 231 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7755 (mp) REVERT: U 83 ASP cc_start: 0.8110 (t70) cc_final: 0.7775 (t0) REVERT: U 91 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7814 (mtpt) REVERT: U 255 GLN cc_start: 0.7637 (tt0) cc_final: 0.7059 (mt0) REVERT: V 94 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7618 (tm-30) REVERT: V 222 ASP cc_start: 0.7722 (p0) cc_final: 0.7247 (t0) REVERT: V 231 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7775 (mp) REVERT: X 94 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7506 (tm-30) REVERT: X 211 ASP cc_start: 0.8134 (p0) cc_final: 0.7886 (p0) REVERT: X 231 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8167 (mp) REVERT: X 242 LYS cc_start: 0.7869 (ttmt) cc_final: 0.7219 (tptm) REVERT: Y 117 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: Z 50 MET cc_start: 0.8346 (mtp) cc_final: 0.7974 (mtt) REVERT: a 87 ASP cc_start: 0.8338 (t0) cc_final: 0.7933 (m-30) REVERT: a 265 GLN cc_start: 0.8041 (mt0) cc_final: 0.7755 (mp10) REVERT: b 7 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8124 (t) REVERT: b 69 GLN cc_start: 0.7353 (mt0) cc_final: 0.7029 (mt0) REVERT: b 106 THR cc_start: 0.6290 (p) cc_final: 0.6021 (m) REVERT: b 177 THR cc_start: 0.7371 (m) cc_final: 0.6951 (p) REVERT: c 133 ASN cc_start: 0.8593 (t0) cc_final: 0.8152 (t0) REVERT: c 151 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7570 (pp20) REVERT: c 262 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7505 (mm110) REVERT: d 40 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7661 (p0) REVERT: d 42 LYS cc_start: 0.6269 (tptt) cc_final: 0.5312 (mtmt) REVERT: d 60 SER cc_start: 0.7920 (t) cc_final: 0.7653 (m) REVERT: d 262 GLN cc_start: 0.7982 (tm-30) cc_final: 0.7381 (tt0) REVERT: e 24 GLU cc_start: 0.8419 (tp30) cc_final: 0.8102 (tp30) REVERT: e 66 ASP cc_start: 0.7579 (m-30) cc_final: 0.7084 (m-30) REVERT: e 131 LYS cc_start: 0.7831 (ptpt) cc_final: 0.7472 (mtmt) REVERT: f 2 LEU cc_start: 0.6286 (mt) cc_final: 0.6052 (tp) REVERT: f 24 GLU cc_start: 0.8141 (tp30) cc_final: 0.7790 (tt0) REVERT: f 151 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.7690 (pp20) REVERT: f 267 ILE cc_start: 0.8958 (tp) cc_final: 0.8655 (tp) REVERT: g 131 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7913 (mtmm) REVERT: h 42 LYS cc_start: 0.5868 (tptt) cc_final: 0.5080 (mtmm) REVERT: h 84 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8622 (p) REVERT: h 265 GLN cc_start: 0.6488 (OUTLIER) cc_final: 0.6133 (mm-40) REVERT: i 92 MET cc_start: 0.8323 (mtp) cc_final: 0.8090 (mtp) REVERT: i 94 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6808 (mt-10) REVERT: i 123 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8786 (tt) REVERT: j 117 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8406 (mt-10) REVERT: j 151 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8006 (pp20) REVERT: k 76 ASP cc_start: 0.8017 (m-30) cc_final: 0.7738 (m-30) REVERT: k 242 LYS cc_start: 0.8416 (mtpt) cc_final: 0.8062 (mttm) outliers start: 188 outliers final: 115 residues processed: 1010 average time/residue: 1.3106 time to fit residues: 1796.6801 Evaluate side-chains 1000 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 853 time to evaluate : 6.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 255 GLN Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 247 GLN Chi-restraints excluded: chain I residue 255 GLN Chi-restraints excluded: chain I residue 269 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain K residue 248 THR Chi-restraints excluded: chain L residue 3 ASN Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 91 LYS Chi-restraints excluded: chain L residue 95 LYS Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 159 THR Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain N residue 115 ASP Chi-restraints excluded: chain N residue 128 THR Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 258 SER Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain O residue 83 ASP Chi-restraints excluded: chain O residue 163 LEU Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 36 LYS Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 115 ASP Chi-restraints excluded: chain P residue 122 GLN Chi-restraints excluded: chain P residue 163 LEU Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 73 SER Chi-restraints excluded: chain Q residue 252 LEU Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 242 LYS Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain S residue 150 ASN Chi-restraints excluded: chain S residue 231 LEU Chi-restraints excluded: chain T residue 55 SER Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain T residue 152 ASP Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain T residue 231 LEU Chi-restraints excluded: chain U residue 75 ILE Chi-restraints excluded: chain U residue 91 LYS Chi-restraints excluded: chain U residue 154 SER Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 232 VAL Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain V residue 13 LEU Chi-restraints excluded: chain V residue 24 GLU Chi-restraints excluded: chain V residue 40 ASN Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain V residue 231 LEU Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 244 GLN Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain X residue 40 ASN Chi-restraints excluded: chain X residue 94 GLU Chi-restraints excluded: chain X residue 231 LEU Chi-restraints excluded: chain X residue 239 GLU Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 117 GLU Chi-restraints excluded: chain Y residue 210 LEU Chi-restraints excluded: chain Y residue 263 THR Chi-restraints excluded: chain Z residue 91 LYS Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 258 SER Chi-restraints excluded: chain a residue 84 THR Chi-restraints excluded: chain a residue 210 LEU Chi-restraints excluded: chain b residue 2 LEU Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 135 VAL Chi-restraints excluded: chain b residue 168 ILE Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 15 LEU Chi-restraints excluded: chain c residue 52 LYS Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain d residue 40 ASN Chi-restraints excluded: chain d residue 108 SER Chi-restraints excluded: chain d residue 168 ILE Chi-restraints excluded: chain d residue 184 THR Chi-restraints excluded: chain d residue 239 GLU Chi-restraints excluded: chain e residue 168 ILE Chi-restraints excluded: chain e residue 232 VAL Chi-restraints excluded: chain e residue 267 ILE Chi-restraints excluded: chain f residue 151 GLU Chi-restraints excluded: chain g residue 131 LYS Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 151 GLU Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 265 GLN Chi-restraints excluded: chain i residue 86 THR Chi-restraints excluded: chain i residue 89 LEU Chi-restraints excluded: chain i residue 123 LEU Chi-restraints excluded: chain i residue 186 ILE Chi-restraints excluded: chain i residue 267 ILE Chi-restraints excluded: chain j residue 92 MET Chi-restraints excluded: chain j residue 117 GLU Chi-restraints excluded: chain j residue 151 GLU Chi-restraints excluded: chain j residue 157 THR Chi-restraints excluded: chain j residue 267 ILE Chi-restraints excluded: chain k residue 55 SER 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: 5.9990 chunk 892 optimal weight: 1.9990 chunk 686 optimal weight: 5.9990 chunk 651 optimal weight: 6.9990 chunk 661 optimal weight: 7.9990 chunk 886 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 498 optimal weight: 0.9990 chunk 666 optimal weight: 2.9990 chunk 458 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 255 GLN C 250 GLN C 255 GLN D 262 GLN E 250 GLN E 262 GLN ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 GLN J 33 ASN L 3 ASN L 262 GLN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 ASN M 155 ASN N 54 GLN O 54 GLN ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 22 ASN P 150 ASN P 255 GLN Q 44 ASN R 54 GLN R 150 ASN S 230 ASN T 150 ASN U 250 GLN V 150 ASN V 247 GLN X 255 GLN ** Z 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 150 ASN Z 230 ASN Z 250 GLN Z 265 GLN a 17 ASN a 19 ASN a 54 GLN a 150 ASN a 262 GLN ** b 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 265 GLN c 129 ASN d 122 GLN d 133 ASN ** f 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 3 ASN h 29 GLN h 262 GLN i 251 GLN k 250 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.116755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.102602 restraints weight = 99947.376| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.41 r_work: 0.3271 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 72816 Z= 0.324 Angle : 0.564 13.677 98753 Z= 0.310 Chirality : 0.040 0.213 12802 Planarity : 0.003 0.111 12617 Dihedral : 4.090 19.275 10064 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.55 % Allowed : 11.30 % Favored : 86.15 % 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: 3.67 (0.08), residues: 9916 helix: 3.40 (0.06), residues: 7474 sheet: -2.34 (0.19), residues: 444 loop : -0.45 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 48 HIS 0.005 0.002 HIS f 213 PHE 0.024 0.002 PHE R 109 ARG 0.006 0.001 ARG Q 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 1040 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 836 time to evaluate : 6.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7957 (m-30) cc_final: 0.7682 (m-30) REVERT: A 151 GLU cc_start: 0.8611 (pm20) cc_final: 0.8396 (pp20) REVERT: A 262 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7567 (mp-120) REVERT: B 178 ASP cc_start: 0.7087 (t0) cc_final: 0.6884 (t0) REVERT: E 87 ASP cc_start: 0.8126 (m-30) cc_final: 0.7922 (m-30) REVERT: E 91 LYS cc_start: 0.7918 (mtpt) cc_final: 0.7650 (mtpm) REVERT: E 106 THR cc_start: 0.6940 (p) cc_final: 0.6676 (m) REVERT: F 86 THR cc_start: 0.8275 (m) cc_final: 0.7893 (p) REVERT: F 101 ASP cc_start: 0.8040 (t0) cc_final: 0.7781 (t0) REVERT: G 24 GLU cc_start: 0.8301 (tt0) cc_final: 0.7838 (mm-30) REVERT: G 151 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7757 (pp20) REVERT: G 255 GLN cc_start: 0.8205 (tt0) cc_final: 0.7999 (mt0) REVERT: H 2 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6045 (tm) REVERT: H 131 LYS cc_start: 0.8384 (ptpt) cc_final: 0.8046 (pttp) REVERT: K 86 THR cc_start: 0.8401 (m) cc_final: 0.8056 (p) REVERT: K 117 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8488 (mt-10) REVERT: L 101 ASP cc_start: 0.5797 (p0) cc_final: 0.5295 (p0) REVERT: L 231 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8180 (mp) REVERT: P 5 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7261 (pp) REVERT: P 31 ARG cc_start: 0.7670 (ttm-80) cc_final: 0.7426 (ttm110) REVERT: P 86 THR cc_start: 0.8148 (m) cc_final: 0.7572 (p) REVERT: P 122 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.6663 (tm-30) REVERT: Q 83 ASP cc_start: 0.6746 (m-30) cc_final: 0.6287 (t0) REVERT: Q 91 LYS cc_start: 0.7807 (tttt) cc_final: 0.7507 (mttt) REVERT: Q 94 GLU cc_start: 0.7393 (tp30) cc_final: 0.6746 (mp0) REVERT: Q 122 GLN cc_start: 0.8156 (mt0) cc_final: 0.7090 (mm-40) REVERT: R 235 ASP cc_start: 0.7725 (p0) cc_final: 0.7412 (p0) REVERT: S 20 SER cc_start: 0.8673 (t) cc_final: 0.8409 (m) REVERT: S 24 GLU cc_start: 0.7806 (tp30) cc_final: 0.7551 (tp30) REVERT: S 37 LYS cc_start: 0.8191 (ptmm) cc_final: 0.7811 (pttp) REVERT: S 75 ILE cc_start: 0.8682 (mt) cc_final: 0.8375 (tt) REVERT: S 122 GLN cc_start: 0.7792 (mt0) cc_final: 0.7133 (tp-100) REVERT: T 76 ASP cc_start: 0.8250 (t70) cc_final: 0.7779 (t70) REVERT: T 122 GLN cc_start: 0.8248 (mt0) cc_final: 0.7218 (tp40) REVERT: U 83 ASP cc_start: 0.8148 (t70) cc_final: 0.7873 (t0) REVERT: U 91 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7966 (mtpt) REVERT: V 13 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7902 (mm) REVERT: V 151 GLU cc_start: 0.8063 (pm20) cc_final: 0.7855 (pm20) REVERT: V 231 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7897 (mp) REVERT: X 37 LYS cc_start: 0.8659 (ttmt) cc_final: 0.7951 (tmtt) REVERT: X 94 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8186 (tt0) REVERT: X 211 ASP cc_start: 0.8171 (p0) cc_final: 0.7951 (p0) REVERT: X 231 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8293 (mp) REVERT: X 242 LYS cc_start: 0.8035 (ttmt) cc_final: 0.7446 (tptm) REVERT: Y 210 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8272 (tt) REVERT: a 87 ASP cc_start: 0.8426 (t0) cc_final: 0.8016 (m-30) REVERT: a 265 GLN cc_start: 0.8082 (mt0) cc_final: 0.7792 (mp10) REVERT: b 7 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8230 (t) REVERT: b 177 THR cc_start: 0.7671 (m) cc_final: 0.7248 (p) REVERT: c 133 ASN cc_start: 0.8623 (t0) cc_final: 0.8168 (t0) REVERT: c 151 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7564 (pp20) REVERT: c 262 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7626 (mt0) REVERT: d 40 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.7914 (p0) REVERT: d 42 LYS cc_start: 0.6352 (tptt) cc_final: 0.5425 (mtmt) REVERT: d 60 SER cc_start: 0.8055 (t) cc_final: 0.7735 (m) REVERT: e 24 GLU cc_start: 0.8460 (tp30) cc_final: 0.8126 (tp30) REVERT: e 66 ASP cc_start: 0.7793 (m-30) cc_final: 0.7248 (m-30) REVERT: e 131 LYS cc_start: 0.7944 (ptpt) cc_final: 0.7522 (mtmt) REVERT: f 2 LEU cc_start: 0.6598 (mt) cc_final: 0.6358 (tp) REVERT: f 24 GLU cc_start: 0.8195 (tp30) cc_final: 0.7844 (tt0) REVERT: f 151 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.7760 (pp20) REVERT: f 267 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8646 (tp) REVERT: g 151 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7959 (pp20) REVERT: h 42 LYS cc_start: 0.5849 (tptt) cc_final: 0.5075 (mtmm) REVERT: h 265 GLN cc_start: 0.6544 (OUTLIER) cc_final: 0.6159 (mm-40) REVERT: i 94 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6822 (mm-30) REVERT: i 123 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8771 (tt) REVERT: j 117 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8464 (mt-10) REVERT: j 151 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8031 (pp20) REVERT: k 76 ASP cc_start: 0.8024 (m-30) cc_final: 0.7760 (m-30) REVERT: k 242 LYS cc_start: 0.8429 (mtpt) cc_final: 0.8104 (mttm) outliers start: 204 outliers final: 112 residues processed: 966 average time/residue: 1.3392 time to fit residues: 1752.0794 Evaluate side-chains 938 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 804 time to evaluate : 6.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 255 GLN Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 185 MET Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 269 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain K residue 248 THR Chi-restraints excluded: chain L residue 3 ASN Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 91 LYS Chi-restraints excluded: chain L residue 95 LYS Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 159 THR Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain N residue 115 ASP Chi-restraints excluded: chain N residue 128 THR Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 258 SER Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 163 LEU Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 122 GLN Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 73 SER Chi-restraints excluded: chain Q residue 252 LEU Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain T residue 55 SER Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain T residue 152 ASP Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 75 ILE Chi-restraints excluded: chain U residue 91 LYS Chi-restraints excluded: chain U residue 154 SER Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 232 VAL Chi-restraints excluded: chain V residue 13 LEU Chi-restraints excluded: chain V residue 40 ASN Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain V residue 231 LEU Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 102 THR Chi-restraints excluded: chain W residue 244 GLN Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain X residue 40 ASN Chi-restraints excluded: chain X residue 94 GLU Chi-restraints excluded: chain X residue 231 LEU Chi-restraints excluded: chain X residue 239 GLU Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 210 LEU Chi-restraints excluded: chain Y residue 263 THR Chi-restraints excluded: chain Z residue 91 LYS Chi-restraints excluded: chain a residue 84 THR Chi-restraints excluded: chain a residue 210 LEU Chi-restraints excluded: chain b residue 2 LEU Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 117 GLU Chi-restraints excluded: chain b residue 168 ILE Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 15 LEU Chi-restraints excluded: chain c residue 52 LYS Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain d residue 40 ASN Chi-restraints excluded: chain d residue 108 SER Chi-restraints excluded: chain d residue 168 ILE Chi-restraints excluded: chain d residue 184 THR Chi-restraints excluded: chain d residue 239 GLU Chi-restraints excluded: chain e residue 85 ILE Chi-restraints excluded: chain e residue 168 ILE Chi-restraints excluded: chain e residue 267 ILE Chi-restraints excluded: chain f residue 151 GLU Chi-restraints excluded: chain f residue 267 ILE Chi-restraints excluded: chain f residue 268 LEU Chi-restraints excluded: chain g residue 151 GLU Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain h residue 128 THR Chi-restraints excluded: chain h residue 151 GLU Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 265 GLN Chi-restraints excluded: chain i residue 86 THR Chi-restraints excluded: chain i residue 89 LEU Chi-restraints excluded: chain i residue 123 LEU Chi-restraints excluded: chain i residue 186 ILE Chi-restraints excluded: chain i residue 267 ILE Chi-restraints excluded: chain j residue 92 MET Chi-restraints excluded: chain j residue 117 GLU Chi-restraints excluded: chain j residue 151 GLU Chi-restraints excluded: chain j residue 157 THR Chi-restraints excluded: chain k residue 55 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 114 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 839 optimal weight: 1.9990 chunk 981 optimal weight: 5.9990 chunk 753 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 843 optimal weight: 2.9990 chunk 811 optimal weight: 0.8980 chunk 253 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 GLN C 133 ASN C 250 GLN C 255 GLN D 262 GLN D 265 GLN E 250 GLN ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 GLN I 105 ASN I 255 GLN L 3 ASN L 72 GLN L 262 GLN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 ASN N 54 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN T 150 ASN V 150 ASN V 261 ASN X 255 GLN Z 150 ASN Z 230 ASN Z 250 GLN a 54 GLN a 122 GLN a 150 ASN a 262 GLN ** b 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 265 GLN c 122 GLN c 265 GLN d 122 GLN d 133 ASN e 262 GLN f 8 ASN ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 133 ASN h 29 GLN h 262 GLN i 251 GLN k 133 ASN k 250 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.122490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.108457 restraints weight = 98258.158| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.38 r_work: 0.3346 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 72816 Z= 0.172 Angle : 0.453 12.093 98753 Z= 0.255 Chirality : 0.033 0.200 12802 Planarity : 0.003 0.081 12617 Dihedral : 3.777 17.218 10064 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.81 % Allowed : 12.24 % Favored : 85.95 % 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: 4.17 (0.09), residues: 9916 helix: 3.78 (0.06), residues: 7474 sheet: -2.19 (0.19), residues: 444 loop : -0.38 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 48 HIS 0.003 0.001 HIS g 213 PHE 0.024 0.001 PHE R 109 ARG 0.004 0.000 ARG d 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 1015 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 870 time to evaluate : 6.406 Fit side-chains REVERT: A 151 GLU cc_start: 0.8597 (pm20) cc_final: 0.8357 (pp20) REVERT: E 87 ASP cc_start: 0.8100 (m-30) cc_final: 0.7849 (m-30) REVERT: E 91 LYS cc_start: 0.7850 (mtpt) cc_final: 0.7490 (mtpp) REVERT: F 86 THR cc_start: 0.8149 (m) cc_final: 0.7789 (p) REVERT: F 101 ASP cc_start: 0.7859 (t0) cc_final: 0.7585 (t0) REVERT: G 24 GLU cc_start: 0.8252 (tt0) cc_final: 0.7846 (mm-30) REVERT: G 151 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7760 (pp20) REVERT: H 2 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6043 (tm) REVERT: H 105 ASN cc_start: 0.8366 (p0) cc_final: 0.8068 (p0) REVERT: H 131 LYS cc_start: 0.8304 (ptpt) cc_final: 0.7909 (pttp) REVERT: I 87 ASP cc_start: 0.8029 (m-30) cc_final: 0.7714 (m-30) REVERT: K 86 THR cc_start: 0.8240 (m) cc_final: 0.7886 (p) REVERT: K 117 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8371 (mt-10) REVERT: L 8 ASN cc_start: 0.8557 (p0) cc_final: 0.8293 (p0) REVERT: L 24 GLU cc_start: 0.8043 (mp0) cc_final: 0.7694 (mt-10) REVERT: L 150 ASN cc_start: 0.8052 (t0) cc_final: 0.7727 (t0) REVERT: L 231 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8146 (mp) REVERT: M 250 GLN cc_start: 0.8613 (tt0) cc_final: 0.8282 (tt0) REVERT: P 2 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6636 (tt) REVERT: P 5 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7063 (pp) REVERT: P 31 ARG cc_start: 0.7700 (ttm-80) cc_final: 0.7411 (ttm110) REVERT: P 122 GLN cc_start: 0.7143 (OUTLIER) cc_final: 0.6622 (tm-30) REVERT: Q 5 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.6863 (tp) REVERT: Q 83 ASP cc_start: 0.6694 (m-30) cc_final: 0.6236 (t0) REVERT: Q 91 LYS cc_start: 0.7663 (tttt) cc_final: 0.7426 (mttt) REVERT: Q 94 GLU cc_start: 0.7436 (tp30) cc_final: 0.6673 (mp0) REVERT: Q 122 GLN cc_start: 0.8051 (mt0) cc_final: 0.7150 (mm-40) REVERT: R 24 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8151 (tp30) REVERT: R 125 LYS cc_start: 0.7851 (mttp) cc_final: 0.6608 (tttt) REVERT: R 235 ASP cc_start: 0.7605 (p0) cc_final: 0.7299 (p0) REVERT: S 24 GLU cc_start: 0.7735 (tp30) cc_final: 0.7474 (tp30) REVERT: S 37 LYS cc_start: 0.8211 (ptmm) cc_final: 0.7791 (pttp) REVERT: S 75 ILE cc_start: 0.8608 (mt) cc_final: 0.8297 (tt) REVERT: S 122 GLN cc_start: 0.7724 (mt0) cc_final: 0.7134 (tp40) REVERT: T 13 LEU cc_start: 0.8177 (mt) cc_final: 0.7790 (mm) REVERT: T 76 ASP cc_start: 0.8163 (t70) cc_final: 0.7722 (t70) REVERT: T 83 ASP cc_start: 0.8419 (t70) cc_final: 0.8034 (t70) REVERT: T 122 GLN cc_start: 0.8191 (mt0) cc_final: 0.7216 (tp40) REVERT: U 83 ASP cc_start: 0.8156 (t70) cc_final: 0.7820 (t0) REVERT: U 91 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7887 (mtpt) REVERT: U 255 GLN cc_start: 0.7616 (tt0) cc_final: 0.7015 (mt0) REVERT: V 231 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7736 (mp) REVERT: X 94 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7484 (tm-30) REVERT: X 211 ASP cc_start: 0.8117 (p0) cc_final: 0.7853 (p0) REVERT: X 242 LYS cc_start: 0.7893 (ttmt) cc_final: 0.7238 (tptm) REVERT: Y 117 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: Z 50 MET cc_start: 0.8338 (mtp) cc_final: 0.7960 (mtt) REVERT: Z 267 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7619 (pt) REVERT: a 87 ASP cc_start: 0.8381 (t0) cc_final: 0.7983 (m-30) REVERT: a 265 GLN cc_start: 0.8066 (mt0) cc_final: 0.7812 (mp10) REVERT: b 7 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8221 (t) REVERT: b 177 THR cc_start: 0.7498 (m) cc_final: 0.7061 (p) REVERT: c 133 ASN cc_start: 0.8555 (t0) cc_final: 0.8142 (t0) REVERT: c 151 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7589 (pp20) REVERT: c 262 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7549 (mm-40) REVERT: d 40 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.7838 (p0) REVERT: d 42 LYS cc_start: 0.6206 (tptt) cc_final: 0.5327 (mtmt) REVERT: d 60 SER cc_start: 0.8056 (t) cc_final: 0.7791 (m) REVERT: d 262 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7327 (tt0) REVERT: e 24 GLU cc_start: 0.8420 (tp30) cc_final: 0.8109 (tp30) REVERT: e 66 ASP cc_start: 0.7613 (m-30) cc_final: 0.7107 (m-30) REVERT: e 110 ASN cc_start: 0.7760 (m-40) cc_final: 0.7531 (m110) REVERT: e 131 LYS cc_start: 0.7835 (ptpt) cc_final: 0.7501 (mtmt) REVERT: f 2 LEU cc_start: 0.6379 (mt) cc_final: 0.6147 (tp) REVERT: f 24 GLU cc_start: 0.8132 (tp30) cc_final: 0.7807 (tt0) REVERT: f 151 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.7723 (pp20) REVERT: f 267 ILE cc_start: 0.8953 (tp) cc_final: 0.8652 (tp) REVERT: h 42 LYS cc_start: 0.5913 (tptt) cc_final: 0.5101 (mtmm) REVERT: h 84 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8595 (p) REVERT: h 265 GLN cc_start: 0.6536 (OUTLIER) cc_final: 0.6181 (mm-40) REVERT: i 94 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6891 (mt-10) REVERT: i 123 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8800 (tt) REVERT: j 83 ASP cc_start: 0.8283 (m-30) cc_final: 0.8049 (m-30) REVERT: j 117 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8406 (mt-10) REVERT: j 151 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8016 (pp20) REVERT: k 76 ASP cc_start: 0.8041 (m-30) cc_final: 0.7764 (m-30) REVERT: k 242 LYS cc_start: 0.8432 (mtpt) cc_final: 0.8080 (mttm) outliers start: 145 outliers final: 90 residues processed: 966 average time/residue: 1.3303 time to fit residues: 1743.1269 Evaluate side-chains 955 residues out of total 7992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 844 time to evaluate : 6.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 255 GLN Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 250 GLN Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 269 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain K residue 248 THR Chi-restraints excluded: chain L residue 3 ASN Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 91 LYS Chi-restraints excluded: chain L residue 95 LYS Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 159 THR Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain N residue 115 ASP Chi-restraints excluded: chain N residue 128 THR Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 258 SER Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 122 GLN Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 73 SER Chi-restraints excluded: chain Q residue 252 LEU Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain T residue 55 SER Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain U residue 75 ILE Chi-restraints excluded: chain U residue 91 LYS Chi-restraints excluded: chain U residue 154 SER Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain U residue 232 VAL Chi-restraints excluded: chain V residue 13 LEU Chi-restraints excluded: chain V residue 40 ASN Chi-restraints excluded: chain V residue 231 LEU Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 244 GLN Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain X residue 40 ASN Chi-restraints excluded: chain X residue 94 GLU Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 117 GLU Chi-restraints excluded: chain Y residue 210 LEU Chi-restraints excluded: chain Y residue 263 THR Chi-restraints excluded: chain Z residue 91 LYS Chi-restraints excluded: chain Z residue 267 ILE Chi-restraints excluded: chain a residue 84 THR Chi-restraints excluded: chain a residue 210 LEU Chi-restraints excluded: chain b residue 2 LEU Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 168 ILE Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 15 LEU Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 175 THR Chi-restraints excluded: chain d residue 40 ASN Chi-restraints excluded: chain d residue 108 SER Chi-restraints excluded: chain d residue 168 ILE Chi-restraints excluded: chain d residue 184 THR Chi-restraints excluded: chain d residue 239 GLU Chi-restraints excluded: chain e residue 168 ILE Chi-restraints excluded: chain e residue 267 ILE Chi-restraints excluded: chain f residue 151 GLU Chi-restraints excluded: chain f residue 268 LEU Chi-restraints excluded: chain g residue 131 LYS Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain h residue 128 THR Chi-restraints excluded: chain h residue 151 GLU Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 265 GLN Chi-restraints excluded: chain i residue 86 THR Chi-restraints excluded: chain i residue 89 LEU Chi-restraints excluded: chain i residue 123 LEU Chi-restraints excluded: chain i residue 186 ILE Chi-restraints excluded: chain i residue 267 ILE Chi-restraints excluded: chain j residue 92 MET Chi-restraints excluded: chain j residue 117 GLU Chi-restraints excluded: chain j residue 151 GLU Chi-restraints excluded: chain j residue 157 THR Chi-restraints excluded: chain j residue 267 ILE Chi-restraints excluded: chain k residue 55 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 321 optimal weight: 4.9990 chunk 379 optimal weight: 2.9990 chunk 981 optimal weight: 0.8980 chunk 966 optimal weight: 4.9990 chunk 942 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 331 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 420 optimal weight: 7.9990 chunk 552 optimal weight: 6.9990 chunk 846 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 255 GLN C 250 GLN C 255 GLN D 262 GLN E 250 GLN E 262 GLN G 255 GLN ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 ASN L 262 GLN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 ASN N 54 GLN O 54 GLN O 122 GLN R 54 GLN S 230 ASN T 150 ASN U 150 ASN V 150 ASN W 150 ASN X 255 GLN ** Z 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 150 ASN Z 230 ASN Z 250 GLN a 17 ASN a 54 GLN a 150 ASN a 262 GLN ** b 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 265 GLN c 122 GLN c 261 ASN d 122 GLN d 133 ASN ** f 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 29 GLN h 262 GLN i 251 GLN k 250 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.104980 restraints weight = 99454.954| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.41 r_work: 0.3304 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 72816 Z= 0.236 Angle : 0.505 12.721 98753 Z= 0.280 Chirality : 0.036 0.207 12802 Planarity : 0.003 0.096 12617 Dihedral : 3.902 18.217 10064 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.76 % Allowed : 12.50 % Favored : 85.74 % 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: 3.95 (0.08), residues: 9916 helix: 3.63 (0.06), residues: 7474 sheet: -2.22 (0.19), residues: 444 loop : -0.46 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 48 HIS 0.004 0.002 HIS f 213 PHE 0.025 0.002 PHE R 109 ARG 0.003 0.000 ARG Q 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 45670.21 seconds wall clock time: 783 minutes 30.53 seconds (47010.53 seconds total)