Starting phenix.real_space_refine on Sat Sep 28 23:00:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cem_45504/09_2024/9cem_45504.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cem_45504/09_2024/9cem_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cem_45504/09_2024/9cem_45504.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cem_45504/09_2024/9cem_45504.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cem_45504/09_2024/9cem_45504.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cem_45504/09_2024/9cem_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-5461/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: 31.74, per 1000 atoms: 0.44 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: 14.29 Conformation dependent library (CDL) restraints added in 7.9 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: 4.48 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: 27.56 Time building geometry restraints manager: 17.11 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: 0.00 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: 11.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 2.340 Check model and map are aligned: 0.420 Set scattering table: 0.560 Process input model: 128.900 Find NCS groups from input model: 3.010 Set up NCS constraints: 0.800 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:12.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.940 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 1408 time to evaluate : 6.293 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: 1.4274 time to fit residues: 2696.3535 Evaluate side-chains 929 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 926 time to evaluate : 6.324 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 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 fitting. rotamer outliers: 223 poor density : 909 time to evaluate : 6.447 Fit side-chains revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8135 (mt-10) REVERT: C 8 ASN cc_start: 0.8519 (p0) cc_final: 0.8285 (p0) REVERT: C 91 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8256 (mtmp) REVERT: D 24 GLU cc_start: 0.7699 (mp0) cc_final: 0.7362 (mt-10) REVERT: D 86 THR cc_start: 0.8386 (m) cc_final: 0.7998 (p) REVERT: F 86 THR cc_start: 0.8207 (m) cc_final: 0.7799 (p) REVERT: F 148 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8515 (mp) REVERT: F 151 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7759 (pp20) REVERT: G 24 GLU cc_start: 0.8155 (tt0) cc_final: 0.7767 (mm-30) REVERT: G 255 GLN cc_start: 0.8116 (tt0) cc_final: 0.7884 (mt0) REVERT: H 94 GLU cc_start: 0.8253 (tp30) cc_final: 0.8050 (mt-10) REVERT: H 131 LYS cc_start: 0.8388 (ptpt) cc_final: 0.8087 (pttp) REVERT: I 52 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7565 (tttp) REVERT: I 87 ASP cc_start: 0.8253 (m-30) cc_final: 0.8006 (m-30) REVERT: J 92 MET cc_start: 0.9051 (mtp) cc_final: 0.8758 (mtp) REVERT: J 131 LYS cc_start: 0.8554 (ptpp) cc_final: 0.8059 (pttp) REVERT: J 255 GLN cc_start: 0.8343 (tt0) cc_final: 0.7967 (mt0) REVERT: K 86 THR cc_start: 0.8283 (m) cc_final: 0.7944 (p) REVERT: K 92 MET cc_start: 0.8949 (mtp) cc_final: 0.8719 (mtp) REVERT: K 117 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8287 (mt-10) REVERT: K 255 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7759 (mm-40) REVERT: L 8 ASN cc_start: 0.8824 (p0) cc_final: 0.8620 (p0) REVERT: L 128 THR cc_start: 0.8185 (m) cc_final: 0.7874 (m) REVERT: L 150 ASN cc_start: 0.8339 (t0) cc_final: 0.7966 (t0) REVERT: O 91 LYS cc_start: 0.7982 (mtpt) cc_final: 0.7778 (mttm) REVERT: O 133 ASN cc_start: 0.8730 (t0) cc_final: 0.8410 (t160) REVERT: P 31 ARG cc_start: 0.8183 (ttm-80) cc_final: 0.7798 (mtm110) REVERT: P 83 ASP cc_start: 0.7725 (m-30) cc_final: 0.7508 (m-30) REVERT: P 86 THR cc_start: 0.8612 (m) cc_final: 0.8288 (p) REVERT: P 255 GLN cc_start: 0.7456 (tt0) cc_final: 0.7214 (tp-100) REVERT: Q 83 ASP cc_start: 0.7154 (m-30) cc_final: 0.6948 (m-30) REVERT: Q 94 GLU cc_start: 0.7614 (tp30) cc_final: 0.7113 (mp0) REVERT: R 125 LYS cc_start: 0.8167 (mttp) cc_final: 0.6746 (pttt) REVERT: R 235 ASP cc_start: 0.7731 (p0) cc_final: 0.7483 (p0) REVERT: R 242 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7841 (ttpp) REVERT: R 252 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7542 (tm) REVERT: S 24 GLU cc_start: 0.8065 (tp30) cc_final: 0.7848 (tp30) REVERT: S 122 GLN cc_start: 0.8118 (mt0) cc_final: 0.7459 (tp40) REVERT: T 13 LEU cc_start: 0.8380 (mt) cc_final: 0.8053 (mm) REVERT: U 93 LYS cc_start: 0.8432 (ttpt) cc_final: 0.8151 (tttm) REVERT: U 239 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8053 (mm-30) REVERT: U 244 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8214 (mm-40) REVERT: W 222 ASP cc_start: 0.7921 (p0) cc_final: 0.7622 (m-30) REVERT: X 94 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7652 (tm-30) REVERT: X 242 LYS cc_start: 0.8161 (ttmt) cc_final: 0.7696 (tptm) REVERT: a 87 ASP cc_start: 0.8502 (t0) cc_final: 0.8125 (m-30) REVERT: a 91 LYS cc_start: 0.8355 (mmtt) cc_final: 0.7812 (mppt) REVERT: a 265 GLN cc_start: 0.8160 (mt0) cc_final: 0.7864 (mp10) REVERT: b 29 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: b 66 ASP cc_start: 0.7627 (m-30) cc_final: 0.7227 (m-30) REVERT: b 177 THR cc_start: 0.7563 (m) cc_final: 0.7133 (p) REVERT: c 133 ASN cc_start: 0.8790 (t0) cc_final: 0.8421 (t0) REVERT: c 177 THR cc_start: 0.7536 (m) cc_final: 0.7111 (p) REVERT: c 262 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7705 (mt0) REVERT: d 42 LYS cc_start: 0.6277 (tptt) cc_final: 0.5560 (mtmt) REVERT: e 24 GLU cc_start: 0.8703 (tp30) cc_final: 0.8086 (mt-10) REVERT: e 66 ASP cc_start: 0.7896 (m-30) cc_final: 0.7559 (m-30) REVERT: e 131 LYS cc_start: 0.7995 (ptpt) cc_final: 0.7577 (pttp) REVERT: e 154 SER cc_start: 0.8894 (OUTLIER) cc_final: 0.8324 (p) REVERT: f 151 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.7939 (pp20) REVERT: f 267 ILE cc_start: 0.8886 (tp) cc_final: 0.8682 (tp) REVERT: g 151 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8069 (pp20) REVERT: h 42 LYS cc_start: 0.6207 (tptt) cc_final: 0.5473 (mtmm) REVERT: h 262 GLN cc_start: 0.8079 (tp-100) cc_final: 0.7758 (tp-100) REVERT: h 265 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.6686 (mm110) REVERT: i 94 GLU cc_start: 0.7491 (mm-30) cc_final: 0.6996 (mt-10) REVERT: j 83 ASP cc_start: 0.8049 (m-30) cc_final: 0.7808 (m-30) REVERT: j 92 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8123 (mtt) REVERT: k 76 ASP cc_start: 0.8013 (m-30) cc_final: 0.7759 (m-30) REVERT: k 117 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.7745 (mm-30) REVERT: k 242 LYS cc_start: 0.8433 (mtpt) cc_final: 0.8092 (mttm) outliers start: 223 outliers final: 104 residues processed: 1046 average time/residue: 1.4375 time to fit residues: 2044.0468 Evaluate side-chains 955 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 836 time to evaluate : 6.434 ------------------------------------------------------------------------------- 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 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 504 optimal weight: 4.9990 chunk 281 optimal weight: 0.9990 chunk 755 optimal weight: 0.9980 chunk 617 optimal weight: 1.9990 chunk 250 optimal weight: 0.7980 chunk 908 optimal weight: 1.9990 chunk 981 optimal weight: 0.9990 chunk 809 optimal weight: 0.9990 chunk 901 optimal weight: 1.9990 chunk 309 optimal weight: 9.9990 chunk 729 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 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: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 72816 Z= 0.152 Angle : 0.435 10.995 98753 Z= 0.245 Chirality : 0.033 0.196 12802 Planarity : 0.003 0.048 12617 Dihedral : 3.818 51.142 10066 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 2.18 % Allowed : 8.90 % Favored : 88.93 % 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: 3.94 (0.09), residues: 9916 helix: 3.52 (0.06), residues: 7511 sheet: -3.24 (0.16), residues: 444 loop : 0.19 (0.15), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP d 48 HIS 0.003 0.001 HIS e 213 PHE 0.015 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 1145 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 971 time to evaluate : 6.434 Fit side-chains REVERT: C 8 ASN cc_start: 0.8230 (p0) cc_final: 0.7985 (p0) REVERT: D 86 THR cc_start: 0.8403 (m) cc_final: 0.7971 (p) REVERT: D 265 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7846 (mm-40) REVERT: E 91 LYS cc_start: 0.8052 (mtpm) cc_final: 0.7824 (mtpp) REVERT: E 239 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7801 (mm-30) REVERT: F 86 THR cc_start: 0.8145 (m) cc_final: 0.7706 (p) REVERT: F 151 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7733 (pp20) REVERT: F 242 LYS cc_start: 0.8309 (mtpt) cc_final: 0.8072 (mtpp) REVERT: G 24 GLU cc_start: 0.8119 (tt0) cc_final: 0.7732 (mm-30) REVERT: G 255 GLN cc_start: 0.8096 (tt0) cc_final: 0.7872 (mt0) REVERT: H 94 GLU cc_start: 0.8236 (tp30) cc_final: 0.7965 (mt-10) REVERT: H 131 LYS cc_start: 0.8210 (ptpt) cc_final: 0.7900 (pttp) REVERT: I 52 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7562 (tttp) REVERT: I 87 ASP cc_start: 0.8218 (m-30) cc_final: 0.7957 (m-30) REVERT: I 255 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.7119 (mm110) REVERT: J 54 GLN cc_start: 0.7383 (mm-40) cc_final: 0.6866 (tt0) REVERT: J 92 MET cc_start: 0.9080 (mtp) cc_final: 0.8730 (mtp) REVERT: K 86 THR cc_start: 0.8127 (m) cc_final: 0.7802 (p) REVERT: K 92 MET cc_start: 0.8925 (mtp) cc_final: 0.8450 (mtp) REVERT: K 117 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8264 (mt-10) REVERT: K 251 GLN cc_start: 0.7205 (tp-100) cc_final: 0.6953 (tp-100) REVERT: L 24 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: L 92 MET cc_start: 0.7507 (mtp) cc_final: 0.7122 (mtp) REVERT: L 128 THR cc_start: 0.8085 (m) cc_final: 0.7780 (m) REVERT: L 150 ASN cc_start: 0.8208 (t0) cc_final: 0.7834 (t0) REVERT: L 231 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8307 (mp) REVERT: M 250 GLN cc_start: 0.8656 (tt0) cc_final: 0.8414 (tt0) REVERT: P 31 ARG cc_start: 0.8065 (ttm-80) cc_final: 0.7768 (ttm110) REVERT: P 83 ASP cc_start: 0.7624 (m-30) cc_final: 0.7349 (m-30) REVERT: P 86 THR cc_start: 0.8433 (m) cc_final: 0.8085 (p) REVERT: P 255 GLN cc_start: 0.7504 (tt0) cc_final: 0.7261 (tp-100) REVERT: Q 83 ASP cc_start: 0.7187 (m-30) cc_final: 0.6976 (m-30) REVERT: Q 94 GLU cc_start: 0.7612 (tp30) cc_final: 0.7051 (mp0) REVERT: Q 122 GLN cc_start: 0.8298 (mt0) cc_final: 0.7446 (mm-40) REVERT: R 125 LYS cc_start: 0.8075 (mttp) cc_final: 0.6846 (tttt) REVERT: S 24 GLU cc_start: 0.7997 (tp30) cc_final: 0.7775 (tp30) REVERT: S 75 ILE cc_start: 0.8684 (mt) cc_final: 0.8446 (tt) REVERT: S 122 GLN cc_start: 0.8020 (mt0) cc_final: 0.7414 (tp40) REVERT: T 13 LEU cc_start: 0.8245 (mt) cc_final: 0.7935 (mm) REVERT: T 76 ASP cc_start: 0.8149 (t70) cc_final: 0.7840 (t70) REVERT: T 83 ASP cc_start: 0.8391 (t70) cc_final: 0.8083 (t70) REVERT: T 122 GLN cc_start: 0.8374 (mt0) cc_final: 0.7358 (tp40) REVERT: U 239 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8056 (mm-30) REVERT: U 244 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8204 (mm-40) REVERT: V 13 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8207 (mm) REVERT: W 222 ASP cc_start: 0.7793 (p0) cc_final: 0.7543 (m-30) REVERT: X 94 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: X 122 GLN cc_start: 0.8024 (tp40) cc_final: 0.7723 (tp-100) REVERT: X 222 ASP cc_start: 0.7579 (p0) cc_final: 0.6910 (m-30) REVERT: X 242 LYS cc_start: 0.7942 (ttmt) cc_final: 0.7414 (tptm) REVERT: a 87 ASP cc_start: 0.8471 (t0) cc_final: 0.8083 (m-30) REVERT: a 91 LYS cc_start: 0.8270 (mmtt) cc_final: 0.7754 (mppt) REVERT: a 265 GLN cc_start: 0.8157 (mt0) cc_final: 0.7824 (mp10) REVERT: b 177 THR cc_start: 0.7573 (m) cc_final: 0.7124 (p) REVERT: c 36 LYS cc_start: 0.8966 (mttt) cc_final: 0.8690 (mttp) REVERT: c 133 ASN cc_start: 0.8664 (t0) cc_final: 0.8297 (t0) REVERT: c 151 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7676 (pp20) REVERT: c 177 THR cc_start: 0.7424 (m) cc_final: 0.6962 (p) REVERT: c 262 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7532 (mm-40) REVERT: d 42 LYS cc_start: 0.6365 (tptt) cc_final: 0.5749 (mtmt) REVERT: d 120 ARG cc_start: 0.7094 (tmm160) cc_final: 0.6866 (tmm160) REVERT: e 24 GLU cc_start: 0.8681 (tp30) cc_final: 0.8048 (mt-10) REVERT: e 66 ASP cc_start: 0.7701 (m-30) cc_final: 0.7366 (m-30) REVERT: e 110 ASN cc_start: 0.7789 (m-40) cc_final: 0.7573 (m110) REVERT: e 131 LYS cc_start: 0.7928 (ptpt) cc_final: 0.7464 (mtmt) REVERT: e 154 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8303 (p) REVERT: f 151 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7833 (pp20) REVERT: f 267 ILE cc_start: 0.8862 (tp) cc_final: 0.8651 (tp) REVERT: h 42 LYS cc_start: 0.6147 (tptt) cc_final: 0.5407 (mtmm) REVERT: h 151 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7959 (pt0) REVERT: h 262 GLN cc_start: 0.7972 (tp-100) cc_final: 0.7658 (tp-100) REVERT: h 265 GLN cc_start: 0.7015 (mm110) cc_final: 0.6704 (mm-40) REVERT: i 94 GLU cc_start: 0.7466 (mm-30) cc_final: 0.6920 (mt-10) REVERT: i 123 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8867 (tt) REVERT: j 151 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8027 (pp20) REVERT: k 76 ASP cc_start: 0.7920 (m-30) cc_final: 0.7664 (m-30) REVERT: k 242 LYS cc_start: 0.8398 (mtpt) cc_final: 0.8043 (mttm) outliers start: 174 outliers final: 65 residues processed: 1073 average time/residue: 1.3255 time to fit residues: 1928.6487 Evaluate side-chains 951 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 873 time to evaluate : 6.346 ------------------------------------------------------------------------------- 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 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 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 263 THR Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 84 THR 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 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 897 optimal weight: 0.9990 chunk 683 optimal weight: 0.7980 chunk 471 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 433 optimal weight: 6.9990 chunk 610 optimal weight: 0.3980 chunk 912 optimal weight: 0.6980 chunk 965 optimal weight: 2.9990 chunk 476 optimal weight: 8.9990 chunk 864 optimal weight: 0.0980 chunk 260 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 29 GLN D 251 GLN D 262 GLN E 155 ASN E 250 GLN E 262 GLN H 262 GLN L 72 GLN L 262 GLN 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 262 GLN Q 250 GLN R 54 GLN S 230 ASN T 255 GLN U 40 ASN ** U 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 124 GLN V 150 ASN W 150 ASN X 40 ASN 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** c 122 GLN c 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 h 29 GLN i 3 ASN i 8 ASN i 110 ASN i 250 GLN j 29 GLN j 122 GLN k 133 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 72816 Z= 0.130 Angle : 0.401 11.231 98753 Z= 0.226 Chirality : 0.032 0.192 12802 Planarity : 0.002 0.055 12617 Dihedral : 3.589 15.678 10064 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 2.13 % Allowed : 10.05 % Favored : 87.83 % 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: 4.38 (0.09), residues: 9916 helix: 3.88 (0.06), residues: 7511 sheet: -2.84 (0.17), residues: 444 loop : 0.10 (0.15), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP d 48 HIS 0.003 0.001 HIS L 213 PHE 0.017 0.001 PHE R 109 ARG 0.004 0.000 ARG Y 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 1171 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1001 time to evaluate : 6.931 Fit side-chains revert: symmetry clash REVERT: D 86 THR cc_start: 0.8406 (m) cc_final: 0.7955 (p) REVERT: D 265 GLN cc_start: 0.7903 (mm-40) cc_final: 0.7565 (mm-40) REVERT: F 86 THR cc_start: 0.8170 (m) cc_final: 0.7713 (p) REVERT: F 151 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7700 (pp20) REVERT: G 24 GLU cc_start: 0.8122 (tt0) cc_final: 0.7729 (mm-30) REVERT: G 151 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7573 (pp20) REVERT: G 255 GLN cc_start: 0.8095 (tt0) cc_final: 0.7870 (mt0) REVERT: H 94 GLU cc_start: 0.8185 (tp30) cc_final: 0.7927 (mt-10) REVERT: I 24 GLU cc_start: 0.7582 (tp30) cc_final: 0.7263 (mm-30) REVERT: I 52 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7554 (tttp) REVERT: I 87 ASP cc_start: 0.8184 (m-30) cc_final: 0.7977 (m-30) REVERT: I 255 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.7149 (mm110) REVERT: J 54 GLN cc_start: 0.7278 (mm-40) cc_final: 0.6831 (tt0) REVERT: J 92 MET cc_start: 0.9014 (mtp) cc_final: 0.8789 (mtp) REVERT: K 86 THR cc_start: 0.8115 (m) cc_final: 0.7773 (p) REVERT: K 92 MET cc_start: 0.8941 (mtp) cc_final: 0.8413 (mtp) REVERT: K 251 GLN cc_start: 0.7293 (tp-100) cc_final: 0.7067 (tp-100) REVERT: K 255 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7741 (mm-40) REVERT: K 270 LEU cc_start: 0.8684 (mt) cc_final: 0.8389 (mm) REVERT: L 24 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7924 (mt-10) REVERT: L 92 MET cc_start: 0.7532 (mtp) cc_final: 0.7267 (mtp) REVERT: L 231 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8130 (mp) REVERT: M 76 ASP cc_start: 0.8274 (m-30) cc_final: 0.8060 (m-30) REVERT: M 250 GLN cc_start: 0.8654 (tt0) cc_final: 0.8434 (tt0) REVERT: O 83 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7160 (m-30) REVERT: P 5 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7402 (pp) REVERT: P 83 ASP cc_start: 0.7483 (m-30) cc_final: 0.7205 (m-30) REVERT: P 86 THR cc_start: 0.8288 (m) cc_final: 0.7882 (p) REVERT: P 255 GLN cc_start: 0.7513 (tt0) cc_final: 0.7275 (tp-100) REVERT: Q 94 GLU cc_start: 0.7483 (tp30) cc_final: 0.6827 (mp0) REVERT: Q 122 GLN cc_start: 0.8159 (mt0) cc_final: 0.7444 (mm-40) REVERT: R 125 LYS cc_start: 0.8062 (mttp) cc_final: 0.6845 (tttt) REVERT: S 24 GLU cc_start: 0.7947 (tp30) cc_final: 0.7728 (tp30) REVERT: S 75 ILE cc_start: 0.8692 (mt) cc_final: 0.8392 (tt) REVERT: S 122 GLN cc_start: 0.7976 (mt0) cc_final: 0.7404 (tp40) REVERT: T 13 LEU cc_start: 0.8080 (mt) cc_final: 0.7815 (mm) REVERT: T 76 ASP cc_start: 0.7977 (t70) cc_final: 0.7725 (t70) REVERT: T 83 ASP cc_start: 0.8348 (t70) cc_final: 0.8040 (t70) REVERT: T 122 GLN cc_start: 0.8273 (mt0) cc_final: 0.7396 (tp40) REVERT: U 83 ASP cc_start: 0.8134 (t70) cc_final: 0.7821 (t0) REVERT: X 122 GLN cc_start: 0.8017 (tp40) cc_final: 0.7743 (tp-100) REVERT: Y 53 MET cc_start: 0.8924 (mmm) cc_final: 0.8688 (mmm) REVERT: Y 117 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: Z 13 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8151 (mm) REVERT: Z 50 MET cc_start: 0.8269 (mtp) cc_final: 0.7977 (mtt) REVERT: a 87 ASP cc_start: 0.8486 (t0) cc_final: 0.8075 (m-30) REVERT: a 265 GLN cc_start: 0.8133 (mt0) cc_final: 0.7828 (mp10) REVERT: b 69 GLN cc_start: 0.7485 (mt0) cc_final: 0.7229 (mt0) REVERT: b 106 THR cc_start: 0.6516 (p) cc_final: 0.6239 (m) REVERT: b 115 ASP cc_start: 0.7183 (m-30) cc_final: 0.6935 (m-30) REVERT: b 150 ASN cc_start: 0.8368 (t0) cc_final: 0.7907 (t0) REVERT: c 133 ASN cc_start: 0.8618 (t0) cc_final: 0.8214 (t0) REVERT: c 262 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7468 (mm-40) REVERT: d 40 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7721 (p0) REVERT: d 42 LYS cc_start: 0.6384 (tptt) cc_final: 0.5564 (mtmt) REVERT: d 262 GLN cc_start: 0.7640 (tm-30) cc_final: 0.7323 (tt0) REVERT: e 131 LYS cc_start: 0.7755 (ptpt) cc_final: 0.7407 (mtmt) REVERT: f 129 ASN cc_start: 0.8350 (m-40) cc_final: 0.8095 (t0) REVERT: f 267 ILE cc_start: 0.8928 (tp) cc_final: 0.8705 (tp) REVERT: g 131 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7729 (mtmm) REVERT: h 42 LYS cc_start: 0.6080 (tptt) cc_final: 0.5383 (mtmm) REVERT: h 151 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7909 (pt0) REVERT: h 265 GLN cc_start: 0.7064 (mm110) cc_final: 0.6860 (mm-40) REVERT: i 94 GLU cc_start: 0.7382 (mm-30) cc_final: 0.6786 (mt-10) REVERT: i 117 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7457 (mp0) REVERT: i 123 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8886 (tt) REVERT: j 117 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8212 (mt-10) REVERT: k 76 ASP cc_start: 0.7838 (m-30) cc_final: 0.7583 (m-30) REVERT: k 242 LYS cc_start: 0.8396 (mtpt) cc_final: 0.8035 (mttm) outliers start: 170 outliers final: 61 residues processed: 1096 average time/residue: 1.3031 time to fit residues: 1949.2806 Evaluate side-chains 961 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 885 time to evaluate : 6.324 ------------------------------------------------------------------------------- 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 D residue 55 SER 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 G residue 151 GLU Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain H residue 84 THR 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 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 231 LEU 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 O residue 83 ASP Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 252 LEU Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain S residue 94 GLU 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 154 SER Chi-restraints excluded: chain U residue 232 VAL Chi-restraints excluded: chain V residue 40 ASN Chi-restraints excluded: chain W residue 244 GLN 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 13 LEU 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 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 d residue 40 ASN Chi-restraints excluded: chain d residue 108 SER 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 52 LYS Chi-restraints excluded: chain g residue 131 LYS Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 151 GLU Chi-restraints excluded: chain i residue 89 LEU Chi-restraints excluded: chain i residue 123 LEU 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 j residue 268 LEU Chi-restraints excluded: chain k residue 55 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 804 optimal weight: 0.7980 chunk 548 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 718 optimal weight: 0.0970 chunk 398 optimal weight: 0.9990 chunk 824 optimal weight: 10.0000 chunk 667 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 493 optimal weight: 7.9990 chunk 866 optimal weight: 1.9990 chunk 243 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 E 250 GLN E 262 GLN H 262 GLN I 40 ASN J 33 ASN L 3 ASN L 72 GLN L 230 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** O 250 GLN P 69 GLN P 150 ASN Q 44 ASN Q 230 ASN R 54 GLN T 150 ASN T 255 GLN U 17 ASN U 250 GLN V 6 ASN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 150 ASN W 150 ASN Y 250 GLN Z 150 ASN 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 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 265 GLN c 122 GLN c 265 GLN d 69 GLN d 72 GLN d 122 GLN d 133 ASN d 230 ASN f 8 ASN ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 133 ASN i 3 ASN i 110 ASN i 250 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 72816 Z= 0.136 Angle : 0.404 10.528 98753 Z= 0.227 Chirality : 0.032 0.204 12802 Planarity : 0.002 0.051 12617 Dihedral : 3.550 16.914 10064 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.10 % Allowed : 10.85 % Favored : 87.05 % 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: 4.49 (0.09), residues: 9916 helix: 3.97 (0.06), residues: 7511 sheet: -2.54 (0.17), residues: 444 loop : 0.01 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP d 48 HIS 0.003 0.001 HIS f 213 PHE 0.010 0.001 PHE i 116 ARG 0.004 0.000 ARG a 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 939 time to evaluate : 6.344 Fit side-chains revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8085 (pp20) REVERT: D 265 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7566 (mm-40) REVERT: F 86 THR cc_start: 0.8176 (m) cc_final: 0.7738 (p) REVERT: F 151 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7691 (pp20) REVERT: G 24 GLU cc_start: 0.8136 (tt0) cc_final: 0.7729 (mm-30) REVERT: G 151 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7592 (pp20) REVERT: G 255 GLN cc_start: 0.8113 (tt0) cc_final: 0.7887 (mt0) REVERT: H 94 GLU cc_start: 0.8204 (tp30) cc_final: 0.7923 (mt-10) REVERT: I 24 GLU cc_start: 0.7520 (tp30) cc_final: 0.7209 (mm-30) REVERT: I 52 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7537 (tttp) REVERT: I 87 ASP cc_start: 0.8198 (m-30) cc_final: 0.7987 (m-30) REVERT: I 255 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.7167 (mm110) REVERT: J 54 GLN cc_start: 0.7005 (mm-40) cc_final: 0.6759 (tt0) REVERT: J 92 MET cc_start: 0.9039 (mtp) cc_final: 0.8758 (mtp) REVERT: K 92 MET cc_start: 0.8933 (mtp) cc_final: 0.8638 (mtp) REVERT: K 251 GLN cc_start: 0.7345 (tp-100) cc_final: 0.7097 (tp-100) REVERT: K 255 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7728 (mm-40) REVERT: K 270 LEU cc_start: 0.8683 (mt) cc_final: 0.8383 (mm) REVERT: L 24 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: L 92 MET cc_start: 0.7526 (mtp) cc_final: 0.7172 (mtp) REVERT: L 231 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8105 (mp) REVERT: M 76 ASP cc_start: 0.8273 (m-30) cc_final: 0.8063 (m-30) REVERT: M 250 GLN cc_start: 0.8649 (tt0) cc_final: 0.8448 (tt0) REVERT: O 83 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7141 (m-30) REVERT: P 83 ASP cc_start: 0.7464 (m-30) cc_final: 0.7147 (m-30) REVERT: P 86 THR cc_start: 0.8278 (m) cc_final: 0.7886 (p) REVERT: P 255 GLN cc_start: 0.7551 (tt0) cc_final: 0.7253 (tp-100) REVERT: Q 94 GLU cc_start: 0.7486 (tp30) cc_final: 0.6846 (mp0) REVERT: Q 122 GLN cc_start: 0.8122 (mt0) cc_final: 0.7444 (mm-40) REVERT: R 125 LYS cc_start: 0.8088 (mttp) cc_final: 0.6956 (tttt) REVERT: R 235 ASP cc_start: 0.7496 (p0) cc_final: 0.7124 (p0) REVERT: S 24 GLU cc_start: 0.7941 (tp30) cc_final: 0.7736 (tp30) REVERT: S 75 ILE cc_start: 0.8691 (mt) cc_final: 0.8388 (tt) REVERT: S 122 GLN cc_start: 0.7970 (mt0) cc_final: 0.7430 (tp40) REVERT: T 13 LEU cc_start: 0.8064 (mt) cc_final: 0.7812 (mm) REVERT: T 76 ASP cc_start: 0.7982 (t70) cc_final: 0.7676 (t70) REVERT: T 83 ASP cc_start: 0.8373 (t70) cc_final: 0.8063 (t70) REVERT: T 122 GLN cc_start: 0.8258 (mt0) cc_final: 0.7505 (tp40) REVERT: U 83 ASP cc_start: 0.8167 (t70) cc_final: 0.7871 (t0) REVERT: U 91 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7937 (mtpt) REVERT: V 222 ASP cc_start: 0.7882 (p0) cc_final: 0.7566 (t0) REVERT: X 122 GLN cc_start: 0.7984 (tp40) cc_final: 0.7702 (tp-100) REVERT: Y 53 MET cc_start: 0.8920 (mmm) cc_final: 0.8690 (mmm) REVERT: Y 117 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: Z 13 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8118 (mm) REVERT: a 87 ASP cc_start: 0.8476 (t0) cc_final: 0.8058 (m-30) REVERT: a 265 GLN cc_start: 0.8112 (mt0) cc_final: 0.7816 (mp10) REVERT: b 69 GLN cc_start: 0.7458 (mt0) cc_final: 0.7167 (mt0) REVERT: b 83 ASP cc_start: 0.7381 (m-30) cc_final: 0.7092 (m-30) REVERT: c 133 ASN cc_start: 0.8600 (t0) cc_final: 0.8194 (t0) REVERT: c 151 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7659 (pp20) REVERT: c 262 GLN cc_start: 0.7660 (mm-40) cc_final: 0.7443 (mm-40) REVERT: d 42 LYS cc_start: 0.6512 (tptt) cc_final: 0.5875 (mtmt) REVERT: d 262 GLN cc_start: 0.7628 (tm-30) cc_final: 0.7272 (tt0) REVERT: e 24 GLU cc_start: 0.8658 (tp30) cc_final: 0.8067 (mt-10) REVERT: e 110 ASN cc_start: 0.7856 (m-40) cc_final: 0.7616 (m110) REVERT: e 131 LYS cc_start: 0.7730 (ptpt) cc_final: 0.7407 (mtmt) REVERT: f 129 ASN cc_start: 0.8354 (m-40) cc_final: 0.8113 (t0) REVERT: f 267 ILE cc_start: 0.8944 (tp) cc_final: 0.8717 (tp) REVERT: h 42 LYS cc_start: 0.6147 (tptt) cc_final: 0.5441 (mtmm) REVERT: h 151 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7911 (pt0) REVERT: h 265 GLN cc_start: 0.6877 (mm110) cc_final: 0.6669 (mm-40) REVERT: i 94 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6782 (mt-10) REVERT: i 117 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7465 (mp0) REVERT: i 123 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8901 (tt) REVERT: j 117 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8226 (mt-10) REVERT: k 76 ASP cc_start: 0.7872 (m-30) cc_final: 0.7625 (m-30) REVERT: k 242 LYS cc_start: 0.8406 (mtpt) cc_final: 0.8050 (mttm) outliers start: 168 outliers final: 88 residues processed: 1039 average time/residue: 1.3006 time to fit residues: 1844.0067 Evaluate side-chains 978 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 875 time to evaluate : 6.466 ------------------------------------------------------------------------------- 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 139 ASP Chi-restraints excluded: chain A residue 151 GLU 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 117 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 D residue 258 SER 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 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 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 24 GLU 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 258 SER Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain O residue 83 ASP Chi-restraints excluded: chain O residue 245 SER Chi-restraints excluded: chain P residue 267 ILE Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 252 LEU Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain S residue 150 ASN Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 55 SER 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 94 GLU Chi-restraints excluded: chain U residue 154 SER Chi-restraints excluded: chain U residue 232 VAL Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 252 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 W residue 7 THR Chi-restraints excluded: chain W residue 40 ASN Chi-restraints excluded: chain W residue 231 LEU Chi-restraints excluded: chain W residue 244 GLN Chi-restraints excluded: chain X residue 40 ASN 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 262 GLN Chi-restraints excluded: chain Y residue 263 THR Chi-restraints excluded: chain Z residue 13 LEU Chi-restraints excluded: chain Z residue 83 ASP 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 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 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 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 h residue 129 ASN 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 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 150 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 324 optimal weight: 6.9990 chunk 869 optimal weight: 6.9990 chunk 190 optimal weight: 8.9990 chunk 566 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 966 optimal weight: 0.6980 chunk 802 optimal weight: 0.9990 chunk 447 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 319 optimal weight: 10.0000 chunk 507 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 E 250 GLN H 255 GLN H 262 GLN ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 261 ASN K 8 ASN L 3 ASN L 72 GLN M 133 ASN M 262 GLN N 54 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 122 GLN Q 44 ASN R 54 GLN S 230 ASN S 265 GLN T 54 GLN T 255 GLN U 247 GLN ** U 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 6 ASN V 29 GLN V 150 ASN W 150 ASN W 198 ASN X 255 GLN Z 150 ASN Z 265 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 17 ASN d 72 GLN d 122 GLN d 133 ASN d 230 ASN e 72 GLN f 8 ASN ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 29 GLN h 262 GLN i 3 ASN i 110 ASN i 251 GLN k 250 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1978 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= 0.154 Angle : 0.420 12.239 98753 Z= 0.235 Chirality : 0.033 0.208 12802 Planarity : 0.002 0.051 12617 Dihedral : 3.591 16.439 10064 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 2.18 % Allowed : 11.10 % Favored : 86.72 % 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: 4.46 (0.09), residues: 9916 helix: 3.95 (0.06), residues: 7511 sheet: -2.35 (0.18), residues: 444 loop : -0.09 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 48 HIS 0.004 0.001 HIS f 213 PHE 0.015 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 1079 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 905 time to evaluate : 6.390 Fit side-chains revert: symmetry clash REVERT: A 148 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7656 (mp) REVERT: A 151 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8039 (pp20) REVERT: A 262 GLN cc_start: 0.7801 (mt0) cc_final: 0.7399 (tp40) REVERT: D 252 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8356 (mp) REVERT: D 265 GLN cc_start: 0.7918 (mm-40) cc_final: 0.7534 (mm-40) REVERT: F 86 THR cc_start: 0.8189 (m) cc_final: 0.7754 (p) REVERT: F 151 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7701 (pp20) REVERT: G 24 GLU cc_start: 0.8153 (tt0) cc_final: 0.7752 (mm-30) REVERT: G 151 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7623 (pp20) REVERT: G 255 GLN cc_start: 0.8105 (tt0) cc_final: 0.7870 (mt0) REVERT: H 2 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6129 (tm) REVERT: H 94 GLU cc_start: 0.8231 (tp30) cc_final: 0.8010 (mt-10) REVERT: I 24 GLU cc_start: 0.7530 (tp30) cc_final: 0.7208 (mm-30) REVERT: I 52 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7502 (tttp) REVERT: I 87 ASP cc_start: 0.8211 (m-30) cc_final: 0.7965 (m-30) REVERT: I 117 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.6798 (mm-30) REVERT: I 255 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.7163 (mm110) REVERT: J 92 MET cc_start: 0.9039 (mtp) cc_final: 0.8711 (mtp) REVERT: K 86 THR cc_start: 0.8174 (m) cc_final: 0.7824 (p) REVERT: K 251 GLN cc_start: 0.7295 (tp-100) cc_final: 0.7048 (tp-100) REVERT: K 255 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7739 (mm-40) REVERT: L 24 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: L 92 MET cc_start: 0.7551 (mtp) cc_final: 0.7207 (mtp) REVERT: L 101 ASP cc_start: 0.5985 (p0) cc_final: 0.5575 (p0) REVERT: L 128 THR cc_start: 0.8174 (m) cc_final: 0.7902 (m) REVERT: L 173 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.8067 (p) REVERT: M 24 GLU cc_start: 0.8055 (tp30) cc_final: 0.7682 (mp0) REVERT: M 76 ASP cc_start: 0.8283 (m-30) cc_final: 0.8082 (m-30) REVERT: M 250 GLN cc_start: 0.8657 (tt0) cc_final: 0.8442 (tt0) REVERT: O 83 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7127 (m-30) REVERT: O 251 GLN cc_start: 0.8345 (mt0) cc_final: 0.8056 (mt0) REVERT: P 36 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8311 (mttp) REVERT: P 86 THR cc_start: 0.8235 (m) cc_final: 0.7795 (p) REVERT: P 255 GLN cc_start: 0.7583 (tt0) cc_final: 0.7221 (tp-100) REVERT: Q 94 GLU cc_start: 0.7551 (tp30) cc_final: 0.6949 (mp0) REVERT: Q 122 GLN cc_start: 0.8155 (mt0) cc_final: 0.7453 (mm-40) REVERT: R 125 LYS cc_start: 0.8108 (mttp) cc_final: 0.6905 (tttt) REVERT: R 235 ASP cc_start: 0.7465 (p0) cc_final: 0.7105 (p0) REVERT: S 24 GLU cc_start: 0.7954 (tp30) cc_final: 0.7741 (tp30) REVERT: S 75 ILE cc_start: 0.8713 (mt) cc_final: 0.8424 (tt) REVERT: S 122 GLN cc_start: 0.7973 (mt0) cc_final: 0.7436 (tp40) REVERT: T 13 LEU cc_start: 0.8134 (mt) cc_final: 0.7871 (mm) REVERT: T 32 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7906 (mm) REVERT: T 76 ASP cc_start: 0.8098 (t70) cc_final: 0.7820 (t70) REVERT: T 83 ASP cc_start: 0.8358 (t70) cc_final: 0.8045 (t70) REVERT: T 122 GLN cc_start: 0.8279 (mt0) cc_final: 0.7493 (tp40) REVERT: T 252 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8085 (tt) REVERT: U 83 ASP cc_start: 0.8160 (t70) cc_final: 0.7863 (t0) REVERT: U 91 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7934 (mtpt) REVERT: V 222 ASP cc_start: 0.7916 (p0) cc_final: 0.7640 (t0) REVERT: X 122 GLN cc_start: 0.8008 (tp40) cc_final: 0.7721 (tp-100) REVERT: X 231 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8168 (mp) REVERT: X 242 LYS cc_start: 0.7915 (ttmt) cc_final: 0.7414 (tptm) REVERT: Y 117 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: Z 13 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8136 (mm) REVERT: Z 50 MET cc_start: 0.8430 (mtp) cc_final: 0.8141 (mtt) REVERT: a 87 ASP cc_start: 0.8458 (t0) cc_final: 0.8067 (m-30) REVERT: a 265 GLN cc_start: 0.8109 (mt0) cc_final: 0.7817 (mp10) REVERT: b 7 THR cc_start: 0.8379 (p) cc_final: 0.8165 (t) REVERT: b 69 GLN cc_start: 0.7458 (mt0) cc_final: 0.7213 (mt0) REVERT: b 83 ASP cc_start: 0.7427 (m-30) cc_final: 0.7159 (m-30) REVERT: c 133 ASN cc_start: 0.8629 (t0) cc_final: 0.8219 (t0) REVERT: c 151 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7656 (pp20) REVERT: c 262 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7479 (mm110) REVERT: d 40 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7684 (p0) REVERT: d 42 LYS cc_start: 0.6537 (tptt) cc_final: 0.5663 (mtmt) REVERT: e 24 GLU cc_start: 0.8680 (tp30) cc_final: 0.8077 (mt-10) REVERT: e 66 ASP cc_start: 0.7720 (m-30) cc_final: 0.7351 (m-30) REVERT: e 110 ASN cc_start: 0.7886 (m-40) cc_final: 0.7630 (m110) REVERT: e 131 LYS cc_start: 0.7860 (ptpt) cc_final: 0.7578 (mtmt) REVERT: f 267 ILE cc_start: 0.8973 (tp) cc_final: 0.8727 (tp) REVERT: h 42 LYS cc_start: 0.6001 (tptt) cc_final: 0.5306 (mtmm) REVERT: h 265 GLN cc_start: 0.6869 (mm110) cc_final: 0.6661 (mm-40) REVERT: i 94 GLU cc_start: 0.7453 (mm-30) cc_final: 0.6832 (mt-10) REVERT: i 117 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7468 (mp0) REVERT: i 123 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8888 (tt) REVERT: j 117 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8260 (mt-10) REVERT: k 76 ASP cc_start: 0.7890 (m-30) cc_final: 0.7630 (m-30) REVERT: k 242 LYS cc_start: 0.8380 (mtpt) cc_final: 0.8037 (mttm) outliers start: 174 outliers final: 96 residues processed: 1013 average time/residue: 1.2922 time to fit residues: 1786.7967 Evaluate side-chains 988 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 868 time to evaluate : 6.403 ------------------------------------------------------------------------------- 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 148 LEU Chi-restraints excluded: chain A residue 151 GLU 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 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 252 LEU Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain E residue 38 VAL 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 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 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 159 THR Chi-restraints excluded: chain L residue 173 THR 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 258 SER Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain O residue 83 ASP Chi-restraints excluded: chain O residue 245 SER Chi-restraints excluded: chain P residue 36 LYS Chi-restraints excluded: chain P residue 115 ASP Chi-restraints excluded: chain P residue 163 LEU Chi-restraints excluded: chain P residue 267 ILE Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 252 LEU Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain S residue 150 ASN Chi-restraints excluded: chain T residue 32 ILE 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 75 ILE 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 U residue 252 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 W residue 7 THR Chi-restraints excluded: chain W residue 40 ASN Chi-restraints excluded: chain W residue 231 LEU Chi-restraints excluded: chain W residue 244 GLN Chi-restraints excluded: chain X residue 40 ASN 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 262 GLN Chi-restraints excluded: chain Y residue 263 THR Chi-restraints excluded: chain Z residue 13 LEU Chi-restraints excluded: chain Z residue 83 ASP Chi-restraints excluded: chain Z residue 84 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 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 c residue 2 LEU Chi-restraints excluded: chain c residue 15 LEU Chi-restraints excluded: chain c residue 52 LYS Chi-restraints excluded: chain c residue 122 GLN 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 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 h residue 128 THR Chi-restraints excluded: chain h residue 129 ASN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 931 optimal weight: 6.9990 chunk 108 optimal weight: 0.0040 chunk 550 optimal weight: 2.9990 chunk 705 optimal weight: 0.1980 chunk 546 optimal weight: 5.9990 chunk 813 optimal weight: 5.9990 chunk 539 optimal weight: 0.2980 chunk 962 optimal weight: 8.9990 chunk 602 optimal weight: 9.9990 chunk 587 optimal weight: 5.9990 chunk 444 optimal weight: 7.9990 overall best weight: 1.8996 ------------------------------------------------------------------------------- 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 251 GLN E 250 GLN E 262 GLN H 262 GLN ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 261 ASN L 3 ASN L 262 GLN L 265 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** R 54 GLN S 265 GLN T 255 GLN ** U 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 150 ASN W 150 ASN X 255 GLN Z 150 ASN Z 265 GLN a 17 ASN a 122 GLN a 150 ASN a 262 GLN ** b 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 265 GLN c 122 GLN c 265 GLN d 17 ASN d 122 GLN d 133 ASN f 8 ASN h 262 GLN i 110 ASN i 250 GLN i 251 GLN j 29 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 72816 Z= 0.204 Angle : 0.468 12.366 98753 Z= 0.261 Chirality : 0.035 0.215 12802 Planarity : 0.003 0.066 12617 Dihedral : 3.783 17.762 10064 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 2.31 % Allowed : 11.27 % Favored : 86.41 % 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 (0.08), residues: 9916 helix: 3.81 (0.06), residues: 7474 sheet: -2.27 (0.19), residues: 444 loop : -0.04 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 48 HIS 0.005 0.002 HIS f 213 PHE 0.015 0.002 PHE f 216 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 1056 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 871 time to evaluate : 6.476 Fit side-chains revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7942 (pp20) REVERT: C 94 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7983 (mt-10) REVERT: D 252 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8396 (mp) REVERT: F 86 THR cc_start: 0.8195 (m) cc_final: 0.7769 (p) REVERT: F 151 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7722 (pp20) REVERT: G 24 GLU cc_start: 0.8162 (tt0) cc_final: 0.7792 (mm-30) REVERT: G 151 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7662 (pp20) REVERT: G 255 GLN cc_start: 0.8103 (tt0) cc_final: 0.7877 (mt0) REVERT: H 2 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6002 (tm) REVERT: H 94 GLU cc_start: 0.8299 (tp30) cc_final: 0.8024 (mt-10) REVERT: I 24 GLU cc_start: 0.7553 (tp30) cc_final: 0.7220 (mm-30) REVERT: I 52 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7546 (tttp) REVERT: I 87 ASP cc_start: 0.8241 (m-30) cc_final: 0.7998 (m-30) REVERT: I 117 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.6844 (mm-30) REVERT: I 255 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.7018 (mm110) REVERT: K 86 THR cc_start: 0.8268 (m) cc_final: 0.7917 (p) REVERT: K 251 GLN cc_start: 0.7278 (tp-100) cc_final: 0.7019 (tp-100) REVERT: K 255 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7741 (mm-40) REVERT: L 24 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7998 (mt-10) REVERT: L 92 MET cc_start: 0.7468 (mtp) cc_final: 0.7088 (mtp) REVERT: L 128 THR cc_start: 0.8184 (m) cc_final: 0.7911 (m) REVERT: M 24 GLU cc_start: 0.8118 (tp30) cc_final: 0.7775 (mp0) REVERT: M 249 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7893 (tmtt) REVERT: N 120 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7499 (ptt90) REVERT: O 83 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7225 (m-30) REVERT: O 251 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8096 (mt0) REVERT: P 5 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7455 (pp) REVERT: P 31 ARG cc_start: 0.8138 (ttm110) cc_final: 0.7778 (ttp-110) REVERT: P 36 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8327 (mttp) REVERT: P 86 THR cc_start: 0.8326 (m) cc_final: 0.7906 (p) REVERT: P 122 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.6983 (tm-30) REVERT: Q 94 GLU cc_start: 0.7674 (tp30) cc_final: 0.7089 (mp0) REVERT: Q 122 GLN cc_start: 0.8226 (mt0) cc_final: 0.7458 (mm-40) REVERT: R 24 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8311 (tp30) REVERT: R 125 LYS cc_start: 0.8145 (mttp) cc_final: 0.6906 (tttt) REVERT: R 235 ASP cc_start: 0.7471 (p0) cc_final: 0.7155 (p0) REVERT: S 24 GLU cc_start: 0.7917 (tp30) cc_final: 0.7694 (tp30) REVERT: S 75 ILE cc_start: 0.8732 (mt) cc_final: 0.8508 (tt) REVERT: S 122 GLN cc_start: 0.7998 (mt0) cc_final: 0.7446 (tp40) REVERT: T 13 LEU cc_start: 0.8271 (mt) cc_final: 0.7958 (mm) REVERT: T 32 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8115 (mm) REVERT: T 76 ASP cc_start: 0.8189 (t70) cc_final: 0.7849 (t70) REVERT: T 122 GLN cc_start: 0.8300 (mt0) cc_final: 0.7434 (tp40) REVERT: T 252 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8151 (tt) REVERT: U 83 ASP cc_start: 0.8183 (t70) cc_final: 0.7898 (t0) REVERT: U 91 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.8020 (mtpt) REVERT: V 222 ASP cc_start: 0.7915 (p0) cc_final: 0.7614 (t0) REVERT: W 231 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8517 (mp) REVERT: X 122 GLN cc_start: 0.7968 (tp40) cc_final: 0.7680 (tp-100) REVERT: X 231 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8307 (mp) REVERT: X 242 LYS cc_start: 0.7997 (ttmt) cc_final: 0.7489 (tptm) REVERT: Y 117 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: a 87 ASP cc_start: 0.8466 (t0) cc_final: 0.8107 (m-30) REVERT: a 117 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.7674 (mm-30) REVERT: a 265 GLN cc_start: 0.8102 (mt0) cc_final: 0.7871 (mp10) REVERT: b 7 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8268 (t) REVERT: c 115 ASP cc_start: 0.7260 (m-30) cc_final: 0.6892 (t0) REVERT: c 133 ASN cc_start: 0.8741 (t0) cc_final: 0.8368 (t0) REVERT: c 151 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7690 (pp20) REVERT: c 262 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7608 (mm110) REVERT: d 42 LYS cc_start: 0.6495 (tptt) cc_final: 0.5830 (mtmt) REVERT: d 262 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7507 (tt0) REVERT: e 24 GLU cc_start: 0.8695 (tp30) cc_final: 0.8483 (tp30) REVERT: e 66 ASP cc_start: 0.7796 (m-30) cc_final: 0.7405 (m-30) REVERT: e 131 LYS cc_start: 0.7879 (ptpt) cc_final: 0.7658 (mtmt) REVERT: f 267 ILE cc_start: 0.8976 (tp) cc_final: 0.8707 (tp) REVERT: h 42 LYS cc_start: 0.6211 (tptt) cc_final: 0.5461 (mtmm) REVERT: h 265 GLN cc_start: 0.6806 (OUTLIER) cc_final: 0.6548 (mm-40) REVERT: i 94 GLU cc_start: 0.7497 (mm-30) cc_final: 0.6945 (mt-10) REVERT: i 117 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7468 (mp0) REVERT: i 123 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8871 (tt) REVERT: j 83 ASP cc_start: 0.7839 (m-30) cc_final: 0.7524 (m-30) REVERT: k 76 ASP cc_start: 0.7935 (m-30) cc_final: 0.7666 (m-30) REVERT: k 242 LYS cc_start: 0.8367 (mtpt) cc_final: 0.8014 (mttm) outliers start: 185 outliers final: 103 residues processed: 982 average time/residue: 1.3238 time to fit residues: 1765.9988 Evaluate side-chains 972 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 840 time to evaluate : 6.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR 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 151 GLU 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 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 D residue 252 LEU 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 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 128 THR Chi-restraints excluded: chain H residue 250 GLN Chi-restraints excluded: chain I residue 52 LYS Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain I residue 185 MET 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 95 LYS Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 249 LYS 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 O residue 83 ASP Chi-restraints excluded: chain O residue 245 SER Chi-restraints excluded: chain O residue 251 GLN Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 36 LYS Chi-restraints excluded: chain P residue 122 GLN Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 25 LEU 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 154 SER Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain S residue 150 ASN Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 55 SER Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain T residue 141 SER 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 75 ILE 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 U residue 252 LEU Chi-restraints excluded: chain V residue 40 ASN Chi-restraints excluded: chain V residue 166 THR Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 40 ASN Chi-restraints excluded: chain W residue 231 LEU Chi-restraints excluded: chain W residue 244 GLN Chi-restraints excluded: chain X residue 40 ASN 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 215 THR Chi-restraints excluded: chain Y residue 263 THR Chi-restraints excluded: chain Z residue 83 ASP Chi-restraints excluded: chain Z residue 84 THR Chi-restraints excluded: chain Z residue 91 LYS Chi-restraints excluded: chain a residue 84 THR Chi-restraints excluded: chain a residue 117 GLU 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 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 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 268 LEU Chi-restraints excluded: chain h residue 128 THR Chi-restraints excluded: chain h residue 129 ASN 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 595 optimal weight: 2.9990 chunk 384 optimal weight: 0.9990 chunk 575 optimal weight: 0.9990 chunk 290 optimal weight: 0.8980 chunk 189 optimal weight: 20.0000 chunk 186 optimal weight: 3.9990 chunk 612 optimal weight: 8.9990 chunk 656 optimal weight: 3.9990 chunk 476 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 756 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 265 GLN E 250 GLN E 262 GLN H 262 GLN ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 ASN L 17 ASN L 262 GLN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 ASN M 230 ASN N 54 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 262 GLN P 255 GLN Q 44 ASN R 54 GLN T 150 ASN ** U 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 150 ASN W 250 GLN X 255 GLN Z 150 ASN Z 265 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 d 122 GLN d 133 ASN f 8 ASN ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 262 GLN i 251 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 72816 Z= 0.171 Angle : 0.441 11.762 98753 Z= 0.247 Chirality : 0.033 0.210 12802 Planarity : 0.003 0.081 12617 Dihedral : 3.711 17.022 10064 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 2.05 % Allowed : 11.79 % Favored : 86.16 % 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: 4.35 (0.08), residues: 9916 helix: 3.88 (0.06), residues: 7474 sheet: -2.19 (0.19), residues: 444 loop : -0.11 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 48 HIS 0.004 0.001 HIS f 213 PHE 0.018 0.001 PHE R 109 ARG 0.005 0.000 ARG d 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 1041 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 877 time to evaluate : 6.425 Fit side-chains REVERT: A 151 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7984 (pp20) REVERT: D 252 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8395 (mp) REVERT: F 86 THR cc_start: 0.8194 (m) cc_final: 0.7752 (p) REVERT: G 24 GLU cc_start: 0.8155 (tt0) cc_final: 0.7753 (mm-30) REVERT: G 151 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7698 (pp20) REVERT: G 255 GLN cc_start: 0.8091 (tt0) cc_final: 0.7865 (mt0) REVERT: H 2 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.5990 (tm) REVERT: H 94 GLU cc_start: 0.8270 (tp30) cc_final: 0.8010 (mt-10) REVERT: I 24 GLU cc_start: 0.7535 (tp30) cc_final: 0.7207 (mm-30) REVERT: I 117 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.6839 (mm-30) REVERT: I 255 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.7073 (mm110) REVERT: K 86 THR cc_start: 0.8202 (m) cc_final: 0.7852 (p) REVERT: K 92 MET cc_start: 0.8907 (mtp) cc_final: 0.8630 (mtp) REVERT: K 251 GLN cc_start: 0.7295 (tp-100) cc_final: 0.7031 (tp-100) REVERT: L 24 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7946 (mt-10) REVERT: L 92 MET cc_start: 0.7462 (mtp) cc_final: 0.7090 (mtp) REVERT: L 101 ASP cc_start: 0.5811 (p0) cc_final: 0.5266 (p0) REVERT: L 128 THR cc_start: 0.8164 (m) cc_final: 0.7902 (m) REVERT: L 150 ASN cc_start: 0.8286 (t0) cc_final: 0.7908 (t0) REVERT: M 24 GLU cc_start: 0.8056 (tp30) cc_final: 0.7700 (mp0) REVERT: M 250 GLN cc_start: 0.8659 (tt0) cc_final: 0.8419 (tt0) REVERT: O 83 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7185 (m-30) REVERT: O 251 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8044 (mt0) REVERT: P 5 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7457 (pp) REVERT: P 36 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8297 (mttp) REVERT: P 86 THR cc_start: 0.8199 (m) cc_final: 0.7736 (p) REVERT: P 122 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.6959 (tm-30) REVERT: Q 44 ASN cc_start: 0.7469 (t0) cc_final: 0.7267 (t0) REVERT: Q 94 GLU cc_start: 0.7717 (tp30) cc_final: 0.7067 (mp0) REVERT: Q 122 GLN cc_start: 0.8218 (mt0) cc_final: 0.7469 (mm-40) REVERT: R 125 LYS cc_start: 0.8134 (mttp) cc_final: 0.6930 (tttt) REVERT: R 242 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7860 (ttpp) REVERT: S 24 GLU cc_start: 0.7964 (tp30) cc_final: 0.7743 (tp30) REVERT: S 75 ILE cc_start: 0.8731 (mt) cc_final: 0.8481 (tt) REVERT: S 122 GLN cc_start: 0.7958 (mt0) cc_final: 0.7415 (tp40) REVERT: T 13 LEU cc_start: 0.8234 (mt) cc_final: 0.7918 (mm) REVERT: T 32 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.8039 (mm) REVERT: T 76 ASP cc_start: 0.8153 (t70) cc_final: 0.7829 (t70) REVERT: T 122 GLN cc_start: 0.8289 (mt0) cc_final: 0.7427 (tp40) REVERT: T 252 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8123 (tt) REVERT: U 83 ASP cc_start: 0.8166 (t70) cc_final: 0.7873 (t0) REVERT: U 91 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.8027 (mtpt) REVERT: U 255 GLN cc_start: 0.7821 (tt0) cc_final: 0.7326 (mt0) REVERT: V 94 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7960 (tm-30) REVERT: V 222 ASP cc_start: 0.7927 (p0) cc_final: 0.7639 (t0) REVERT: V 231 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8087 (mp) REVERT: X 122 GLN cc_start: 0.8015 (tp40) cc_final: 0.7726 (tp-100) REVERT: X 231 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8244 (mp) REVERT: X 242 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7438 (tptm) REVERT: Y 117 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7903 (mp0) REVERT: a 87 ASP cc_start: 0.8470 (t0) cc_final: 0.8067 (m-30) REVERT: a 117 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.7674 (mm-30) REVERT: a 265 GLN cc_start: 0.8109 (mt0) cc_final: 0.7872 (mp10) REVERT: b 69 GLN cc_start: 0.7486 (mt0) cc_final: 0.7151 (mt0) REVERT: c 115 ASP cc_start: 0.7168 (m-30) cc_final: 0.6916 (t0) REVERT: c 133 ASN cc_start: 0.8715 (t0) cc_final: 0.8337 (t0) REVERT: c 151 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7672 (pp20) REVERT: c 262 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7553 (mm110) REVERT: d 40 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.7800 (p0) REVERT: d 42 LYS cc_start: 0.6560 (tptt) cc_final: 0.5683 (mtmt) REVERT: d 262 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7484 (tt0) REVERT: e 24 GLU cc_start: 0.8698 (tp30) cc_final: 0.8484 (tp30) REVERT: e 66 ASP cc_start: 0.7772 (m-30) cc_final: 0.7369 (m-30) REVERT: f 151 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.7832 (pp20) REVERT: f 267 ILE cc_start: 0.8977 (tp) cc_final: 0.8714 (tp) REVERT: h 42 LYS cc_start: 0.6245 (tptt) cc_final: 0.5489 (mtmm) REVERT: h 265 GLN cc_start: 0.6791 (OUTLIER) cc_final: 0.6539 (mm-40) REVERT: i 94 GLU cc_start: 0.7502 (mm-30) cc_final: 0.6943 (mt-10) REVERT: i 117 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7460 (mp0) REVERT: i 123 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8877 (tt) REVERT: k 76 ASP cc_start: 0.7934 (m-30) cc_final: 0.7657 (m-30) REVERT: k 242 LYS cc_start: 0.8387 (mtpt) cc_final: 0.8029 (mttm) outliers start: 164 outliers final: 102 residues processed: 975 average time/residue: 1.3415 time to fit residues: 1772.7770 Evaluate side-chains 971 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 843 time to evaluate : 6.287 ------------------------------------------------------------------------------- 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 151 GLU 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 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 252 LEU Chi-restraints excluded: chain E residue 38 VAL 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 139 ASP Chi-restraints excluded: chain H residue 250 GLN Chi-restraints excluded: chain I residue 97 LEU 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 95 LYS Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain N residue 115 ASP 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 O residue 83 ASP Chi-restraints excluded: chain O residue 245 SER Chi-restraints excluded: chain O residue 251 GLN 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 25 LEU 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 154 SER Chi-restraints excluded: chain R residue 242 LYS Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain S residue 150 ASN Chi-restraints excluded: chain T residue 32 ILE 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 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 252 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 24 GLU Chi-restraints excluded: chain W residue 40 ASN Chi-restraints excluded: chain W residue 231 LEU Chi-restraints excluded: chain W residue 244 GLN Chi-restraints excluded: chain X residue 40 ASN 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 262 GLN Chi-restraints excluded: chain Y residue 263 THR Chi-restraints excluded: chain Z residue 83 ASP Chi-restraints excluded: chain Z residue 84 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 117 GLU 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 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 8 ASN Chi-restraints excluded: chain f residue 151 GLU Chi-restraints excluded: chain f residue 268 LEU Chi-restraints excluded: chain h residue 128 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 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 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 875 optimal weight: 2.9990 chunk 922 optimal weight: 4.9990 chunk 841 optimal weight: 3.9990 chunk 897 optimal weight: 1.9990 chunk 540 optimal weight: 20.0000 chunk 390 optimal weight: 2.9990 chunk 704 optimal weight: 4.9990 chunk 275 optimal weight: 0.7980 chunk 810 optimal weight: 9.9990 chunk 848 optimal weight: 6.9990 chunk 894 optimal weight: 0.0000 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 251 GLN B 255 GLN C 250 GLN C 255 GLN E 250 GLN H 262 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 ** both conformations clash, **PLEASE CHECK MANUALLY** P 255 GLN R 54 GLN S 230 ASN T 150 ASN ** U 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 150 ASN W 150 ASN W 250 GLN X 255 GLN Z 150 ASN Z 265 GLN a 17 ASN a 122 GLN a 150 ASN a 262 GLN ** b 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 265 GLN d 122 GLN d 133 ASN f 8 ASN h 262 GLN i 250 GLN i 251 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2019 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= 0.195 Angle : 0.463 11.788 98753 Z= 0.258 Chirality : 0.034 0.209 12802 Planarity : 0.003 0.082 12617 Dihedral : 3.765 17.458 10064 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 2.04 % Allowed : 11.94 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.23 (0.08), residues: 9916 helix: 3.79 (0.06), residues: 7474 sheet: -2.18 (0.19), residues: 444 loop : -0.18 (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 0.021 0.002 PHE R 109 ARG 0.005 0.000 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 1020 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 857 time to evaluate : 6.449 Fit side-chains REVERT: A 151 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7953 (pp20) REVERT: A 262 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7650 (mp-120) REVERT: C 94 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: D 252 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8371 (mp) REVERT: F 86 THR cc_start: 0.8197 (m) cc_final: 0.7771 (p) REVERT: G 24 GLU cc_start: 0.8163 (tt0) cc_final: 0.7763 (mm-30) REVERT: G 151 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7667 (pp20) REVERT: G 255 GLN cc_start: 0.8095 (tt0) cc_final: 0.7868 (mt0) REVERT: H 2 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6007 (tm) REVERT: H 94 GLU cc_start: 0.8297 (tp30) cc_final: 0.8073 (mt-10) REVERT: I 24 GLU cc_start: 0.7553 (tp30) cc_final: 0.7223 (mm-30) REVERT: I 117 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.6839 (mm-30) REVERT: I 255 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.7020 (mm110) REVERT: K 86 THR cc_start: 0.8262 (m) cc_final: 0.7914 (p) REVERT: K 251 GLN cc_start: 0.7304 (tp-100) cc_final: 0.7040 (tp-100) REVERT: L 24 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7996 (mt-10) REVERT: L 92 MET cc_start: 0.7461 (mtp) cc_final: 0.7090 (mtp) REVERT: L 101 ASP cc_start: 0.5950 (p0) cc_final: 0.5492 (p0) REVERT: L 128 THR cc_start: 0.8170 (m) cc_final: 0.7904 (m) REVERT: L 150 ASN cc_start: 0.8265 (t0) cc_final: 0.7915 (t0) REVERT: M 24 GLU cc_start: 0.8104 (tp30) cc_final: 0.7755 (mp0) REVERT: M 250 GLN cc_start: 0.8661 (tt0) cc_final: 0.8456 (tt0) REVERT: O 83 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7216 (m-30) REVERT: O 251 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8086 (mt0) REVERT: P 5 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7477 (pp) REVERT: P 31 ARG cc_start: 0.8088 (ttm110) cc_final: 0.7762 (ttp-110) REVERT: P 36 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8265 (mttp) REVERT: P 86 THR cc_start: 0.8237 (m) cc_final: 0.7764 (p) REVERT: P 122 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.6980 (tm-30) REVERT: Q 83 ASP cc_start: 0.6962 (m-30) cc_final: 0.6713 (t0) REVERT: Q 94 GLU cc_start: 0.7750 (tp30) cc_final: 0.7109 (mp0) REVERT: Q 122 GLN cc_start: 0.8241 (mt0) cc_final: 0.7478 (mm-40) REVERT: R 125 LYS cc_start: 0.8117 (mttp) cc_final: 0.6890 (tttt) REVERT: R 235 ASP cc_start: 0.7573 (p0) cc_final: 0.7191 (p0) REVERT: S 24 GLU cc_start: 0.7913 (tp30) cc_final: 0.7682 (tp30) REVERT: S 75 ILE cc_start: 0.8726 (mt) cc_final: 0.8477 (tt) REVERT: S 122 GLN cc_start: 0.7991 (mt0) cc_final: 0.7447 (tp40) REVERT: T 13 LEU cc_start: 0.8281 (mt) cc_final: 0.7953 (mm) REVERT: T 32 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.8097 (mm) REVERT: T 76 ASP cc_start: 0.8175 (t70) cc_final: 0.7878 (t70) REVERT: T 122 GLN cc_start: 0.8299 (mt0) cc_final: 0.7436 (tp40) REVERT: T 231 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8122 (mp) REVERT: T 252 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8156 (tt) REVERT: U 83 ASP cc_start: 0.8190 (t70) cc_final: 0.7907 (t0) REVERT: U 91 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8013 (mtpt) REVERT: U 255 GLN cc_start: 0.7873 (tt0) cc_final: 0.7412 (mt0) REVERT: V 94 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7917 (tm-30) REVERT: V 222 ASP cc_start: 0.7937 (p0) cc_final: 0.7657 (t0) REVERT: V 231 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8108 (mp) REVERT: X 25 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7984 (tt) REVERT: X 122 GLN cc_start: 0.8015 (tp40) cc_final: 0.7719 (tp-100) REVERT: X 231 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8271 (mp) REVERT: X 242 LYS cc_start: 0.7992 (ttmt) cc_final: 0.7479 (tptm) REVERT: Y 117 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7901 (mp0) REVERT: a 87 ASP cc_start: 0.8478 (t0) cc_final: 0.8083 (m-30) REVERT: a 117 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.7680 (mm-30) REVERT: a 265 GLN cc_start: 0.8079 (mt0) cc_final: 0.7826 (mp10) REVERT: b 7 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8291 (t) REVERT: b 69 GLN cc_start: 0.7519 (mt0) cc_final: 0.7163 (mt0) REVERT: b 177 THR cc_start: 0.7421 (m) cc_final: 0.7061 (p) REVERT: c 133 ASN cc_start: 0.8742 (t0) cc_final: 0.8357 (t0) REVERT: c 151 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7691 (pp20) REVERT: c 262 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7591 (mm110) REVERT: d 40 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.7904 (p0) REVERT: d 42 LYS cc_start: 0.6542 (tptt) cc_final: 0.5695 (mtmt) REVERT: e 24 GLU cc_start: 0.8689 (tp30) cc_final: 0.8476 (tp30) REVERT: e 66 ASP cc_start: 0.7794 (m-30) cc_final: 0.7399 (m-30) REVERT: f 151 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.7815 (pp20) REVERT: f 267 ILE cc_start: 0.8959 (tp) cc_final: 0.8693 (tp) REVERT: h 42 LYS cc_start: 0.6204 (tptt) cc_final: 0.5460 (mtmm) REVERT: h 239 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6590 (tp30) REVERT: h 265 GLN cc_start: 0.6794 (OUTLIER) cc_final: 0.6536 (mm-40) REVERT: i 94 GLU cc_start: 0.7508 (mm-30) cc_final: 0.6954 (mt-10) REVERT: i 117 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7482 (mp0) REVERT: i 123 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8874 (tt) REVERT: k 76 ASP cc_start: 0.7940 (m-30) cc_final: 0.7675 (m-30) REVERT: k 242 LYS cc_start: 0.8362 (mtpt) cc_final: 0.8010 (mttm) outliers start: 163 outliers final: 110 residues processed: 955 average time/residue: 1.3115 time to fit residues: 1707.1171 Evaluate side-chains 975 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 834 time to evaluate : 6.359 ------------------------------------------------------------------------------- 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 151 GLU 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 32 ILE 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 252 LEU Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain E residue 38 VAL 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 128 THR Chi-restraints excluded: chain H residue 250 GLN Chi-restraints excluded: chain I residue 97 LEU 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 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 95 LYS Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain N residue 115 ASP 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 O residue 83 ASP Chi-restraints excluded: chain O residue 245 SER Chi-restraints excluded: chain O residue 251 GLN 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 25 LEU 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 154 SER 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 32 ILE Chi-restraints excluded: chain T residue 55 SER Chi-restraints excluded: chain T residue 91 LYS 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 T residue 252 LEU 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 U residue 252 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 24 GLU Chi-restraints excluded: chain W residue 40 ASN 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 X residue 25 LEU Chi-restraints excluded: chain X residue 40 ASN 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 215 THR Chi-restraints excluded: chain Y residue 263 THR Chi-restraints excluded: chain Z residue 83 ASP Chi-restraints excluded: chain Z residue 84 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 117 GLU 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 97 LEU Chi-restraints excluded: chain b residue 135 VAL Chi-restraints excluded: chain b residue 168 ILE 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 f residue 268 LEU Chi-restraints excluded: chain h residue 128 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 239 GLU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 589 optimal weight: 2.9990 chunk 948 optimal weight: 5.9990 chunk 579 optimal weight: 0.0020 chunk 450 optimal weight: 7.9990 chunk 659 optimal weight: 5.9990 chunk 995 optimal weight: 5.9990 chunk 916 optimal weight: 5.9990 chunk 792 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 612 optimal weight: 8.9990 chunk 485 optimal weight: 5.9990 overall best weight: 3.9996 ------------------------------------------------------------------------------- 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 E 250 GLN E 262 GLN F 262 GLN H 262 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 M 155 ASN N 54 GLN N 133 ASN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 262 GLN P 255 GLN ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN T 150 ASN ** U 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 124 GLN V 150 ASN V 247 GLN W 250 GLN X 255 GLN Y 29 GLN ** Z 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 150 ASN Z 230 ASN Z 265 GLN a 19 ASN a 150 ASN a 262 GLN b 17 ASN ** b 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 265 GLN d 6 ASN d 122 GLN d 133 ASN ** f 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 3 ASN h 262 GLN i 250 GLN i 251 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 72816 Z= 0.355 Angle : 0.585 13.748 98753 Z= 0.322 Chirality : 0.041 0.223 12802 Planarity : 0.004 0.104 12617 Dihedral : 4.131 20.233 10064 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.08 % Allowed : 12.05 % Favored : 85.87 % 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: 3.60 (0.08), residues: 9916 helix: 3.34 (0.06), residues: 7474 sheet: -2.33 (0.19), residues: 444 loop : -0.46 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP U 48 HIS 0.006 0.002 HIS f 213 PHE 0.023 0.003 PHE R 109 ARG 0.008 0.001 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 982 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 816 time to evaluate : 6.414 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8217 (m-30) cc_final: 0.7990 (m-30) REVERT: A 151 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7914 (pp20) REVERT: D 252 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8388 (mp) REVERT: E 106 THR cc_start: 0.7144 (p) cc_final: 0.6914 (m) REVERT: F 86 THR cc_start: 0.8323 (m) cc_final: 0.7927 (p) REVERT: G 24 GLU cc_start: 0.8212 (tt0) cc_final: 0.7755 (mm-30) REVERT: G 151 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7719 (pp20) REVERT: G 255 GLN cc_start: 0.8113 (tt0) cc_final: 0.7898 (mt0) REVERT: H 2 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6076 (tm) REVERT: K 86 THR cc_start: 0.8434 (m) cc_final: 0.8093 (p) REVERT: L 101 ASP cc_start: 0.5919 (p0) cc_final: 0.5355 (p0) REVERT: L 128 THR cc_start: 0.8188 (m) cc_final: 0.7902 (m) REVERT: L 232 VAL cc_start: 0.8578 (OUTLIER) cc_final: 0.8366 (p) REVERT: M 24 GLU cc_start: 0.8215 (tp30) cc_final: 0.7921 (mp0) REVERT: M 76 ASP cc_start: 0.8413 (m-30) cc_final: 0.8205 (m-30) REVERT: O 251 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8163 (mt0) REVERT: P 5 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7534 (pp) REVERT: P 31 ARG cc_start: 0.8160 (ttm110) cc_final: 0.7866 (ttp-110) REVERT: P 86 THR cc_start: 0.8317 (m) cc_final: 0.7917 (p) REVERT: P 122 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7190 (tm-30) REVERT: Q 94 GLU cc_start: 0.7810 (tp30) cc_final: 0.7260 (mp0) REVERT: Q 122 GLN cc_start: 0.8329 (mt0) cc_final: 0.7411 (mm-40) REVERT: R 235 ASP cc_start: 0.7720 (p0) cc_final: 0.7377 (p0) REVERT: R 242 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7920 (ttpp) REVERT: R 252 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7633 (tm) REVERT: S 20 SER cc_start: 0.8719 (t) cc_final: 0.8515 (m) REVERT: S 24 GLU cc_start: 0.7967 (tp30) cc_final: 0.7733 (tp30) REVERT: S 75 ILE cc_start: 0.8796 (mt) cc_final: 0.8551 (tt) REVERT: S 122 GLN cc_start: 0.8023 (mt0) cc_final: 0.7418 (tp-100) REVERT: T 122 GLN cc_start: 0.8357 (mt0) cc_final: 0.7396 (tp40) REVERT: V 231 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8316 (mp) REVERT: X 37 LYS cc_start: 0.8761 (ttmt) cc_final: 0.8177 (tmtt) REVERT: X 122 GLN cc_start: 0.7972 (tp40) cc_final: 0.7636 (tp-100) REVERT: X 231 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8435 (mp) REVERT: X 242 LYS cc_start: 0.8154 (ttmt) cc_final: 0.7668 (tptm) REVERT: Y 117 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: Y 210 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8528 (tt) REVERT: a 87 ASP cc_start: 0.8495 (t0) cc_final: 0.8133 (m-30) REVERT: a 117 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.7725 (mm-30) REVERT: a 265 GLN cc_start: 0.8113 (mt0) cc_final: 0.7860 (mp10) REVERT: b 177 THR cc_start: 0.7682 (m) cc_final: 0.7284 (p) REVERT: c 115 ASP cc_start: 0.7410 (m-30) cc_final: 0.6956 (t0) REVERT: c 133 ASN cc_start: 0.8798 (t0) cc_final: 0.8413 (t0) REVERT: c 151 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7709 (pp20) REVERT: c 262 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7636 (mm110) REVERT: d 40 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.8113 (p0) REVERT: d 42 LYS cc_start: 0.6506 (tptt) cc_final: 0.5686 (mtmt) REVERT: d 262 GLN cc_start: 0.8193 (tm-30) cc_final: 0.7613 (tt0) REVERT: e 24 GLU cc_start: 0.8736 (tp30) cc_final: 0.8497 (tp30) REVERT: e 66 ASP cc_start: 0.7936 (m-30) cc_final: 0.7519 (m-30) REVERT: f 151 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.7844 (pp20) REVERT: f 267 ILE cc_start: 0.8986 (tp) cc_final: 0.8714 (tp) REVERT: h 42 LYS cc_start: 0.6305 (tptt) cc_final: 0.5542 (mtmm) REVERT: h 265 GLN cc_start: 0.6846 (OUTLIER) cc_final: 0.6552 (mm-40) REVERT: i 92 MET cc_start: 0.8412 (mtp) cc_final: 0.8208 (mtp) REVERT: i 94 GLU cc_start: 0.7346 (mm-30) cc_final: 0.6972 (mm-30) REVERT: i 123 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8859 (tt) REVERT: j 83 ASP cc_start: 0.8293 (m-30) cc_final: 0.7910 (m-30) REVERT: k 76 ASP cc_start: 0.7981 (m-30) cc_final: 0.7731 (m-30) REVERT: k 242 LYS cc_start: 0.8361 (mtpt) cc_final: 0.8019 (mttm) outliers start: 166 outliers final: 101 residues processed: 922 average time/residue: 1.3896 time to fit residues: 1741.2443 Evaluate side-chains 918 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 797 time to evaluate : 6.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 222 ASP 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 252 LEU 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 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 128 THR Chi-restraints excluded: chain H residue 250 GLN 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 95 LYS Chi-restraints excluded: chain L residue 166 THR 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 133 ASN 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 O residue 245 SER Chi-restraints excluded: chain O residue 251 GLN 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 118 SER Chi-restraints excluded: chain Q residue 252 LEU Chi-restraints excluded: chain R residue 154 SER 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 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 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 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 24 GLU Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 244 GLN Chi-restraints excluded: chain X residue 40 ASN 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 215 THR Chi-restraints excluded: chain Y residue 263 THR Chi-restraints excluded: chain Z residue 84 THR Chi-restraints excluded: chain Z residue 91 LYS Chi-restraints excluded: chain a residue 24 GLU Chi-restraints excluded: chain a residue 84 THR Chi-restraints excluded: chain a residue 117 GLU Chi-restraints excluded: chain a residue 210 LEU Chi-restraints excluded: chain b residue 2 LEU Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 168 ILE 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 268 LEU Chi-restraints excluded: chain h residue 128 THR 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 629 optimal weight: 2.9990 chunk 844 optimal weight: 2.9990 chunk 242 optimal weight: 0.9990 chunk 730 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 793 optimal weight: 7.9990 chunk 332 optimal weight: 8.9990 chunk 815 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 133 ASN C 250 GLN C 255 GLN E 250 GLN H 262 GLN I 44 ASN I 255 GLN L 3 ASN 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** R 54 GLN T 150 ASN ** U 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 150 ASN V 261 ASN W 250 GLN X 40 ASN X 255 GLN ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 150 ASN Z 230 ASN Z 265 GLN a 150 ASN a 262 GLN b 265 GLN c 265 GLN d 122 GLN d 133 ASN f 8 ASN ** h 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 262 GLN ** i 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 250 GLN i 251 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.121826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.107607 restraints weight = 99070.119| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.42 r_work: 0.3341 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1996 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= 0.169 Angle : 0.456 12.024 98753 Z= 0.257 Chirality : 0.034 0.200 12802 Planarity : 0.003 0.084 12617 Dihedral : 3.808 17.636 10064 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 1.70 % Allowed : 12.70 % Favored : 85.60 % 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: 3.77 (0.06), residues: 7474 sheet: -2.16 (0.19), residues: 444 loop : -0.39 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 48 HIS 0.004 0.001 HIS f 213 PHE 0.023 0.001 PHE R 109 ARG 0.007 0.000 ARG d 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26969.17 seconds wall clock time: 463 minutes 8.36 seconds (27788.36 seconds total)