Starting phenix.real_space_refine on Mon Oct 14 18:33:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxk_42767/10_2024/8uxk_42767.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxk_42767/10_2024/8uxk_42767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxk_42767/10_2024/8uxk_42767.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxk_42767/10_2024/8uxk_42767.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxk_42767/10_2024/8uxk_42767.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxk_42767/10_2024/8uxk_42767.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 148 5.16 5 C 44511 2.51 5 N 12432 2.21 5 O 15281 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 72372 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "B" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "C" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "D" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "E" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "F" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "G" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "H" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "I" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "J" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "K" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "L" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "M" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "N" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "O" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "P" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "Q" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "R" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "S" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "T" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "U" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "V" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "W" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "X" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "Y" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "Z" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "a" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "b" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "c" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "d" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "e" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "f" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "g" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "h" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "i" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "j" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Chain: "k" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1956 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 2, 'TRANS': 267} Time building chain proxies: 30.34, per 1000 atoms: 0.42 Number of scatterers: 72372 At special positions: 0 Unit cell: (138.444, 135.942, 331.098, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 148 16.00 O 15281 8.00 N 12432 7.00 C 44511 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.90 Conformation dependent library (CDL) restraints added in 7.5 seconds 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18722 Finding SS restraints... Secondary structure from input PDB file: 276 helices and 38 sheets defined 77.3% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.37 Creating SS restraints... Processing helix chain 'A' and resid 8 through 35 removed outlier: 3.934A pdb=" N LEU A 12 " --> pdb=" O ASN A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 101 removed outlier: 3.796A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASN A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N SER A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 129 Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.626A pdb=" N GLY A 169 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 233 removed outlier: 4.083A pdb=" N ALA A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 263 removed outlier: 3.763A pdb=" N GLU A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 271 removed outlier: 3.513A pdb=" N LEU A 268 " --> pdb=" O GLN A 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 35 removed outlier: 3.629A pdb=" N LEU B 12 " --> pdb=" O ASN B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 100 removed outlier: 4.456A pdb=" N ASN B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N SER B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 129 removed outlier: 3.502A pdb=" N LYS B 125 " --> pdb=" O ASP B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 169 removed outlier: 3.571A pdb=" N GLY B 169 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 233 removed outlier: 4.031A pdb=" N ALA B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 263 removed outlier: 3.864A pdb=" N GLU B 239 " --> pdb=" O ASP B 235 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLN B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 271 Processing helix chain 'C' and resid 8 through 35 removed outlier: 3.546A pdb=" N LEU C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 60 Processing helix chain 'C' and resid 60 through 101 removed outlier: 4.073A pdb=" N VAL C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 129 Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.647A pdb=" N GLY C 169 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 233 removed outlier: 4.085A pdb=" N ALA C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 262 removed outlier: 3.500A pdb=" N GLU C 239 " --> pdb=" O ASP C 235 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 241 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLN C 244 " --> pdb=" O SER C 240 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 271 Processing helix chain 'D' and resid 8 through 35 removed outlier: 3.863A pdb=" N LEU D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 100 removed outlier: 3.749A pdb=" N LEU D 61 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASN D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N SER D 63 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 129 Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.195A pdb=" N GLY D 134 " --> pdb=" O LYS D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 169 removed outlier: 3.640A pdb=" N GLY D 169 " --> pdb=" O THR D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 233 removed outlier: 4.148A pdb=" N ALA D 187 " --> pdb=" O LYS D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 262 removed outlier: 3.744A pdb=" N GLU D 239 " --> pdb=" O ASP D 235 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA D 241 " --> pdb=" O ALA D 237 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN D 262 " --> pdb=" O SER D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 271 removed outlier: 3.520A pdb=" N THR D 266 " --> pdb=" O THR D 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 35 Processing helix chain 'E' and resid 44 through 60 Processing helix chain 'E' and resid 60 through 101 removed outlier: 4.109A pdb=" N VAL E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP E 87 " --> pdb=" O ASP E 83 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP E 101 " --> pdb=" O LEU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 129 Processing helix chain 'E' and resid 164 through 169 removed outlier: 3.595A pdb=" N GLY E 169 " --> pdb=" O THR E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 233 removed outlier: 3.836A pdb=" N ALA E 187 " --> pdb=" O LYS E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 263 removed outlier: 3.588A pdb=" N ALA E 241 " --> pdb=" O ALA E 237 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLN E 244 " --> pdb=" O SER E 240 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN E 262 " --> pdb=" O SER E 258 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR E 263 " --> pdb=" O ILE E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 271 removed outlier: 4.094A pdb=" N LEU E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE E 271 " --> pdb=" O ILE E 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 266 through 271' Processing helix chain 'F' and resid 8 through 35 Processing helix chain 'F' and resid 44 through 60 Processing helix chain 'F' and resid 60 through 101 removed outlier: 4.091A pdb=" N VAL F 64 " --> pdb=" O SER F 60 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR F 84 " --> pdb=" O ALA F 80 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP F 87 " --> pdb=" O ASP F 83 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP F 101 " --> pdb=" O LEU F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 129 Processing helix chain 'F' and resid 164 through 169 removed outlier: 3.573A pdb=" N GLY F 169 " --> pdb=" O THR F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 233 removed outlier: 4.038A pdb=" N THR F 184 " --> pdb=" O ALA F 180 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA F 187 " --> pdb=" O LYS F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 263 removed outlier: 3.843A pdb=" N GLN F 244 " --> pdb=" O SER F 240 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN F 262 " --> pdb=" O SER F 258 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR F 263 " --> pdb=" O ILE F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 271 Processing helix chain 'G' and resid 8 through 35 Processing helix chain 'G' and resid 44 through 60 Processing helix chain 'G' and resid 60 through 100 removed outlier: 3.970A pdb=" N VAL G 64 " --> pdb=" O SER G 60 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR G 84 " --> pdb=" O ALA G 80 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP G 87 " --> pdb=" O ASP G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 129 Processing helix chain 'G' and resid 164 through 169 removed outlier: 3.552A pdb=" N GLY G 169 " --> pdb=" O THR G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 233 removed outlier: 3.976A pdb=" N THR G 184 " --> pdb=" O ALA G 180 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA G 187 " --> pdb=" O LYS G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 262 removed outlier: 3.639A pdb=" N ALA G 241 " --> pdb=" O ALA G 237 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN G 244 " --> pdb=" O SER G 240 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN G 262 " --> pdb=" O SER G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 265 No H-bonds generated for 'chain 'G' and resid 263 through 265' Processing helix chain 'G' and resid 266 through 271 removed outlier: 3.902A pdb=" N LEU G 270 " --> pdb=" O THR G 266 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE G 271 " --> pdb=" O ILE G 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 266 through 271' Processing helix chain 'H' and resid 8 through 35 Processing helix chain 'H' and resid 44 through 101 removed outlier: 3.595A pdb=" N TRP H 48 " --> pdb=" O ASN H 44 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU H 61 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER H 63 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL H 64 " --> pdb=" O SER H 60 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR H 84 " --> pdb=" O ALA H 80 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP H 101 " --> pdb=" O LEU H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 129 Processing helix chain 'H' and resid 178 through 233 removed outlier: 3.988A pdb=" N THR H 184 " --> pdb=" O ALA H 180 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA H 187 " --> pdb=" O LYS H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 262 removed outlier: 3.857A pdb=" N ALA H 241 " --> pdb=" O ALA H 237 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN H 244 " --> pdb=" O SER H 240 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN H 262 " --> pdb=" O SER H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 271 removed outlier: 3.815A pdb=" N SER H 269 " --> pdb=" O GLN H 265 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU H 270 " --> pdb=" O THR H 266 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE H 271 " --> pdb=" O ILE H 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 265 through 271' Processing helix chain 'I' and resid 8 through 35 Processing helix chain 'I' and resid 44 through 60 Processing helix chain 'I' and resid 60 through 100 removed outlier: 4.208A pdb=" N VAL I 64 " --> pdb=" O SER I 60 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR I 84 " --> pdb=" O ALA I 80 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP I 87 " --> pdb=" O ASP I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 129 Processing helix chain 'I' and resid 164 through 169 removed outlier: 3.644A pdb=" N GLY I 169 " --> pdb=" O THR I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 233 removed outlier: 3.796A pdb=" N ALA I 187 " --> pdb=" O LYS I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 235 through 263 removed outlier: 3.756A pdb=" N ALA I 241 " --> pdb=" O ALA I 237 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR I 248 " --> pdb=" O GLN I 244 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN I 262 " --> pdb=" O SER I 258 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR I 263 " --> pdb=" O ILE I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 271 removed outlier: 3.575A pdb=" N LEU I 268 " --> pdb=" O GLN I 265 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 35 removed outlier: 3.538A pdb=" N LEU J 12 " --> pdb=" O ASN J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 60 Processing helix chain 'J' and resid 60 through 100 removed outlier: 4.043A pdb=" N VAL J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR J 84 " --> pdb=" O ALA J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 129 Processing helix chain 'J' and resid 164 through 168 Processing helix chain 'J' and resid 178 through 233 removed outlier: 3.910A pdb=" N ALA J 187 " --> pdb=" O LYS J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 235 through 261 removed outlier: 4.035A pdb=" N ALA J 241 " --> pdb=" O ALA J 237 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR J 248 " --> pdb=" O GLN J 244 " (cutoff:3.500A) Processing helix chain 'J' and resid 262 through 271 Processing helix chain 'K' and resid 8 through 35 removed outlier: 3.961A pdb=" N LEU K 12 " --> pdb=" O ASN K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 100 removed outlier: 3.887A pdb=" N LEU K 61 " --> pdb=" O THR K 57 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN K 62 " --> pdb=" O ALA K 58 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER K 63 " --> pdb=" O SER K 59 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL K 64 " --> pdb=" O SER K 60 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR K 84 " --> pdb=" O ALA K 80 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP K 87 " --> pdb=" O ASP K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 129 Processing helix chain 'K' and resid 164 through 169 Processing helix chain 'K' and resid 178 through 233 removed outlier: 3.832A pdb=" N ALA K 187 " --> pdb=" O LYS K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 235 through 262 removed outlier: 3.831A pdb=" N ALA K 241 " --> pdb=" O ALA K 237 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR K 248 " --> pdb=" O GLN K 244 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN K 262 " --> pdb=" O SER K 258 " (cutoff:3.500A) Processing helix chain 'K' and resid 263 through 271 removed outlier: 3.625A pdb=" N THR K 266 " --> pdb=" O THR K 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 35 removed outlier: 3.739A pdb=" N LEU L 12 " --> pdb=" O ASN L 8 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 60 Processing helix chain 'L' and resid 60 through 100 removed outlier: 3.870A pdb=" N VAL L 64 " --> pdb=" O SER L 60 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR L 84 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 130 removed outlier: 3.882A pdb=" N ALA L 130 " --> pdb=" O ALA L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 168 Processing helix chain 'L' and resid 178 through 233 removed outlier: 3.825A pdb=" N ALA L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 235 through 263 removed outlier: 4.122A pdb=" N ALA L 241 " --> pdb=" O ALA L 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 271 removed outlier: 3.660A pdb=" N LEU L 270 " --> pdb=" O ILE L 267 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 35 removed outlier: 3.817A pdb=" N LEU M 12 " --> pdb=" O ASN M 8 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 100 removed outlier: 3.640A pdb=" N LEU M 61 " --> pdb=" O THR M 57 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN M 62 " --> pdb=" O ALA M 58 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N SER M 63 " --> pdb=" O SER M 59 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL M 64 " --> pdb=" O SER M 60 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR M 84 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 129 Processing helix chain 'M' and resid 164 through 169 removed outlier: 4.114A pdb=" N GLY M 169 " --> pdb=" O THR M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 178 through 233 removed outlier: 3.914A pdb=" N ALA M 187 " --> pdb=" O LYS M 183 " (cutoff:3.500A) Processing helix chain 'M' and resid 235 through 263 removed outlier: 4.074A pdb=" N ALA M 241 " --> pdb=" O ALA M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 271 Processing helix chain 'N' and resid 8 through 35 removed outlier: 3.673A pdb=" N LEU N 12 " --> pdb=" O ASN N 8 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 100 removed outlier: 3.939A pdb=" N LEU N 61 " --> pdb=" O THR N 57 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ASN N 62 " --> pdb=" O ALA N 58 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N SER N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL N 64 " --> pdb=" O SER N 60 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR N 84 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 130 removed outlier: 3.625A pdb=" N ALA N 130 " --> pdb=" O ALA N 126 " (cutoff:3.500A) Processing helix chain 'N' and resid 164 through 169 removed outlier: 3.987A pdb=" N GLY N 169 " --> pdb=" O THR N 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 178 through 233 removed outlier: 3.756A pdb=" N ALA N 187 " --> pdb=" O LYS N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 235 through 263 removed outlier: 4.052A pdb=" N ALA N 241 " --> pdb=" O ALA N 237 " (cutoff:3.500A) Processing helix chain 'N' and resid 264 through 271 removed outlier: 3.650A pdb=" N ILE N 267 " --> pdb=" O PRO N 264 " (cutoff:3.500A) Processing helix chain 'O' and resid 8 through 35 removed outlier: 3.638A pdb=" N LEU O 12 " --> pdb=" O ASN O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 100 removed outlier: 4.273A pdb=" N ASN O 62 " --> pdb=" O ALA O 58 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER O 63 " --> pdb=" O SER O 59 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL O 64 " --> pdb=" O SER O 60 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR O 84 " --> pdb=" O ALA O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 129 Processing helix chain 'O' and resid 165 through 169 removed outlier: 3.712A pdb=" N GLY O 169 " --> pdb=" O THR O 166 " (cutoff:3.500A) Processing helix chain 'O' and resid 178 through 233 removed outlier: 3.793A pdb=" N ALA O 187 " --> pdb=" O LYS O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 235 through 262 removed outlier: 4.071A pdb=" N ALA O 241 " --> pdb=" O ALA O 237 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN O 262 " --> pdb=" O SER O 258 " (cutoff:3.500A) Processing helix chain 'O' and resid 263 through 271 Processing helix chain 'P' and resid 9 through 35 Processing helix chain 'P' and resid 44 through 60 Processing helix chain 'P' and resid 60 through 100 removed outlier: 3.958A pdb=" N VAL P 64 " --> pdb=" O SER P 60 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR P 84 " --> pdb=" O ALA P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 130 removed outlier: 3.594A pdb=" N ASN P 129 " --> pdb=" O LYS P 125 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA P 130 " --> pdb=" O ALA P 126 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 169 removed outlier: 3.915A pdb=" N GLY P 169 " --> pdb=" O THR P 166 " (cutoff:3.500A) Processing helix chain 'P' and resid 178 through 233 removed outlier: 3.799A pdb=" N ALA P 187 " --> pdb=" O LYS P 183 " (cutoff:3.500A) Processing helix chain 'P' and resid 235 through 262 removed outlier: 3.927A pdb=" N ALA P 241 " --> pdb=" O ALA P 237 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN P 262 " --> pdb=" O SER P 258 " (cutoff:3.500A) Processing helix chain 'P' and resid 263 through 271 removed outlier: 3.511A pdb=" N ILE P 267 " --> pdb=" O PRO P 264 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 35 removed outlier: 3.734A pdb=" N LEU Q 12 " --> pdb=" O ASN Q 8 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 100 removed outlier: 3.827A pdb=" N LEU Q 61 " --> pdb=" O THR Q 57 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN Q 62 " --> pdb=" O ALA Q 58 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER Q 63 " --> pdb=" O SER Q 59 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR Q 84 " --> pdb=" O ALA Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 130 removed outlier: 3.799A pdb=" N ALA Q 130 " --> pdb=" O ALA Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 169 removed outlier: 3.984A pdb=" N GLY Q 169 " --> pdb=" O THR Q 166 " (cutoff:3.500A) Processing helix chain 'Q' and resid 178 through 233 removed outlier: 3.701A pdb=" N ALA Q 187 " --> pdb=" O LYS Q 183 " (cutoff:3.500A) Processing helix chain 'Q' and resid 235 through 262 removed outlier: 3.721A pdb=" N GLN Q 262 " --> pdb=" O SER Q 258 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 271 Processing helix chain 'R' and resid 8 through 35 removed outlier: 3.871A pdb=" N LEU R 12 " --> pdb=" O ASN R 8 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU R 24 " --> pdb=" O SER R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 101 removed outlier: 3.776A pdb=" N LEU R 61 " --> pdb=" O THR R 57 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASN R 62 " --> pdb=" O ALA R 58 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N SER R 63 " --> pdb=" O SER R 59 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL R 64 " --> pdb=" O SER R 60 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR R 84 " --> pdb=" O ALA R 80 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP R 101 " --> pdb=" O LEU R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 129 Processing helix chain 'R' and resid 164 through 169 removed outlier: 3.978A pdb=" N GLY R 169 " --> pdb=" O THR R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 233 removed outlier: 3.934A pdb=" N ALA R 187 " --> pdb=" O LYS R 183 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU R 231 " --> pdb=" O GLY R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 235 through 263 removed outlier: 3.652A pdb=" N GLU R 239 " --> pdb=" O ASP R 235 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 271 Processing helix chain 'S' and resid 8 through 35 removed outlier: 3.861A pdb=" N LEU S 12 " --> pdb=" O ASN S 8 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 60 Processing helix chain 'S' and resid 60 through 100 removed outlier: 3.925A pdb=" N VAL S 64 " --> pdb=" O SER S 60 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR S 84 " --> pdb=" O ALA S 80 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP S 87 " --> pdb=" O ASP S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 105 through 130 removed outlier: 3.638A pdb=" N ALA S 130 " --> pdb=" O ALA S 126 " (cutoff:3.500A) Processing helix chain 'S' and resid 178 through 233 removed outlier: 3.931A pdb=" N ALA S 187 " --> pdb=" O LYS S 183 " (cutoff:3.500A) Processing helix chain 'S' and resid 235 through 263 Processing helix chain 'S' and resid 264 through 271 removed outlier: 3.913A pdb=" N PHE S 271 " --> pdb=" O LEU S 268 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 35 removed outlier: 4.118A pdb=" N LEU T 12 " --> pdb=" O ASN T 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 60 Processing helix chain 'T' and resid 60 through 101 removed outlier: 3.818A pdb=" N VAL T 64 " --> pdb=" O SER T 60 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR T 84 " --> pdb=" O ALA T 80 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP T 87 " --> pdb=" O ASP T 83 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP T 101 " --> pdb=" O LEU T 97 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 130 removed outlier: 3.617A pdb=" N ALA T 130 " --> pdb=" O ALA T 126 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 169 removed outlier: 3.649A pdb=" N GLY T 169 " --> pdb=" O THR T 166 " (cutoff:3.500A) Processing helix chain 'T' and resid 178 through 233 removed outlier: 3.873A pdb=" N ALA T 187 " --> pdb=" O LYS T 183 " (cutoff:3.500A) Processing helix chain 'T' and resid 235 through 263 Processing helix chain 'T' and resid 266 through 271 removed outlier: 3.807A pdb=" N LEU T 270 " --> pdb=" O THR T 266 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE T 271 " --> pdb=" O ILE T 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 266 through 271' Processing helix chain 'U' and resid 9 through 35 Processing helix chain 'U' and resid 44 through 60 removed outlier: 3.920A pdb=" N SER U 60 " --> pdb=" O ALA U 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 60 through 100 removed outlier: 4.203A pdb=" N THR U 84 " --> pdb=" O ALA U 80 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP U 87 " --> pdb=" O ASP U 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 105 through 129 removed outlier: 3.526A pdb=" N ASN U 129 " --> pdb=" O LYS U 125 " (cutoff:3.500A) Processing helix chain 'U' and resid 164 through 169 removed outlier: 3.777A pdb=" N GLY U 169 " --> pdb=" O THR U 166 " (cutoff:3.500A) Processing helix chain 'U' and resid 178 through 233 removed outlier: 3.956A pdb=" N ALA U 187 " --> pdb=" O LYS U 183 " (cutoff:3.500A) Processing helix chain 'U' and resid 235 through 263 Processing helix chain 'U' and resid 264 through 271 removed outlier: 3.710A pdb=" N PHE U 271 " --> pdb=" O LEU U 268 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 34 removed outlier: 3.672A pdb=" N LEU V 12 " --> pdb=" O ASN V 8 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU V 24 " --> pdb=" O SER V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 60 Processing helix chain 'V' and resid 60 through 100 removed outlier: 3.951A pdb=" N VAL V 64 " --> pdb=" O SER V 60 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR V 84 " --> pdb=" O ALA V 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 105 through 130 removed outlier: 3.548A pdb=" N ASN V 129 " --> pdb=" O LYS V 125 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA V 130 " --> pdb=" O ALA V 126 " (cutoff:3.500A) Processing helix chain 'V' and resid 178 through 233 removed outlier: 4.030A pdb=" N ALA V 187 " --> pdb=" O LYS V 183 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN V 198 " --> pdb=" O GLN V 194 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP V 222 " --> pdb=" O GLY V 218 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU V 231 " --> pdb=" O GLY V 227 " (cutoff:3.500A) Processing helix chain 'V' and resid 235 through 263 removed outlier: 3.829A pdb=" N GLN V 251 " --> pdb=" O GLN V 247 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU V 252 " --> pdb=" O THR V 248 " (cutoff:3.500A) Processing helix chain 'V' and resid 264 through 271 Processing helix chain 'W' and resid 8 through 35 removed outlier: 3.606A pdb=" N LEU W 12 " --> pdb=" O ASN W 8 " (cutoff:3.500A) Processing helix chain 'W' and resid 44 through 60 Processing helix chain 'W' and resid 60 through 100 removed outlier: 3.935A pdb=" N VAL W 64 " --> pdb=" O SER W 60 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR W 84 " --> pdb=" O ALA W 80 " (cutoff:3.500A) Processing helix chain 'W' and resid 105 through 129 removed outlier: 3.559A pdb=" N ASN W 129 " --> pdb=" O LYS W 125 " (cutoff:3.500A) Processing helix chain 'W' and resid 164 through 169 removed outlier: 3.799A pdb=" N GLY W 169 " --> pdb=" O THR W 166 " (cutoff:3.500A) Processing helix chain 'W' and resid 178 through 233 removed outlier: 3.988A pdb=" N ALA W 187 " --> pdb=" O LYS W 183 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP W 222 " --> pdb=" O GLY W 218 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU W 231 " --> pdb=" O GLY W 227 " (cutoff:3.500A) Processing helix chain 'W' and resid 235 through 263 removed outlier: 3.790A pdb=" N GLN W 251 " --> pdb=" O GLN W 247 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU W 252 " --> pdb=" O THR W 248 " (cutoff:3.500A) Processing helix chain 'W' and resid 264 through 271 removed outlier: 3.889A pdb=" N LEU W 268 " --> pdb=" O GLN W 265 " (cutoff:3.500A) Processing helix chain 'X' and resid 8 through 35 removed outlier: 3.884A pdb=" N LEU X 12 " --> pdb=" O ASN X 8 " (cutoff:3.500A) Processing helix chain 'X' and resid 44 through 60 Processing helix chain 'X' and resid 60 through 100 removed outlier: 3.993A pdb=" N VAL X 64 " --> pdb=" O SER X 60 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR X 84 " --> pdb=" O ALA X 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 130 removed outlier: 3.648A pdb=" N ALA X 130 " --> pdb=" O ALA X 126 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 169 removed outlier: 3.843A pdb=" N GLY X 169 " --> pdb=" O THR X 166 " (cutoff:3.500A) Processing helix chain 'X' and resid 178 through 233 removed outlier: 3.869A pdb=" N ALA X 187 " --> pdb=" O LYS X 183 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN X 198 " --> pdb=" O GLN X 194 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP X 222 " --> pdb=" O GLY X 218 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU X 231 " --> pdb=" O GLY X 227 " (cutoff:3.500A) Processing helix chain 'X' and resid 235 through 263 removed outlier: 3.630A pdb=" N GLN X 251 " --> pdb=" O GLN X 247 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU X 252 " --> pdb=" O THR X 248 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 271 removed outlier: 3.629A pdb=" N LEU X 268 " --> pdb=" O GLN X 265 " (cutoff:3.500A) Processing helix chain 'Y' and resid 8 through 35 removed outlier: 3.770A pdb=" N LEU Y 12 " --> pdb=" O ASN Y 8 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 60 removed outlier: 3.778A pdb=" N TRP Y 48 " --> pdb=" O ASN Y 44 " (cutoff:3.500A) Processing helix chain 'Y' and resid 60 through 100 removed outlier: 4.125A pdb=" N VAL Y 64 " --> pdb=" O SER Y 60 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR Y 84 " --> pdb=" O ALA Y 80 " (cutoff:3.500A) Processing helix chain 'Y' and resid 105 through 130 removed outlier: 3.515A pdb=" N ALA Y 130 " --> pdb=" O ALA Y 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 164 through 168 Processing helix chain 'Y' and resid 178 through 233 removed outlier: 4.298A pdb=" N ALA Y 187 " --> pdb=" O LYS Y 183 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR Y 188 " --> pdb=" O THR Y 184 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP Y 222 " --> pdb=" O GLY Y 218 " (cutoff:3.500A) Processing helix chain 'Y' and resid 235 through 263 removed outlier: 3.964A pdb=" N ALA Y 241 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS Y 242 " --> pdb=" O LYS Y 238 " (cutoff:3.500A) Processing helix chain 'Y' and resid 264 through 271 removed outlier: 3.874A pdb=" N ILE Y 267 " --> pdb=" O PRO Y 264 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU Y 268 " --> pdb=" O GLN Y 265 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE Y 271 " --> pdb=" O LEU Y 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 8 through 35 removed outlier: 3.505A pdb=" N LEU Z 12 " --> pdb=" O ASN Z 8 " (cutoff:3.500A) Processing helix chain 'Z' and resid 44 through 100 removed outlier: 4.297A pdb=" N ASN Z 62 " --> pdb=" O ALA Z 58 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER Z 63 " --> pdb=" O SER Z 59 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL Z 64 " --> pdb=" O SER Z 60 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA Z 78 " --> pdb=" O THR Z 74 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR Z 84 " --> pdb=" O ALA Z 80 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP Z 87 " --> pdb=" O ASP Z 83 " (cutoff:3.500A) Processing helix chain 'Z' and resid 105 through 130 removed outlier: 3.646A pdb=" N ALA Z 130 " --> pdb=" O ALA Z 126 " (cutoff:3.500A) Processing helix chain 'Z' and resid 164 through 169 removed outlier: 3.859A pdb=" N GLY Z 169 " --> pdb=" O THR Z 166 " (cutoff:3.500A) Processing helix chain 'Z' and resid 178 through 233 removed outlier: 4.342A pdb=" N ALA Z 187 " --> pdb=" O LYS Z 183 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR Z 188 " --> pdb=" O THR Z 184 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP Z 222 " --> pdb=" O GLY Z 218 " (cutoff:3.500A) Processing helix chain 'Z' and resid 235 through 263 removed outlier: 3.811A pdb=" N ALA Z 241 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS Z 242 " --> pdb=" O LYS Z 238 " (cutoff:3.500A) Processing helix chain 'Z' and resid 264 through 271 removed outlier: 3.725A pdb=" N PHE Z 271 " --> pdb=" O LEU Z 268 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 35 removed outlier: 3.639A pdb=" N LEU a 12 " --> pdb=" O ASN a 8 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 99 removed outlier: 4.068A pdb=" N ASN a 62 " --> pdb=" O ALA a 58 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER a 63 " --> pdb=" O SER a 59 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL a 64 " --> pdb=" O SER a 60 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR a 84 " --> pdb=" O ALA a 80 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP a 87 " --> pdb=" O ASP a 83 " (cutoff:3.500A) Processing helix chain 'a' and resid 105 through 130 removed outlier: 3.504A pdb=" N GLN a 124 " --> pdb=" O ARG a 120 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN a 129 " --> pdb=" O LYS a 125 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA a 130 " --> pdb=" O ALA a 126 " (cutoff:3.500A) Processing helix chain 'a' and resid 178 through 233 removed outlier: 4.100A pdb=" N ALA a 187 " --> pdb=" O LYS a 183 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR a 188 " --> pdb=" O THR a 184 " (cutoff:3.500A) Processing helix chain 'a' and resid 235 through 263 removed outlier: 3.698A pdb=" N GLU a 239 " --> pdb=" O ASP a 235 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA a 241 " --> pdb=" O ALA a 237 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLN a 251 " --> pdb=" O GLN a 247 " (cutoff:3.500A) Processing helix chain 'a' and resid 264 through 271 removed outlier: 3.508A pdb=" N PHE a 271 " --> pdb=" O LEU a 268 " (cutoff:3.500A) Processing helix chain 'b' and resid 8 through 35 removed outlier: 4.031A pdb=" N LEU b 12 " --> pdb=" O ASN b 8 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 60 removed outlier: 3.744A pdb=" N SER b 60 " --> pdb=" O ALA b 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 60 through 100 removed outlier: 3.894A pdb=" N VAL b 64 " --> pdb=" O SER b 60 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL b 77 " --> pdb=" O SER b 73 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA b 78 " --> pdb=" O THR b 74 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP b 87 " --> pdb=" O ASP b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 105 through 129 Processing helix chain 'b' and resid 178 through 233 removed outlier: 3.811A pdb=" N ILE b 186 " --> pdb=" O ALA b 182 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA b 187 " --> pdb=" O LYS b 183 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR b 188 " --> pdb=" O THR b 184 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP b 222 " --> pdb=" O GLY b 218 " (cutoff:3.500A) Processing helix chain 'b' and resid 235 through 263 removed outlier: 4.285A pdb=" N ALA b 241 " --> pdb=" O ALA b 237 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS b 242 " --> pdb=" O LYS b 238 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN b 251 " --> pdb=" O GLN b 247 " (cutoff:3.500A) Processing helix chain 'b' and resid 264 through 271 Processing helix chain 'c' and resid 8 through 35 removed outlier: 3.631A pdb=" N LEU c 12 " --> pdb=" O ASN c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 60 removed outlier: 3.903A pdb=" N SER c 60 " --> pdb=" O ALA c 56 " (cutoff:3.500A) Processing helix chain 'c' and resid 60 through 99 removed outlier: 4.011A pdb=" N VAL c 64 " --> pdb=" O SER c 60 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR c 84 " --> pdb=" O ALA c 80 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP c 87 " --> pdb=" O ASP c 83 " (cutoff:3.500A) Processing helix chain 'c' and resid 105 through 129 removed outlier: 3.645A pdb=" N LYS c 125 " --> pdb=" O ASP c 121 " (cutoff:3.500A) Processing helix chain 'c' and resid 164 through 169 removed outlier: 3.638A pdb=" N GLY c 169 " --> pdb=" O THR c 166 " (cutoff:3.500A) Processing helix chain 'c' and resid 178 through 233 removed outlier: 4.094A pdb=" N ILE c 186 " --> pdb=" O ALA c 182 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA c 187 " --> pdb=" O LYS c 183 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR c 188 " --> pdb=" O THR c 184 " (cutoff:3.500A) Processing helix chain 'c' and resid 235 through 263 removed outlier: 4.308A pdb=" N ALA c 241 " --> pdb=" O ALA c 237 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS c 242 " --> pdb=" O LYS c 238 " (cutoff:3.500A) Processing helix chain 'c' and resid 264 through 271 removed outlier: 3.557A pdb=" N SER c 269 " --> pdb=" O THR c 266 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE c 271 " --> pdb=" O LEU c 268 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 35 removed outlier: 3.647A pdb=" N LEU d 12 " --> pdb=" O ASN d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 60 Processing helix chain 'd' and resid 61 through 99 removed outlier: 3.915A pdb=" N SER d 67 " --> pdb=" O SER d 63 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL d 77 " --> pdb=" O SER d 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA d 78 " --> pdb=" O THR d 74 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR d 84 " --> pdb=" O ALA d 80 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP d 87 " --> pdb=" O ASP d 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 129 removed outlier: 3.674A pdb=" N GLN d 124 " --> pdb=" O ARG d 120 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS d 125 " --> pdb=" O ASP d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 164 through 168 Processing helix chain 'd' and resid 178 through 233 removed outlier: 3.929A pdb=" N ILE d 186 " --> pdb=" O ALA d 182 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ALA d 187 " --> pdb=" O LYS d 183 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR d 188 " --> pdb=" O THR d 184 " (cutoff:3.500A) Processing helix chain 'd' and resid 235 through 263 removed outlier: 3.637A pdb=" N GLU d 239 " --> pdb=" O ASP d 235 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA d 241 " --> pdb=" O ALA d 237 " (cutoff:3.500A) Processing helix chain 'd' and resid 264 through 271 Processing helix chain 'e' and resid 8 through 35 removed outlier: 3.688A pdb=" N LEU e 12 " --> pdb=" O ASN e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 100 removed outlier: 4.589A pdb=" N ASN e 62 " --> pdb=" O ALA e 58 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N SER e 63 " --> pdb=" O SER e 59 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL e 64 " --> pdb=" O SER e 60 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA e 78 " --> pdb=" O THR e 74 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR e 84 " --> pdb=" O ALA e 80 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP e 87 " --> pdb=" O ASP e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 105 through 129 Processing helix chain 'e' and resid 164 through 169 Processing helix chain 'e' and resid 178 through 233 removed outlier: 4.602A pdb=" N ALA e 187 " --> pdb=" O LYS e 183 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR e 188 " --> pdb=" O THR e 184 " (cutoff:3.500A) Processing helix chain 'e' and resid 235 through 266 removed outlier: 4.230A pdb=" N ALA e 241 " --> pdb=" O ALA e 237 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS e 242 " --> pdb=" O LYS e 238 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN e 251 " --> pdb=" O GLN e 247 " (cutoff:3.500A) Proline residue: e 264 - end of helix Processing helix chain 'e' and resid 267 through 271 removed outlier: 3.589A pdb=" N PHE e 271 " --> pdb=" O LEU e 268 " (cutoff:3.500A) Processing helix chain 'f' and resid 8 through 35 removed outlier: 4.011A pdb=" N LEU f 12 " --> pdb=" O ASN f 8 " (cutoff:3.500A) Processing helix chain 'f' and resid 44 through 100 removed outlier: 4.508A pdb=" N ASN f 62 " --> pdb=" O ALA f 58 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N SER f 63 " --> pdb=" O SER f 59 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL f 64 " --> pdb=" O SER f 60 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR f 84 " --> pdb=" O ALA f 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP f 87 " --> pdb=" O ASP f 83 " (cutoff:3.500A) Processing helix chain 'f' and resid 105 through 129 Processing helix chain 'f' and resid 165 through 169 Processing helix chain 'f' and resid 178 through 233 removed outlier: 4.413A pdb=" N ALA f 187 " --> pdb=" O LYS f 183 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR f 188 " --> pdb=" O THR f 184 " (cutoff:3.500A) Processing helix chain 'f' and resid 235 through 263 removed outlier: 3.947A pdb=" N ALA f 241 " --> pdb=" O ALA f 237 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN f 251 " --> pdb=" O GLN f 247 " (cutoff:3.500A) Processing helix chain 'f' and resid 264 through 271 removed outlier: 3.567A pdb=" N PHE f 271 " --> pdb=" O LEU f 268 " (cutoff:3.500A) Processing helix chain 'g' and resid 8 through 35 removed outlier: 3.718A pdb=" N LEU g 12 " --> pdb=" O ASN g 8 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 61 Processing helix chain 'g' and resid 61 through 100 removed outlier: 3.542A pdb=" N SER g 67 " --> pdb=" O SER g 63 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR g 84 " --> pdb=" O ALA g 80 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP g 87 " --> pdb=" O ASP g 83 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER g 100 " --> pdb=" O ALA g 96 " (cutoff:3.500A) Processing helix chain 'g' and resid 105 through 129 Processing helix chain 'g' and resid 164 through 169 removed outlier: 3.520A pdb=" N GLY g 169 " --> pdb=" O THR g 166 " (cutoff:3.500A) Processing helix chain 'g' and resid 178 through 233 removed outlier: 4.292A pdb=" N ALA g 187 " --> pdb=" O LYS g 183 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR g 188 " --> pdb=" O THR g 184 " (cutoff:3.500A) Processing helix chain 'g' and resid 235 through 263 removed outlier: 3.911A pdb=" N ALA g 241 " --> pdb=" O ALA g 237 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN g 251 " --> pdb=" O GLN g 247 " (cutoff:3.500A) Processing helix chain 'g' and resid 264 through 271 Processing helix chain 'h' and resid 8 through 35 removed outlier: 4.021A pdb=" N LEU h 12 " --> pdb=" O ASN h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 44 through 60 removed outlier: 3.701A pdb=" N SER h 60 " --> pdb=" O ALA h 56 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 100 removed outlier: 3.951A pdb=" N THR h 84 " --> pdb=" O ALA h 80 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP h 87 " --> pdb=" O ASP h 83 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER h 100 " --> pdb=" O ALA h 96 " (cutoff:3.500A) Processing helix chain 'h' and resid 105 through 129 Processing helix chain 'h' and resid 164 through 169 removed outlier: 3.944A pdb=" N GLY h 169 " --> pdb=" O THR h 166 " (cutoff:3.500A) Processing helix chain 'h' and resid 178 through 233 removed outlier: 4.331A pdb=" N ALA h 187 " --> pdb=" O LYS h 183 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR h 188 " --> pdb=" O THR h 184 " (cutoff:3.500A) Processing helix chain 'h' and resid 235 through 263 removed outlier: 4.187A pdb=" N ALA h 241 " --> pdb=" O ALA h 237 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS h 242 " --> pdb=" O LYS h 238 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN h 251 " --> pdb=" O GLN h 247 " (cutoff:3.500A) Processing helix chain 'h' and resid 264 through 271 Processing helix chain 'i' and resid 8 through 35 removed outlier: 3.654A pdb=" N LEU i 12 " --> pdb=" O ASN i 8 " (cutoff:3.500A) Processing helix chain 'i' and resid 44 through 60 Processing helix chain 'i' and resid 60 through 101 removed outlier: 4.109A pdb=" N VAL i 64 " --> pdb=" O SER i 60 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR i 84 " --> pdb=" O ALA i 80 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP i 87 " --> pdb=" O ASP i 83 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP i 101 " --> pdb=" O LEU i 97 " (cutoff:3.500A) Processing helix chain 'i' and resid 105 through 129 removed outlier: 3.615A pdb=" N GLN i 124 " --> pdb=" O ARG i 120 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS i 125 " --> pdb=" O ASP i 121 " (cutoff:3.500A) Processing helix chain 'i' and resid 165 through 169 Processing helix chain 'i' and resid 178 through 233 removed outlier: 4.293A pdb=" N ALA i 187 " --> pdb=" O LYS i 183 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR i 188 " --> pdb=" O THR i 184 " (cutoff:3.500A) Processing helix chain 'i' and resid 235 through 263 removed outlier: 3.874A pdb=" N ALA i 241 " --> pdb=" O ALA i 237 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN i 251 " --> pdb=" O GLN i 247 " (cutoff:3.500A) Processing helix chain 'i' and resid 264 through 271 Processing helix chain 'j' and resid 8 through 35 removed outlier: 3.574A pdb=" N LEU j 12 " --> pdb=" O ASN j 8 " (cutoff:3.500A) Processing helix chain 'j' and resid 44 through 100 removed outlier: 4.413A pdb=" N ASN j 62 " --> pdb=" O ALA j 58 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N SER j 63 " --> pdb=" O SER j 59 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL j 64 " --> pdb=" O SER j 60 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR j 84 " --> pdb=" O ALA j 80 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP j 87 " --> pdb=" O ASP j 83 " (cutoff:3.500A) Processing helix chain 'j' and resid 105 through 129 Processing helix chain 'j' and resid 164 through 169 removed outlier: 3.699A pdb=" N GLY j 169 " --> pdb=" O THR j 166 " (cutoff:3.500A) Processing helix chain 'j' and resid 178 through 233 removed outlier: 3.866A pdb=" N ALA j 187 " --> pdb=" O LYS j 183 " (cutoff:3.500A) Processing helix chain 'j' and resid 235 through 263 removed outlier: 4.010A pdb=" N ALA j 241 " --> pdb=" O ALA j 237 " (cutoff:3.500A) Processing helix chain 'j' and resid 264 through 271 Processing helix chain 'k' and resid 8 through 35 Processing helix chain 'k' and resid 44 through 100 removed outlier: 3.778A pdb=" N LEU k 61 " --> pdb=" O THR k 57 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN k 62 " --> pdb=" O ALA k 58 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER k 63 " --> pdb=" O SER k 59 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL k 64 " --> pdb=" O SER k 60 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL k 77 " --> pdb=" O SER k 73 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA k 78 " --> pdb=" O THR k 74 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR k 84 " --> pdb=" O ALA k 80 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP k 87 " --> pdb=" O ASP k 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 105 through 129 Processing helix chain 'k' and resid 178 through 233 removed outlier: 4.084A pdb=" N ALA k 187 " --> pdb=" O LYS k 183 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR k 188 " --> pdb=" O THR k 184 " (cutoff:3.500A) Processing helix chain 'k' and resid 235 through 263 removed outlier: 4.275A pdb=" N ALA k 241 " --> pdb=" O ALA k 237 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS k 242 " --> pdb=" O LYS k 238 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN k 251 " --> pdb=" O GLN k 247 " (cutoff:3.500A) Processing helix chain 'k' and resid 264 through 271 removed outlier: 3.575A pdb=" N ILE k 267 " --> pdb=" O PRO k 264 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER k 269 " --> pdb=" O THR k 266 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE k 271 " --> pdb=" O LEU k 268 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 148 Processing sheet with id=AA2, first strand: chain 'B' and resid 144 through 148 Processing sheet with id=AA3, first strand: chain 'C' and resid 144 through 148 Processing sheet with id=AA4, first strand: chain 'D' and resid 144 through 148 Processing sheet with id=AA5, first strand: chain 'E' and resid 144 through 148 Processing sheet with id=AA6, first strand: chain 'F' and resid 144 through 148 Processing sheet with id=AA7, first strand: chain 'G' and resid 144 through 148 Processing sheet with id=AA8, first strand: chain 'H' and resid 144 through 148 removed outlier: 3.696A pdb=" N PHE H 147 " --> pdb=" O PHE H 156 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 144 through 148 Processing sheet with id=AB1, first strand: chain 'J' and resid 144 through 148 Processing sheet with id=AB2, first strand: chain 'K' and resid 144 through 148 Processing sheet with id=AB3, first strand: chain 'L' and resid 144 through 148 removed outlier: 3.557A pdb=" N LEU L 145 " --> pdb=" O VAL L 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 144 through 148 Processing sheet with id=AB5, first strand: chain 'N' and resid 144 through 148 Processing sheet with id=AB6, first strand: chain 'O' and resid 144 through 148 Processing sheet with id=AB7, first strand: chain 'P' and resid 144 through 148 Processing sheet with id=AB8, first strand: chain 'R' and resid 131 through 132 Processing sheet with id=AB9, first strand: chain 'R' and resid 144 through 148 Processing sheet with id=AC1, first strand: chain 'S' and resid 144 through 148 Processing sheet with id=AC2, first strand: chain 'T' and resid 144 through 148 Processing sheet with id=AC3, first strand: chain 'U' and resid 131 through 132 Processing sheet with id=AC4, first strand: chain 'U' and resid 144 through 148 Processing sheet with id=AC5, first strand: chain 'V' and resid 144 through 148 removed outlier: 3.758A pdb=" N PHE V 147 " --> pdb=" O PHE V 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'W' and resid 144 through 148 removed outlier: 3.538A pdb=" N PHE W 147 " --> pdb=" O PHE W 156 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'X' and resid 144 through 148 Processing sheet with id=AC8, first strand: chain 'Y' and resid 144 through 148 removed outlier: 3.825A pdb=" N PHE Y 147 " --> pdb=" O PHE Y 156 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Z' and resid 144 through 148 removed outlier: 3.561A pdb=" N PHE Z 147 " --> pdb=" O PHE Z 156 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'a' and resid 144 through 148 Processing sheet with id=AD2, first strand: chain 'b' and resid 144 through 148 Processing sheet with id=AD3, first strand: chain 'c' and resid 144 through 145 Processing sheet with id=AD4, first strand: chain 'd' and resid 144 through 145 Processing sheet with id=AD5, first strand: chain 'e' and resid 144 through 148 Processing sheet with id=AD6, first strand: chain 'f' and resid 144 through 148 Processing sheet with id=AD7, first strand: chain 'g' and resid 144 through 148 Processing sheet with id=AD8, first strand: chain 'h' and resid 144 through 145 Processing sheet with id=AD9, first strand: chain 'i' and resid 144 through 148 Processing sheet with id=AE1, first strand: chain 'j' and resid 144 through 148 Processing sheet with id=AE2, first strand: chain 'k' and resid 144 through 148 removed outlier: 3.518A pdb=" N PHE k 147 " --> pdb=" O PHE k 156 " (cutoff:3.500A) 6398 hydrogen bonds defined for protein. 18558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 27.10 Time building geometry restraints manager: 16.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 17005 1.33 - 1.45: 13224 1.45 - 1.58: 42291 1.58 - 1.70: 0 1.70 - 1.82: 296 Bond restraints: 72816 Sorted by residual: bond pdb=" N VAL R 232 " pdb=" CA VAL R 232 " ideal model delta sigma weight residual 1.460 1.503 -0.043 1.21e-02 6.83e+03 1.29e+01 bond pdb=" N VAL c 232 " pdb=" CA VAL c 232 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.11e+01 bond pdb=" N ASP R 233 " pdb=" CA ASP R 233 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.27e-02 6.20e+03 8.61e+00 bond pdb=" N ASP T 115 " pdb=" CA ASP T 115 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 6.99e+00 bond pdb=" N LEU R 231 " pdb=" CA LEU R 231 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.28e+00 ... (remaining 72811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 96798 1.84 - 3.69: 1635 3.69 - 5.53: 268 5.53 - 7.38: 39 7.38 - 9.22: 13 Bond angle restraints: 98753 Sorted by residual: angle pdb=" C LEU a 231 " pdb=" N VAL a 232 " pdb=" CA VAL a 232 " ideal model delta sigma weight residual 122.66 118.89 3.77 9.70e-01 1.06e+00 1.51e+01 angle pdb=" C ASN f 8 " pdb=" CA ASN f 8 " pdb=" CB ASN f 8 " ideal model delta sigma weight residual 110.02 115.79 -5.77 1.50e+00 4.44e-01 1.48e+01 angle pdb=" C ALA R 234 " pdb=" N ASP R 235 " pdb=" CA ASP R 235 " ideal model delta sigma weight residual 120.82 115.68 5.14 1.41e+00 5.03e-01 1.33e+01 angle pdb=" C LEU F 231 " pdb=" N VAL F 232 " pdb=" CA VAL F 232 " ideal model delta sigma weight residual 122.77 118.96 3.81 1.05e+00 9.07e-01 1.31e+01 angle pdb=" CA GLU c 117 " pdb=" CB GLU c 117 " pdb=" CG GLU c 117 " ideal model delta sigma weight residual 114.10 121.09 -6.99 2.00e+00 2.50e-01 1.22e+01 ... (remaining 98748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 40729 17.91 - 35.82: 3169 35.82 - 53.72: 479 53.72 - 71.63: 121 71.63 - 89.54: 87 Dihedral angle restraints: 44585 sinusoidal: 15910 harmonic: 28675 Sorted by residual: dihedral pdb=" CA GLU N 151 " pdb=" C GLU N 151 " pdb=" N ASP N 152 " pdb=" CA ASP N 152 " ideal model delta harmonic sigma weight residual 180.00 -155.92 -24.08 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA ASN S 155 " pdb=" C ASN S 155 " pdb=" N PHE S 156 " pdb=" CA PHE S 156 " ideal model delta harmonic sigma weight residual 180.00 157.23 22.77 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA ASN M 155 " pdb=" C ASN M 155 " pdb=" N PHE M 156 " pdb=" CA PHE M 156 " ideal model delta harmonic sigma weight residual 180.00 157.82 22.18 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 44582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 10937 0.052 - 0.105: 1693 0.105 - 0.157: 153 0.157 - 0.210: 16 0.210 - 0.262: 3 Chirality restraints: 12802 Sorted by residual: chirality pdb=" CA THR a 263 " pdb=" N THR a 263 " pdb=" C THR a 263 " pdb=" CB THR a 263 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB ILE T 85 " pdb=" CA ILE T 85 " pdb=" CG1 ILE T 85 " pdb=" CG2 ILE T 85 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB VAL R 232 " pdb=" CA VAL R 232 " pdb=" CG1 VAL R 232 " pdb=" CG2 VAL R 232 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 12799 not shown) Planarity restraints: 12617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP T 48 " -0.031 2.00e-02 2.50e+03 2.34e-02 1.36e+01 pdb=" CG TRP T 48 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP T 48 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP T 48 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP T 48 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP T 48 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP T 48 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP T 48 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP T 48 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP T 48 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN f 8 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.41e+00 pdb=" C ASN f 8 " -0.044 2.00e-02 2.50e+03 pdb=" O ASN f 8 " 0.016 2.00e-02 2.50e+03 pdb=" N PRO f 9 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN P 8 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO P 9 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO P 9 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO P 9 " -0.029 5.00e-02 4.00e+02 ... (remaining 12614 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 845 2.60 - 3.18: 67911 3.18 - 3.75: 120895 3.75 - 4.33: 158011 4.33 - 4.90: 262693 Nonbonded interactions: 610355 Sorted by model distance: nonbonded pdb=" OG SER f 245 " pdb=" O ILE i 5 " model vdw 2.027 3.040 nonbonded pdb=" OG SER f 4 " pdb=" OD2 ASP g 233 " model vdw 2.079 3.040 nonbonded pdb=" OG SER f 136 " pdb=" OD1 ASP f 139 " model vdw 2.083 3.040 nonbonded pdb=" OG SER D 4 " pdb=" O THR D 7 " model vdw 2.115 3.040 nonbonded pdb=" OE1 GLU h 117 " pdb=" NH2 ARG h 120 " model vdw 2.121 3.120 ... (remaining 610350 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 7.700 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: 0.090 Extract box with map and model: 2.090 Check model and map are aligned: 0.410 Set scattering table: 0.500 Process input model: 121.380 Find NCS groups from input model: 2.900 Set up NCS constraints: 0.810 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 72816 Z= 0.196 Angle : 0.632 9.224 98753 Z= 0.355 Chirality : 0.037 0.262 12802 Planarity : 0.004 0.052 12617 Dihedral : 13.863 89.541 25863 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.55 % Favored : 98.37 % Rotamer: Outliers : 0.08 % Allowed : 0.38 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.07), residues: 9916 helix: -0.26 (0.04), residues: 7363 sheet: -3.57 (0.22), residues: 370 loop : 1.66 (0.15), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP T 48 HIS 0.005 0.001 HIS Q 213 PHE 0.026 0.001 PHE J 156 ARG 0.007 0.001 ARG e 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1361 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1355 time to evaluate : 6.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ASP cc_start: 0.8213 (m-30) cc_final: 0.7904 (m-30) REVERT: B 233 ASP cc_start: 0.8364 (m-30) cc_final: 0.8163 (m-30) REVERT: G 8 ASN cc_start: 0.8642 (p0) cc_final: 0.8389 (p0) REVERT: G 50 MET cc_start: 0.9078 (mtp) cc_final: 0.8862 (mtp) REVERT: H 242 LYS cc_start: 0.8704 (tppt) cc_final: 0.8432 (tppt) REVERT: I 128 THR cc_start: 0.8724 (t) cc_final: 0.8466 (m) REVERT: J 254 VAL cc_start: 0.7720 (p) cc_final: 0.7188 (t) REVERT: K 83 ASP cc_start: 0.7109 (m-30) cc_final: 0.6905 (m-30) REVERT: K 117 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8656 (mt-10) REVERT: K 201 SER cc_start: 0.8766 (t) cc_final: 0.8375 (m) REVERT: K 252 LEU cc_start: 0.8635 (mm) cc_final: 0.8146 (tt) REVERT: K 270 LEU cc_start: 0.7778 (mt) cc_final: 0.7536 (tt) REVERT: L 116 PHE cc_start: 0.6797 (t80) cc_final: 0.6550 (t80) REVERT: L 117 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7355 (mm-30) REVERT: L 219 LYS cc_start: 0.7695 (mttp) cc_final: 0.7211 (tppt) REVERT: N 117 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7281 (mp0) REVERT: O 94 GLU cc_start: 0.5920 (mm-30) cc_final: 0.5121 (tt0) REVERT: P 15 LEU cc_start: 0.8114 (mt) cc_final: 0.7419 (tp) REVERT: P 201 SER cc_start: 0.9252 (t) cc_final: 0.9042 (p) REVERT: Q 175 THR cc_start: 0.8062 (t) cc_final: 0.7737 (m) REVERT: Q 262 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7802 (pp30) REVERT: R 94 GLU cc_start: 0.5613 (mm-30) cc_final: 0.4652 (mt-10) REVERT: S 122 GLN cc_start: 0.8718 (mt0) cc_final: 0.8021 (tp-100) REVERT: S 141 SER cc_start: 0.9007 (t) cc_final: 0.8677 (m) REVERT: W 17 ASN cc_start: 0.7401 (m-40) cc_final: 0.6916 (m110) REVERT: W 122 GLN cc_start: 0.8197 (mp10) cc_final: 0.7558 (mp10) REVERT: W 238 LYS cc_start: 0.6741 (mtpt) cc_final: 0.6231 (mptt) REVERT: X 42 LYS cc_start: 0.5285 (tptt) cc_final: 0.4673 (tppt) REVERT: Y 20 SER cc_start: 0.8617 (t) cc_final: 0.8199 (p) REVERT: Z 37 LYS cc_start: 0.7732 (mmtt) cc_final: 0.7262 (mptt) REVERT: Z 251 GLN cc_start: 0.8303 (mp10) cc_final: 0.7937 (mp10) REVERT: a 13 LEU cc_start: 0.7857 (mt) cc_final: 0.7467 (mt) REVERT: a 151 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6707 (tp30) REVERT: b 36 LYS cc_start: 0.7313 (mtpt) cc_final: 0.6702 (mmtt) REVERT: c 31 ARG cc_start: 0.8343 (mtm-85) cc_final: 0.8129 (mtm-85) REVERT: c 238 LYS cc_start: 0.8197 (ttmm) cc_final: 0.7994 (mttp) REVERT: f 84 THR cc_start: 0.8381 (m) cc_final: 0.8180 (m) REVERT: f 262 GLN cc_start: 0.8025 (tp40) cc_final: 0.7811 (tp40) REVERT: i 185 MET cc_start: 0.8123 (tpp) cc_final: 0.7717 (tpp) REVERT: j 2 LEU cc_start: 0.8703 (mp) cc_final: 0.8068 (tt) REVERT: j 115 ASP cc_start: 0.8260 (t70) cc_final: 0.8056 (t0) REVERT: j 262 GLN cc_start: 0.7849 (mt0) cc_final: 0.7573 (tp40) REVERT: k 94 GLU cc_start: 0.8699 (tp30) cc_final: 0.8374 (tp30) REVERT: k 194 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8239 (tp40) outliers start: 6 outliers final: 2 residues processed: 1359 average time/residue: 0.6010 time to fit residues: 1463.4072 Evaluate side-chains 1047 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1045 time to evaluate : 6.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain c residue 231 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 843 optimal weight: 4.9990 chunk 757 optimal weight: 4.9990 chunk 420 optimal weight: 9.9990 chunk 258 optimal weight: 10.0000 chunk 510 optimal weight: 5.9990 chunk 404 optimal weight: 4.9990 chunk 783 optimal weight: 6.9990 chunk 303 optimal weight: 9.9990 chunk 476 optimal weight: 6.9990 chunk 582 optimal weight: 9.9990 chunk 907 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN B 213 HIS C 6 ASN ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN D 230 ASN ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 ASN F 262 GLN G 29 GLN ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 GLN H 150 ASN I 247 GLN J 29 GLN ** J 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 251 GLN ** J 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 133 ASN K 155 ASN K 194 GLN K 198 ASN ** L 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 GLN M 198 ASN M 262 GLN N 3 ASN ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 194 GLN ** O 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 44 ASN ** P 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 29 GLN ** Q 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 155 ASN Q 255 GLN R 122 GLN S 22 ASN ** S 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 3 ASN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 122 GLN V 155 ASN W 29 GLN W 129 ASN X 262 GLN Y 6 ASN ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN ** Y 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 3 ASN Z 44 ASN a 122 GLN a 129 ASN ** b 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 150 ASN c 6 ASN ** c 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 124 GLN c 133 ASN d 6 ASN d 105 ASN d 250 GLN e 261 ASN ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 198 ASN h 129 ASN i 29 GLN i 72 GLN i 250 GLN j 230 ASN k 72 GLN k 110 ASN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 72816 Z= 0.456 Angle : 0.691 11.014 98753 Z= 0.368 Chirality : 0.042 0.234 12802 Planarity : 0.004 0.055 12617 Dihedral : 4.567 46.714 10068 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.71 % Allowed : 8.61 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.08), residues: 9916 helix: 1.97 (0.06), residues: 7289 sheet: -3.31 (0.23), residues: 370 loop : 0.68 (0.14), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP T 48 HIS 0.007 0.002 HIS E 213 PHE 0.027 0.003 PHE b 109 ARG 0.007 0.001 ARG T 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1013 time to evaluate : 6.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ASP cc_start: 0.8324 (m-30) cc_final: 0.8040 (m-30) REVERT: G 50 MET cc_start: 0.9138 (mtp) cc_final: 0.8771 (mtp) REVERT: G 267 ILE cc_start: 0.8770 (mm) cc_final: 0.8428 (mm) REVERT: H 242 LYS cc_start: 0.8773 (tppt) cc_final: 0.8422 (tppt) REVERT: K 31 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.8233 (ttm-80) REVERT: K 83 ASP cc_start: 0.7134 (m-30) cc_final: 0.6926 (m-30) REVERT: K 252 LEU cc_start: 0.8735 (mm) cc_final: 0.8115 (tt) REVERT: K 270 LEU cc_start: 0.7614 (mt) cc_final: 0.7376 (tt) REVERT: L 219 LYS cc_start: 0.7775 (mttp) cc_final: 0.7259 (tppt) REVERT: P 201 SER cc_start: 0.9309 (t) cc_final: 0.9063 (p) REVERT: Q 230 ASN cc_start: 0.7751 (m-40) cc_final: 0.7439 (m-40) REVERT: R 94 GLU cc_start: 0.5665 (mm-30) cc_final: 0.4673 (mt-10) REVERT: R 211 ASP cc_start: 0.8007 (m-30) cc_final: 0.7792 (m-30) REVERT: T 267 ILE cc_start: 0.8340 (mm) cc_final: 0.8121 (mt) REVERT: W 238 LYS cc_start: 0.7189 (mtpt) cc_final: 0.6608 (mptt) REVERT: W 239 GLU cc_start: 0.8356 (tp30) cc_final: 0.8102 (tp30) REVERT: X 38 VAL cc_start: 0.7651 (m) cc_final: 0.7302 (t) REVERT: X 42 LYS cc_start: 0.5293 (tptt) cc_final: 0.4715 (tppt) REVERT: Z 37 LYS cc_start: 0.7888 (mmtt) cc_final: 0.7134 (mptt) REVERT: Z 251 GLN cc_start: 0.8306 (mp10) cc_final: 0.7898 (mp10) REVERT: a 255 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8409 (tp40) REVERT: c 117 GLU cc_start: 0.7917 (mp0) cc_final: 0.7676 (mp0) REVERT: i 185 MET cc_start: 0.8111 (tpp) cc_final: 0.7568 (tpp) REVERT: j 115 ASP cc_start: 0.8616 (t70) cc_final: 0.8122 (t0) REVERT: k 194 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8356 (mm-40) outliers start: 137 outliers final: 96 residues processed: 1099 average time/residue: 0.5982 time to fit residues: 1178.0968 Evaluate side-chains 1019 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 923 time to evaluate : 6.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain F residue 250 GLN Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain J residue 69 GLN Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 163 LEU Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 165 LEU Chi-restraints excluded: chain Q residue 255 GLN Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain R residue 15 LEU Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain T residue 135 VAL Chi-restraints excluded: chain V residue 47 ILE Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain X residue 266 THR Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 128 THR Chi-restraints excluded: chain Y residue 173 THR Chi-restraints excluded: chain Y residue 248 THR Chi-restraints excluded: chain Y residue 252 LEU Chi-restraints excluded: chain Y residue 259 ILE Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain Z residue 100 SER Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 232 VAL Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 87 ASP Chi-restraints excluded: chain a residue 261 ASN Chi-restraints excluded: chain b residue 32 ILE Chi-restraints excluded: chain b residue 177 THR Chi-restraints excluded: chain b residue 217 VAL Chi-restraints excluded: chain b residue 228 VAL Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain d residue 32 ILE Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain d residue 265 GLN Chi-restraints excluded: chain e residue 171 THR Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 265 GLN Chi-restraints excluded: chain e residue 270 LEU Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain g residue 4 SER Chi-restraints excluded: chain g residue 268 LEU Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 185 MET Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 265 GLN Chi-restraints excluded: chain h residue 266 THR Chi-restraints excluded: chain h residue 267 ILE Chi-restraints excluded: chain i residue 2 LEU Chi-restraints excluded: chain i residue 72 GLN Chi-restraints excluded: chain i residue 101 ASP Chi-restraints excluded: chain i residue 171 THR Chi-restraints excluded: chain j residue 263 THR Chi-restraints excluded: chain k residue 2 LEU Chi-restraints excluded: chain k residue 5 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 504 optimal weight: 0.8980 chunk 281 optimal weight: 0.9990 chunk 755 optimal weight: 0.6980 chunk 617 optimal weight: 5.9990 chunk 250 optimal weight: 0.9980 chunk 908 optimal weight: 0.9990 chunk 981 optimal weight: 0.9990 chunk 809 optimal weight: 0.9980 chunk 901 optimal weight: 1.9990 chunk 309 optimal weight: 5.9990 chunk 729 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 ASN ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 ASN F 262 GLN ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 124 GLN J 29 GLN J 62 ASN ** J 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 ASN L 124 GLN L 250 GLN M 262 GLN N 29 GLN N 124 GLN N 150 ASN O 6 ASN O 17 ASN ** O 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 29 GLN ** Q 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 198 ASN S 54 GLN ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 198 ASN U 29 GLN V 3 ASN V 29 GLN W 29 GLN ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 133 ASN Y 250 GLN Z 3 ASN b 17 ASN b 124 GLN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 122 GLN ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 124 GLN i 250 GLN j 16 GLN ** k 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 72816 Z= 0.154 Angle : 0.477 10.147 98753 Z= 0.259 Chirality : 0.034 0.217 12802 Planarity : 0.003 0.046 12617 Dihedral : 4.000 23.770 10066 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.09 % Allowed : 10.75 % Favored : 88.16 % 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: 3.23 (0.08), residues: 9916 helix: 2.92 (0.06), residues: 7400 sheet: -2.94 (0.24), residues: 370 loop : 0.27 (0.14), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP T 48 HIS 0.003 0.001 HIS R 213 PHE 0.016 0.001 PHE X 216 ARG 0.004 0.000 ARG W 31 *********************** 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 1324 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1237 time to evaluate : 6.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 139 ASP cc_start: 0.7969 (t0) cc_final: 0.7614 (t0) REVERT: F 242 LYS cc_start: 0.8263 (tttt) cc_final: 0.8035 (mtpp) REVERT: G 8 ASN cc_start: 0.8262 (p0) cc_final: 0.8004 (p0) REVERT: G 50 MET cc_start: 0.9132 (mtp) cc_final: 0.8858 (mtp) REVERT: G 267 ILE cc_start: 0.8576 (mm) cc_final: 0.8219 (mm) REVERT: H 242 LYS cc_start: 0.8705 (tppt) cc_final: 0.8388 (tppt) REVERT: I 76 ASP cc_start: 0.7468 (m-30) cc_final: 0.7229 (m-30) REVERT: I 97 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8090 (tt) REVERT: K 31 ARG cc_start: 0.8614 (ttm-80) cc_final: 0.8375 (ttm-80) REVERT: K 83 ASP cc_start: 0.7049 (m-30) cc_final: 0.6825 (m-30) REVERT: K 252 LEU cc_start: 0.8704 (mm) cc_final: 0.8056 (tt) REVERT: L 87 ASP cc_start: 0.8351 (m-30) cc_final: 0.8085 (m-30) REVERT: L 219 LYS cc_start: 0.7759 (mttp) cc_final: 0.7289 (tppt) REVERT: N 37 LYS cc_start: 0.8494 (ptpt) cc_final: 0.8275 (ptpt) REVERT: O 161 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7487 (mm-40) REVERT: P 15 LEU cc_start: 0.8247 (mt) cc_final: 0.7594 (tp) REVERT: P 185 MET cc_start: 0.9240 (tpp) cc_final: 0.8957 (tpp) REVERT: P 201 SER cc_start: 0.9253 (t) cc_final: 0.9027 (p) REVERT: R 94 GLU cc_start: 0.5610 (mm-30) cc_final: 0.4700 (mt-10) REVERT: R 148 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8272 (mm) REVERT: S 122 GLN cc_start: 0.8717 (mt0) cc_final: 0.7901 (tp-100) REVERT: S 258 SER cc_start: 0.8621 (t) cc_final: 0.8253 (p) REVERT: U 32 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7495 (mp) REVERT: W 17 ASN cc_start: 0.7461 (m-40) cc_final: 0.7031 (m110) REVERT: W 238 LYS cc_start: 0.6900 (mtpt) cc_final: 0.6355 (mptt) REVERT: X 42 LYS cc_start: 0.5196 (tptt) cc_final: 0.4700 (tppt) REVERT: X 230 ASN cc_start: 0.8490 (m-40) cc_final: 0.8102 (m-40) REVERT: Y 20 SER cc_start: 0.8621 (t) cc_final: 0.8195 (p) REVERT: Y 133 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7780 (t0) REVERT: Z 37 LYS cc_start: 0.7694 (mmtt) cc_final: 0.7203 (mptt) REVERT: Z 244 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8202 (mp10) REVERT: Z 251 GLN cc_start: 0.8188 (mp10) cc_final: 0.7614 (mp10) REVERT: b 50 MET cc_start: 0.7872 (mtp) cc_final: 0.6802 (mtm) REVERT: b 101 ASP cc_start: 0.7996 (t0) cc_final: 0.7776 (t70) REVERT: c 238 LYS cc_start: 0.8327 (ttmm) cc_final: 0.7868 (tptt) REVERT: h 255 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.7152 (mp10) REVERT: i 185 MET cc_start: 0.8128 (tpp) cc_final: 0.7846 (tpp) REVERT: j 2 LEU cc_start: 0.8760 (mp) cc_final: 0.7950 (tt) REVERT: j 115 ASP cc_start: 0.8496 (t70) cc_final: 0.8209 (t0) REVERT: j 262 GLN cc_start: 0.7807 (mt0) cc_final: 0.7537 (tm-30) REVERT: k 94 GLU cc_start: 0.8948 (tp30) cc_final: 0.8654 (tp30) REVERT: k 117 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: k 194 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8120 (tp40) outliers start: 87 outliers final: 41 residues processed: 1283 average time/residue: 0.6258 time to fit residues: 1444.4712 Evaluate side-chains 1074 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1026 time to evaluate : 6.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain F residue 129 ASN Chi-restraints excluded: chain F residue 250 GLN Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 265 GLN Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain W residue 15 LEU Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 133 ASN Chi-restraints excluded: chain Y residue 252 LEU Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain Z residue 244 GLN Chi-restraints excluded: chain b residue 32 ILE Chi-restraints excluded: chain d residue 105 ASN Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 265 GLN Chi-restraints excluded: chain e residue 270 LEU Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain h residue 255 GLN Chi-restraints excluded: chain h residue 265 GLN Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 117 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 897 optimal weight: 4.9990 chunk 683 optimal weight: 0.9990 chunk 471 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 433 optimal weight: 3.9990 chunk 610 optimal weight: 9.9990 chunk 912 optimal weight: 4.9990 chunk 965 optimal weight: 6.9990 chunk 476 optimal weight: 6.9990 chunk 864 optimal weight: 9.9990 chunk 260 optimal weight: 0.0970 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 GLN I 247 GLN ** J 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 ASN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 262 GLN N 29 GLN N 150 ASN O 17 ASN O 29 GLN O 129 ASN O 155 ASN O 251 GLN ** Q 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 54 GLN ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 GLN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 29 GLN W 122 GLN W 261 ASN X 150 ASN ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 265 GLN b 40 ASN b 124 GLN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 124 GLN ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 247 GLN i 124 GLN ** i 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 250 GLN ** i 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 72816 Z= 0.194 Angle : 0.489 8.996 98753 Z= 0.265 Chirality : 0.034 0.215 12802 Planarity : 0.003 0.041 12617 Dihedral : 3.917 23.863 10064 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.61 % Allowed : 12.27 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.56 (0.09), residues: 9916 helix: 3.18 (0.06), residues: 7363 sheet: -2.70 (0.24), residues: 370 loop : 0.31 (0.14), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP T 48 HIS 0.004 0.001 HIS U 213 PHE 0.023 0.002 PHE b 109 ARG 0.008 0.000 ARG a 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1234 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1105 time to evaluate : 6.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 210 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8023 (mp) REVERT: F 242 LYS cc_start: 0.8254 (tttt) cc_final: 0.8047 (mtpp) REVERT: G 8 ASN cc_start: 0.8312 (p0) cc_final: 0.7972 (p0) REVERT: G 50 MET cc_start: 0.9124 (mtp) cc_final: 0.8842 (mtp) REVERT: G 119 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8555 (mp) REVERT: G 267 ILE cc_start: 0.8600 (mm) cc_final: 0.8255 (mm) REVERT: H 242 LYS cc_start: 0.8716 (tppt) cc_final: 0.8407 (tppt) REVERT: I 76 ASP cc_start: 0.7520 (m-30) cc_final: 0.7270 (m-30) REVERT: I 97 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8147 (tt) REVERT: K 31 ARG cc_start: 0.8568 (ttm-80) cc_final: 0.8300 (ttm-80) REVERT: K 83 ASP cc_start: 0.7038 (m-30) cc_final: 0.6810 (m-30) REVERT: K 252 LEU cc_start: 0.8734 (mm) cc_final: 0.8068 (tt) REVERT: L 87 ASP cc_start: 0.8361 (m-30) cc_final: 0.8080 (m-30) REVERT: L 219 LYS cc_start: 0.7793 (mttp) cc_final: 0.7350 (tppt) REVERT: O 161 GLN cc_start: 0.8296 (mm-40) cc_final: 0.7520 (mm-40) REVERT: P 201 SER cc_start: 0.9263 (t) cc_final: 0.9048 (p) REVERT: Q 94 GLU cc_start: 0.7787 (tp30) cc_final: 0.7471 (tp30) REVERT: R 94 GLU cc_start: 0.5641 (mm-30) cc_final: 0.4765 (mt-10) REVERT: T 52 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7224 (ttmm) REVERT: T 210 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8259 (mp) REVERT: U 32 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7506 (mp) REVERT: U 235 ASP cc_start: 0.7548 (t0) cc_final: 0.7325 (t70) REVERT: V 5 ILE cc_start: 0.8484 (tp) cc_final: 0.8068 (tp) REVERT: W 238 LYS cc_start: 0.7065 (mtpt) cc_final: 0.6482 (mptt) REVERT: X 42 LYS cc_start: 0.5309 (tptt) cc_final: 0.4776 (tppt) REVERT: Y 93 LYS cc_start: 0.7612 (mtmt) cc_final: 0.6846 (mmtm) REVERT: Y 94 GLU cc_start: 0.7279 (mp0) cc_final: 0.6909 (tt0) REVERT: Y 131 LYS cc_start: 0.8082 (ptpp) cc_final: 0.7882 (ptpp) REVERT: Z 37 LYS cc_start: 0.7713 (mmtt) cc_final: 0.7268 (mptt) REVERT: Z 244 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8161 (mp10) REVERT: Z 251 GLN cc_start: 0.8202 (mp10) cc_final: 0.7702 (mp10) REVERT: b 101 ASP cc_start: 0.7979 (t0) cc_final: 0.7638 (t70) REVERT: b 185 MET cc_start: 0.7558 (tpt) cc_final: 0.7277 (tpp) REVERT: h 53 MET cc_start: 0.8322 (mmm) cc_final: 0.8062 (mmt) REVERT: h 255 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6974 (mp10) REVERT: i 185 MET cc_start: 0.8089 (tpp) cc_final: 0.7764 (tpp) REVERT: j 2 LEU cc_start: 0.8730 (mp) cc_final: 0.8019 (tt) REVERT: j 115 ASP cc_start: 0.8615 (t70) cc_final: 0.8085 (t0) REVERT: j 262 GLN cc_start: 0.7868 (mt0) cc_final: 0.7561 (tm-30) REVERT: k 94 GLU cc_start: 0.8980 (tp30) cc_final: 0.8737 (mm-30) outliers start: 129 outliers final: 73 residues processed: 1192 average time/residue: 0.5818 time to fit residues: 1246.3621 Evaluate side-chains 1088 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1007 time to evaluate : 6.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 250 GLN Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 163 LEU Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 150 ASN Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 210 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 52 LYS Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain T residue 210 LEU Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain V residue 92 MET Chi-restraints excluded: chain W residue 15 LEU Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 238 LYS Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 252 LEU Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain Z residue 244 GLN Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain a residue 261 ASN Chi-restraints excluded: chain b residue 32 ILE Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 92 MET Chi-restraints excluded: chain d residue 105 ASN Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 265 GLN Chi-restraints excluded: chain e residue 171 THR Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 265 GLN Chi-restraints excluded: chain e residue 270 LEU Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 255 GLN Chi-restraints excluded: chain h residue 265 GLN Chi-restraints excluded: chain h residue 266 THR Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 267 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 804 optimal weight: 4.9990 chunk 548 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 718 optimal weight: 3.9990 chunk 398 optimal weight: 9.9990 chunk 824 optimal weight: 10.0000 chunk 667 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 493 optimal weight: 6.9990 chunk 866 optimal weight: 1.9990 chunk 243 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 261 ASN L 124 GLN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 29 GLN O 122 GLN ** Q 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 54 GLN S 255 GLN ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 GLN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 122 GLN X 250 GLN ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 133 ASN Y 150 ASN a 22 ASN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 124 GLN c 129 ASN d 72 GLN ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 250 GLN ** i 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 72816 Z= 0.240 Angle : 0.513 9.447 98753 Z= 0.276 Chirality : 0.036 0.213 12802 Planarity : 0.003 0.062 12617 Dihedral : 3.964 24.070 10064 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.80 % Allowed : 13.38 % Favored : 84.82 % 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: 3.53 (0.08), residues: 9916 helix: 3.18 (0.06), residues: 7363 sheet: -2.54 (0.25), residues: 370 loop : 0.16 (0.14), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP T 48 HIS 0.005 0.001 HIS U 213 PHE 0.031 0.002 PHE i 132 ARG 0.008 0.001 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 1183 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1039 time to evaluate : 6.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 210 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8080 (mp) REVERT: F 242 LYS cc_start: 0.8284 (tttt) cc_final: 0.8023 (mtpp) REVERT: G 8 ASN cc_start: 0.8395 (p0) cc_final: 0.8092 (p0) REVERT: G 50 MET cc_start: 0.9127 (mtp) cc_final: 0.8765 (mtp) REVERT: G 267 ILE cc_start: 0.8634 (mm) cc_final: 0.8292 (mm) REVERT: H 242 LYS cc_start: 0.8716 (tppt) cc_final: 0.8409 (tppt) REVERT: I 97 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8164 (tt) REVERT: K 31 ARG cc_start: 0.8566 (ttm-80) cc_final: 0.8269 (ttm-80) REVERT: K 83 ASP cc_start: 0.7067 (m-30) cc_final: 0.6844 (m-30) REVERT: K 252 LEU cc_start: 0.8760 (mm) cc_final: 0.8093 (tt) REVERT: L 87 ASP cc_start: 0.8395 (m-30) cc_final: 0.8112 (m-30) REVERT: L 219 LYS cc_start: 0.7766 (mttp) cc_final: 0.7292 (tppt) REVERT: O 161 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7507 (mm-40) REVERT: P 201 SER cc_start: 0.9272 (t) cc_final: 0.9053 (p) REVERT: R 94 GLU cc_start: 0.5655 (mm-30) cc_final: 0.4770 (mt-10) REVERT: T 210 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8283 (mp) REVERT: U 32 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7405 (mp) REVERT: U 235 ASP cc_start: 0.7607 (t0) cc_final: 0.7387 (t70) REVERT: V 5 ILE cc_start: 0.8496 (tp) cc_final: 0.8084 (tp) REVERT: W 238 LYS cc_start: 0.6912 (mtpt) cc_final: 0.6321 (mptt) REVERT: X 42 LYS cc_start: 0.5337 (tptt) cc_final: 0.4743 (tppt) REVERT: X 175 THR cc_start: 0.8891 (t) cc_final: 0.8493 (m) REVERT: Y 93 LYS cc_start: 0.7667 (mtmt) cc_final: 0.6864 (mmtm) REVERT: Y 94 GLU cc_start: 0.7287 (mp0) cc_final: 0.6899 (tt0) REVERT: Z 37 LYS cc_start: 0.7772 (mmtt) cc_final: 0.7143 (mptt) REVERT: Z 244 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8139 (mp10) REVERT: Z 251 GLN cc_start: 0.8223 (mp10) cc_final: 0.7698 (mp10) REVERT: b 101 ASP cc_start: 0.7971 (t0) cc_final: 0.7654 (t70) REVERT: b 185 MET cc_start: 0.7534 (tpt) cc_final: 0.7256 (tpp) REVERT: e 88 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8184 (tt) REVERT: h 53 MET cc_start: 0.8397 (mmm) cc_final: 0.8127 (mmt) REVERT: h 255 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6899 (mp10) REVERT: i 185 MET cc_start: 0.8095 (tpp) cc_final: 0.7745 (tpp) REVERT: j 2 LEU cc_start: 0.8769 (mp) cc_final: 0.8081 (tt) REVERT: j 115 ASP cc_start: 0.8665 (t70) cc_final: 0.8124 (t0) REVERT: j 262 GLN cc_start: 0.7914 (mt0) cc_final: 0.7576 (tm-30) REVERT: k 117 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8066 (mt-10) outliers start: 144 outliers final: 101 residues processed: 1130 average time/residue: 0.5899 time to fit residues: 1199.4731 Evaluate side-chains 1083 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 974 time to evaluate : 5.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 250 GLN Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain L residue 163 LEU Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain P residue 83 ASP Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 210 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 207 SER Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain T residue 158 VAL Chi-restraints excluded: chain T residue 210 LEU Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain U residue 146 SER Chi-restraints excluded: chain V residue 92 MET Chi-restraints excluded: chain W residue 15 LEU Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 238 LYS Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 173 THR Chi-restraints excluded: chain Y residue 252 LEU Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain Z residue 244 GLN Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 115 ASP Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain a residue 261 ASN Chi-restraints excluded: chain b residue 32 ILE Chi-restraints excluded: chain b residue 268 LEU Chi-restraints excluded: chain c residue 212 THR Chi-restraints excluded: chain d residue 32 ILE Chi-restraints excluded: chain d residue 105 ASN Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 265 GLN Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 88 LEU Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 117 GLU Chi-restraints excluded: chain e residue 171 THR Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 265 GLN Chi-restraints excluded: chain e residue 270 LEU Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain g residue 232 VAL Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 255 GLN Chi-restraints excluded: chain h residue 265 GLN Chi-restraints excluded: chain h residue 266 THR Chi-restraints excluded: chain i residue 101 ASP Chi-restraints excluded: chain k residue 2 LEU Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 117 GLU Chi-restraints excluded: chain k residue 135 VAL Chi-restraints excluded: chain k residue 171 THR Chi-restraints excluded: chain k residue 267 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 324 optimal weight: 9.9990 chunk 869 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 chunk 566 optimal weight: 1.9990 chunk 238 optimal weight: 6.9990 chunk 966 optimal weight: 1.9990 chunk 802 optimal weight: 2.9990 chunk 447 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 319 optimal weight: 2.9990 chunk 507 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 150 ASN ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 29 GLN O 122 GLN ** Q 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 54 GLN ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 GLN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 122 GLN ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 40 ASN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 124 GLN ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 72816 Z= 0.212 Angle : 0.497 9.593 98753 Z= 0.269 Chirality : 0.035 0.230 12802 Planarity : 0.003 0.046 12617 Dihedral : 3.921 23.536 10064 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.93 % Allowed : 13.84 % Favored : 84.23 % 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: 3.59 (0.08), residues: 9916 helix: 3.24 (0.06), residues: 7363 sheet: -2.37 (0.25), residues: 370 loop : 0.08 (0.14), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP T 48 HIS 0.004 0.001 HIS U 213 PHE 0.025 0.002 PHE W 216 ARG 0.008 0.001 ARG a 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1224 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1070 time to evaluate : 6.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.8455 (tpt) cc_final: 0.8224 (tpt) REVERT: E 210 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8040 (mp) REVERT: F 242 LYS cc_start: 0.8275 (tttt) cc_final: 0.8022 (mtpp) REVERT: G 8 ASN cc_start: 0.8340 (p0) cc_final: 0.8016 (p0) REVERT: G 50 MET cc_start: 0.9136 (mtp) cc_final: 0.8857 (mtp) REVERT: G 267 ILE cc_start: 0.8637 (mm) cc_final: 0.8295 (mm) REVERT: H 242 LYS cc_start: 0.8728 (tppt) cc_final: 0.8427 (tppt) REVERT: I 76 ASP cc_start: 0.7535 (m-30) cc_final: 0.7318 (m-30) REVERT: I 97 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8175 (tt) REVERT: I 151 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6831 (tp30) REVERT: K 31 ARG cc_start: 0.8566 (ttm-80) cc_final: 0.8262 (ttm-80) REVERT: K 83 ASP cc_start: 0.7097 (m-30) cc_final: 0.6887 (m-30) REVERT: K 94 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: K 252 LEU cc_start: 0.8755 (mm) cc_final: 0.8080 (tt) REVERT: L 87 ASP cc_start: 0.8320 (m-30) cc_final: 0.8063 (m-30) REVERT: L 219 LYS cc_start: 0.7808 (mttp) cc_final: 0.7310 (tppt) REVERT: M 161 GLN cc_start: 0.8050 (mp10) cc_final: 0.7714 (mp10) REVERT: O 94 GLU cc_start: 0.6020 (mm-30) cc_final: 0.5236 (tt0) REVERT: O 161 GLN cc_start: 0.8282 (mm-40) cc_final: 0.7509 (mm-40) REVERT: P 201 SER cc_start: 0.9266 (t) cc_final: 0.9049 (p) REVERT: P 262 GLN cc_start: 0.8588 (mp10) cc_final: 0.8210 (mp10) REVERT: R 94 GLU cc_start: 0.5648 (mm-30) cc_final: 0.4792 (mt-10) REVERT: S 122 GLN cc_start: 0.8823 (mt0) cc_final: 0.8003 (tp-100) REVERT: T 210 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8277 (mp) REVERT: U 32 ILE cc_start: 0.7657 (OUTLIER) cc_final: 0.7311 (mp) REVERT: U 94 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7857 (mt-10) REVERT: U 151 GLU cc_start: 0.6045 (tp30) cc_final: 0.5681 (tm-30) REVERT: V 5 ILE cc_start: 0.8481 (tp) cc_final: 0.8075 (tp) REVERT: W 238 LYS cc_start: 0.6865 (mtpt) cc_final: 0.6311 (mptt) REVERT: X 42 LYS cc_start: 0.5359 (tptt) cc_final: 0.4794 (tppt) REVERT: X 175 THR cc_start: 0.8860 (t) cc_final: 0.8477 (m) REVERT: Y 94 GLU cc_start: 0.7268 (mp0) cc_final: 0.6907 (tt0) REVERT: Z 37 LYS cc_start: 0.7705 (mmtt) cc_final: 0.7080 (mptt) REVERT: Z 251 GLN cc_start: 0.8225 (mp10) cc_final: 0.7696 (mp10) REVERT: b 101 ASP cc_start: 0.7937 (t0) cc_final: 0.7632 (t70) REVERT: b 185 MET cc_start: 0.7541 (tpt) cc_final: 0.7264 (tpp) REVERT: c 109 PHE cc_start: 0.8011 (t80) cc_final: 0.7795 (t80) REVERT: e 88 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8179 (tt) REVERT: e 185 MET cc_start: 0.6867 (tpp) cc_final: 0.6663 (tpp) REVERT: h 53 MET cc_start: 0.8389 (mmm) cc_final: 0.8149 (mmt) REVERT: h 255 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6854 (mp10) REVERT: i 185 MET cc_start: 0.8092 (tpp) cc_final: 0.7736 (tpp) REVERT: j 2 LEU cc_start: 0.8774 (mp) cc_final: 0.8094 (tt) REVERT: j 115 ASP cc_start: 0.8647 (t70) cc_final: 0.8103 (t0) REVERT: j 262 GLN cc_start: 0.7919 (mt0) cc_final: 0.7606 (tm-30) REVERT: k 94 GLU cc_start: 0.9021 (tp30) cc_final: 0.8733 (mm-30) REVERT: k 117 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8002 (mt-10) outliers start: 154 outliers final: 117 residues processed: 1175 average time/residue: 0.6243 time to fit residues: 1323.5416 Evaluate side-chains 1113 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 986 time to evaluate : 6.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 250 GLN Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 202 SER Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain L residue 163 LEU Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 159 THR Chi-restraints excluded: chain P residue 83 ASP Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain P residue 177 THR Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 210 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 52 LYS Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain T residue 158 VAL Chi-restraints excluded: chain T residue 210 LEU Chi-restraints excluded: chain U residue 24 GLU Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 94 GLU Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain U residue 146 SER Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 92 MET Chi-restraints excluded: chain W residue 15 LEU Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 173 THR Chi-restraints excluded: chain Y residue 252 LEU Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain Z residue 104 LEU Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain Z residue 244 GLN Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 115 ASP Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain a residue 261 ASN Chi-restraints excluded: chain a residue 263 THR Chi-restraints excluded: chain b residue 32 ILE Chi-restraints excluded: chain b residue 252 LEU Chi-restraints excluded: chain c residue 92 MET Chi-restraints excluded: chain d residue 32 ILE Chi-restraints excluded: chain d residue 105 ASN Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 265 GLN Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 88 LEU Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 117 GLU Chi-restraints excluded: chain e residue 171 THR Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 265 GLN Chi-restraints excluded: chain e residue 270 LEU Chi-restraints excluded: chain f residue 158 VAL Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain g residue 232 VAL Chi-restraints excluded: chain g residue 268 LEU Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 255 GLN Chi-restraints excluded: chain h residue 265 GLN Chi-restraints excluded: chain h residue 266 THR Chi-restraints excluded: chain i residue 101 ASP Chi-restraints excluded: chain i residue 171 THR Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 117 GLU Chi-restraints excluded: chain k residue 135 VAL Chi-restraints excluded: chain k residue 171 THR Chi-restraints excluded: chain k residue 267 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 931 optimal weight: 0.6980 chunk 108 optimal weight: 9.9990 chunk 550 optimal weight: 6.9990 chunk 705 optimal weight: 4.9990 chunk 546 optimal weight: 0.9980 chunk 813 optimal weight: 6.9990 chunk 539 optimal weight: 2.9990 chunk 962 optimal weight: 5.9990 chunk 602 optimal weight: 3.9990 chunk 587 optimal weight: 9.9990 chunk 444 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 19 ASN ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 29 GLN O 122 GLN P 29 GLN ** Q 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 54 GLN ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 GLN V 3 ASN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 124 GLN ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 72816 Z= 0.239 Angle : 0.521 12.302 98753 Z= 0.280 Chirality : 0.036 0.242 12802 Planarity : 0.003 0.048 12617 Dihedral : 3.958 23.447 10064 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.15 % Allowed : 14.55 % Favored : 83.30 % 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: 3.49 (0.08), residues: 9916 helix: 3.18 (0.06), residues: 7363 sheet: -2.32 (0.25), residues: 370 loop : -0.02 (0.14), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP T 48 HIS 0.005 0.001 HIS U 213 PHE 0.026 0.002 PHE W 216 ARG 0.009 0.001 ARG a 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1197 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1025 time to evaluate : 6.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 210 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8061 (mp) REVERT: F 242 LYS cc_start: 0.8284 (tttt) cc_final: 0.8017 (mtpp) REVERT: G 8 ASN cc_start: 0.8391 (p0) cc_final: 0.8090 (p0) REVERT: G 50 MET cc_start: 0.9138 (mtp) cc_final: 0.8772 (mtp) REVERT: G 267 ILE cc_start: 0.8674 (mm) cc_final: 0.8340 (mm) REVERT: H 242 LYS cc_start: 0.8753 (tppt) cc_final: 0.8428 (tppt) REVERT: I 97 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8168 (tt) REVERT: I 151 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6840 (tp30) REVERT: K 31 ARG cc_start: 0.8518 (ttm-80) cc_final: 0.8196 (ttm-80) REVERT: K 83 ASP cc_start: 0.7133 (m-30) cc_final: 0.6905 (m-30) REVERT: K 94 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: K 252 LEU cc_start: 0.8749 (mm) cc_final: 0.8068 (tt) REVERT: L 87 ASP cc_start: 0.8328 (m-30) cc_final: 0.8072 (m-30) REVERT: L 219 LYS cc_start: 0.7785 (mttp) cc_final: 0.7269 (tppt) REVERT: M 161 GLN cc_start: 0.8070 (mp10) cc_final: 0.7691 (mp10) REVERT: O 94 GLU cc_start: 0.6029 (mm-30) cc_final: 0.5241 (tt0) REVERT: O 161 GLN cc_start: 0.8285 (mm-40) cc_final: 0.7501 (mm-40) REVERT: P 201 SER cc_start: 0.9272 (t) cc_final: 0.9053 (p) REVERT: P 262 GLN cc_start: 0.8627 (mp10) cc_final: 0.8234 (mp10) REVERT: R 94 GLU cc_start: 0.5657 (mm-30) cc_final: 0.4804 (mt-10) REVERT: S 122 GLN cc_start: 0.8798 (mt0) cc_final: 0.7965 (tp-100) REVERT: T 210 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8293 (mp) REVERT: U 32 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7232 (mp) REVERT: U 94 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: V 5 ILE cc_start: 0.8504 (tp) cc_final: 0.8101 (tp) REVERT: W 238 LYS cc_start: 0.6834 (mtpt) cc_final: 0.6283 (mptt) REVERT: X 42 LYS cc_start: 0.5475 (tptt) cc_final: 0.4886 (tppt) REVERT: X 175 THR cc_start: 0.8903 (t) cc_final: 0.8500 (m) REVERT: Y 94 GLU cc_start: 0.7335 (mp0) cc_final: 0.6852 (tt0) REVERT: Z 37 LYS cc_start: 0.7730 (mmtt) cc_final: 0.7095 (mptt) REVERT: Z 251 GLN cc_start: 0.8233 (mp10) cc_final: 0.7694 (mp10) REVERT: b 101 ASP cc_start: 0.8014 (t0) cc_final: 0.7709 (t70) REVERT: b 185 MET cc_start: 0.7554 (tpt) cc_final: 0.7265 (tpp) REVERT: e 88 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8200 (tt) REVERT: e 244 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8363 (mt0) REVERT: f 133 ASN cc_start: 0.8314 (t0) cc_final: 0.8074 (t0) REVERT: g 251 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8311 (mp10) REVERT: h 53 MET cc_start: 0.8379 (mmm) cc_final: 0.8155 (mmt) REVERT: h 255 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6844 (mp10) REVERT: i 54 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.7972 (mm110) REVERT: i 185 MET cc_start: 0.8099 (tpp) cc_final: 0.7729 (tpp) REVERT: j 2 LEU cc_start: 0.8798 (mp) cc_final: 0.8133 (tt) REVERT: j 115 ASP cc_start: 0.8667 (t70) cc_final: 0.8104 (t0) REVERT: j 262 GLN cc_start: 0.7956 (mt0) cc_final: 0.7629 (tm-30) REVERT: k 94 GLU cc_start: 0.9021 (tp30) cc_final: 0.8659 (tp30) REVERT: k 117 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8032 (mt-10) outliers start: 172 outliers final: 135 residues processed: 1141 average time/residue: 0.5784 time to fit residues: 1184.8389 Evaluate side-chains 1125 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 978 time to evaluate : 6.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 250 GLN Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 202 SER Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 159 THR Chi-restraints excluded: chain O residue 245 SER Chi-restraints excluded: chain P residue 83 ASP Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain P residue 177 THR Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 210 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 207 SER Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 52 LYS Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain T residue 158 VAL Chi-restraints excluded: chain T residue 210 LEU Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 94 GLU Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain U residue 146 SER Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain W residue 15 LEU Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 150 ASN Chi-restraints excluded: chain Y residue 170 LEU Chi-restraints excluded: chain Y residue 173 THR Chi-restraints excluded: chain Y residue 252 LEU Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain Z residue 104 LEU Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 200 LEU Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain Z residue 244 GLN Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 115 ASP Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain a residue 261 ASN Chi-restraints excluded: chain a residue 263 THR Chi-restraints excluded: chain b residue 32 ILE Chi-restraints excluded: chain b residue 116 PHE Chi-restraints excluded: chain b residue 252 LEU Chi-restraints excluded: chain c residue 92 MET Chi-restraints excluded: chain c residue 212 THR Chi-restraints excluded: chain c residue 263 THR Chi-restraints excluded: chain d residue 32 ILE Chi-restraints excluded: chain d residue 105 ASN Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 265 GLN Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 88 LEU Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 117 GLU Chi-restraints excluded: chain e residue 168 ILE Chi-restraints excluded: chain e residue 171 THR Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain e residue 195 THR Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 244 GLN Chi-restraints excluded: chain e residue 265 GLN Chi-restraints excluded: chain e residue 270 LEU Chi-restraints excluded: chain f residue 158 VAL Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain g residue 232 VAL Chi-restraints excluded: chain g residue 268 LEU Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 135 VAL Chi-restraints excluded: chain h residue 255 GLN Chi-restraints excluded: chain h residue 265 GLN Chi-restraints excluded: chain h residue 266 THR Chi-restraints excluded: chain i residue 54 GLN Chi-restraints excluded: chain i residue 101 ASP Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain i residue 269 SER Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 117 GLU Chi-restraints excluded: chain k residue 135 VAL Chi-restraints excluded: chain k residue 171 THR Chi-restraints excluded: chain k residue 267 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 595 optimal weight: 7.9990 chunk 384 optimal weight: 0.9980 chunk 575 optimal weight: 3.9990 chunk 290 optimal weight: 5.9990 chunk 189 optimal weight: 20.0000 chunk 186 optimal weight: 3.9990 chunk 612 optimal weight: 2.9990 chunk 656 optimal weight: 6.9990 chunk 476 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 756 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 247 GLN ** J 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 ASN N 29 GLN ** N 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 262 GLN ** P 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 54 GLN ** S 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 GLN V 3 ASN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 40 ASN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 124 GLN ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 72816 Z= 0.243 Angle : 0.528 13.676 98753 Z= 0.284 Chirality : 0.036 0.301 12802 Planarity : 0.003 0.047 12617 Dihedral : 3.974 23.321 10064 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.15 % Allowed : 14.98 % Favored : 82.87 % 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: 3.44 (0.08), residues: 9916 helix: 3.16 (0.06), residues: 7363 sheet: -2.30 (0.25), residues: 370 loop : -0.10 (0.14), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP T 48 HIS 0.005 0.001 HIS U 213 PHE 0.027 0.002 PHE W 216 ARG 0.009 0.001 ARG a 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19832 Ramachandran restraints generated. 9916 Oldfield, 0 Emsley, 9916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1170 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 998 time to evaluate : 6.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 210 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8061 (mp) REVERT: F 242 LYS cc_start: 0.8327 (tttt) cc_final: 0.8046 (mtpp) REVERT: G 8 ASN cc_start: 0.8385 (p0) cc_final: 0.8081 (p0) REVERT: G 50 MET cc_start: 0.9138 (mtp) cc_final: 0.8774 (mtp) REVERT: H 242 LYS cc_start: 0.8717 (tppt) cc_final: 0.8436 (tppt) REVERT: I 97 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8171 (tt) REVERT: I 151 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6803 (tp30) REVERT: K 31 ARG cc_start: 0.8523 (ttm-80) cc_final: 0.8194 (ttm-80) REVERT: K 83 ASP cc_start: 0.7108 (m-30) cc_final: 0.6852 (m-30) REVERT: K 94 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7810 (mp0) REVERT: K 252 LEU cc_start: 0.8751 (mm) cc_final: 0.8066 (tt) REVERT: L 87 ASP cc_start: 0.8331 (m-30) cc_final: 0.8073 (m-30) REVERT: L 219 LYS cc_start: 0.7782 (mttp) cc_final: 0.7251 (tppt) REVERT: M 161 GLN cc_start: 0.8084 (mp10) cc_final: 0.7686 (mp10) REVERT: O 94 GLU cc_start: 0.6036 (mm-30) cc_final: 0.5256 (tt0) REVERT: O 161 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7501 (mm-40) REVERT: P 201 SER cc_start: 0.9272 (t) cc_final: 0.9054 (p) REVERT: P 262 GLN cc_start: 0.8623 (mp10) cc_final: 0.8213 (mp10) REVERT: R 94 GLU cc_start: 0.5671 (mm-30) cc_final: 0.4825 (mt-10) REVERT: S 122 GLN cc_start: 0.8785 (mt0) cc_final: 0.7960 (tp-100) REVERT: T 210 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8298 (mp) REVERT: U 32 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7202 (mp) REVERT: U 94 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7865 (mt-10) REVERT: U 151 GLU cc_start: 0.6062 (tp30) cc_final: 0.5666 (tm-30) REVERT: W 238 LYS cc_start: 0.6626 (mtpt) cc_final: 0.6072 (mptt) REVERT: X 42 LYS cc_start: 0.5478 (tptt) cc_final: 0.4840 (tppt) REVERT: X 175 THR cc_start: 0.8918 (t) cc_final: 0.8501 (m) REVERT: Y 94 GLU cc_start: 0.7351 (mp0) cc_final: 0.6831 (tt0) REVERT: Z 37 LYS cc_start: 0.7736 (mmtt) cc_final: 0.7087 (mptt) REVERT: Z 251 GLN cc_start: 0.8234 (mp10) cc_final: 0.7711 (mp10) REVERT: b 101 ASP cc_start: 0.8063 (t0) cc_final: 0.7761 (t70) REVERT: b 185 MET cc_start: 0.7564 (tpt) cc_final: 0.7266 (tpp) REVERT: e 88 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8218 (tt) REVERT: e 244 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8369 (mt0) REVERT: f 133 ASN cc_start: 0.8321 (t0) cc_final: 0.8100 (t0) REVERT: g 251 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8313 (mp10) REVERT: h 53 MET cc_start: 0.8367 (mmm) cc_final: 0.8159 (mmt) REVERT: h 255 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.6843 (mp10) REVERT: i 54 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.7975 (mm110) REVERT: i 185 MET cc_start: 0.8099 (tpp) cc_final: 0.7725 (tpp) REVERT: j 2 LEU cc_start: 0.8797 (mp) cc_final: 0.8181 (tt) REVERT: j 115 ASP cc_start: 0.8667 (t70) cc_final: 0.8104 (t0) REVERT: j 262 GLN cc_start: 0.7986 (mt0) cc_final: 0.7622 (tm-30) REVERT: k 94 GLU cc_start: 0.9020 (tp30) cc_final: 0.8713 (tp30) REVERT: k 117 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8057 (mt-10) outliers start: 172 outliers final: 137 residues processed: 1115 average time/residue: 0.5826 time to fit residues: 1167.7260 Evaluate side-chains 1112 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 963 time to evaluate : 5.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 250 GLN Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 202 SER Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 159 THR Chi-restraints excluded: chain O residue 245 SER Chi-restraints excluded: chain P residue 83 ASP Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain P residue 177 THR Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 210 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 207 SER Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 52 LYS Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain T residue 158 VAL Chi-restraints excluded: chain T residue 210 LEU Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 94 GLU Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain U residue 146 SER Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 92 MET Chi-restraints excluded: chain W residue 15 LEU Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 150 ASN Chi-restraints excluded: chain Y residue 170 LEU Chi-restraints excluded: chain Y residue 173 THR Chi-restraints excluded: chain Y residue 252 LEU Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain Z residue 104 LEU Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain Z residue 244 GLN Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 115 ASP Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain a residue 261 ASN Chi-restraints excluded: chain a residue 263 THR Chi-restraints excluded: chain b residue 32 ILE Chi-restraints excluded: chain b residue 116 PHE Chi-restraints excluded: chain c residue 92 MET Chi-restraints excluded: chain c residue 212 THR Chi-restraints excluded: chain d residue 32 ILE Chi-restraints excluded: chain d residue 105 ASN Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 265 GLN Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 88 LEU Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 117 GLU Chi-restraints excluded: chain e residue 168 ILE Chi-restraints excluded: chain e residue 171 THR Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain e residue 195 THR Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 244 GLN Chi-restraints excluded: chain e residue 265 GLN Chi-restraints excluded: chain e residue 270 LEU Chi-restraints excluded: chain f residue 158 VAL Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain g residue 232 VAL Chi-restraints excluded: chain g residue 268 LEU Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 255 GLN Chi-restraints excluded: chain h residue 265 GLN Chi-restraints excluded: chain h residue 266 THR Chi-restraints excluded: chain i residue 54 GLN Chi-restraints excluded: chain i residue 101 ASP Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain i residue 269 SER Chi-restraints excluded: chain k residue 2 LEU Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 117 GLU Chi-restraints excluded: chain k residue 135 VAL Chi-restraints excluded: chain k residue 171 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 875 optimal weight: 3.9990 chunk 922 optimal weight: 6.9990 chunk 841 optimal weight: 2.9990 chunk 897 optimal weight: 1.9990 chunk 540 optimal weight: 20.0000 chunk 390 optimal weight: 8.9990 chunk 704 optimal weight: 5.9990 chunk 275 optimal weight: 0.7980 chunk 810 optimal weight: 1.9990 chunk 848 optimal weight: 0.9980 chunk 894 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 133 ASN I 250 GLN ** J 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN N 29 GLN ** N 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 29 GLN ** Q 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 54 GLN ** S 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 GLN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 44 ASN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 161 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 72816 Z= 0.174 Angle : 0.495 13.174 98753 Z= 0.267 Chirality : 0.034 0.311 12802 Planarity : 0.003 0.054 12617 Dihedral : 3.842 21.839 10064 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.83 % Allowed : 15.50 % Favored : 82.67 % 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: 3.65 (0.09), residues: 9916 helix: 3.33 (0.06), residues: 7363 sheet: -2.19 (0.25), residues: 370 loop : -0.09 (0.14), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP T 48 HIS 0.003 0.001 HIS Q 213 PHE 0.029 0.001 PHE W 216 ARG 0.010 0.001 ARG a 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 1234 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1088 time to evaluate : 6.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 210 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8012 (mp) REVERT: G 8 ASN cc_start: 0.8220 (p0) cc_final: 0.7857 (p0) REVERT: G 50 MET cc_start: 0.9125 (mtp) cc_final: 0.8855 (mtp) REVERT: H 242 LYS cc_start: 0.8715 (tppt) cc_final: 0.8423 (tppt) REVERT: I 97 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8114 (tt) REVERT: K 31 ARG cc_start: 0.8561 (ttm-80) cc_final: 0.8254 (ttm-80) REVERT: K 83 ASP cc_start: 0.7079 (m-30) cc_final: 0.6840 (m-30) REVERT: K 94 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7817 (mp0) REVERT: K 252 LEU cc_start: 0.8746 (mm) cc_final: 0.8083 (tt) REVERT: L 87 ASP cc_start: 0.8231 (m-30) cc_final: 0.7983 (m-30) REVERT: L 219 LYS cc_start: 0.7810 (mttp) cc_final: 0.7287 (tppt) REVERT: O 94 GLU cc_start: 0.5976 (mm-30) cc_final: 0.5265 (tt0) REVERT: O 161 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7499 (mm-40) REVERT: P 201 SER cc_start: 0.9253 (t) cc_final: 0.9032 (p) REVERT: P 259 ILE cc_start: 0.8982 (mt) cc_final: 0.8617 (mp) REVERT: P 262 GLN cc_start: 0.8578 (mp10) cc_final: 0.8165 (mp10) REVERT: Q 94 GLU cc_start: 0.7955 (tp30) cc_final: 0.7541 (tp30) REVERT: Q 175 THR cc_start: 0.7854 (t) cc_final: 0.7637 (m) REVERT: R 94 GLU cc_start: 0.5620 (mm-30) cc_final: 0.4755 (mt-10) REVERT: S 122 GLN cc_start: 0.8783 (mt0) cc_final: 0.7996 (tp-100) REVERT: S 258 SER cc_start: 0.8680 (t) cc_final: 0.8318 (p) REVERT: T 210 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8258 (mp) REVERT: U 32 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.7135 (mp) REVERT: U 94 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: U 151 GLU cc_start: 0.5742 (tp30) cc_final: 0.5415 (tm-30) REVERT: X 42 LYS cc_start: 0.5449 (tptt) cc_final: 0.4817 (tppt) REVERT: X 175 THR cc_start: 0.8844 (t) cc_final: 0.8483 (m) REVERT: Y 20 SER cc_start: 0.8639 (t) cc_final: 0.8202 (p) REVERT: Y 94 GLU cc_start: 0.7256 (mp0) cc_final: 0.6810 (tt0) REVERT: Z 37 LYS cc_start: 0.7653 (mmtt) cc_final: 0.7196 (mptt) REVERT: Z 251 GLN cc_start: 0.8206 (mp10) cc_final: 0.7653 (mp10) REVERT: b 101 ASP cc_start: 0.8012 (t0) cc_final: 0.7726 (t70) REVERT: b 116 PHE cc_start: 0.6945 (t80) cc_final: 0.6708 (m-80) REVERT: c 124 GLN cc_start: 0.7650 (tp-100) cc_final: 0.7354 (pt0) REVERT: e 88 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8204 (tt) REVERT: e 185 MET cc_start: 0.6829 (tpp) cc_final: 0.6625 (tpp) REVERT: f 53 MET cc_start: 0.9256 (mmm) cc_final: 0.8901 (mmm) REVERT: f 133 ASN cc_start: 0.8309 (t0) cc_final: 0.8097 (t0) REVERT: h 255 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.6882 (mp10) REVERT: i 185 MET cc_start: 0.8055 (tpp) cc_final: 0.7702 (tpp) REVERT: j 2 LEU cc_start: 0.8760 (mp) cc_final: 0.8153 (tt) REVERT: j 115 ASP cc_start: 0.8615 (t70) cc_final: 0.8079 (t0) REVERT: j 262 GLN cc_start: 0.7895 (mt0) cc_final: 0.7624 (tm-30) REVERT: k 94 GLU cc_start: 0.8959 (tp30) cc_final: 0.8716 (mm-30) REVERT: k 261 ASN cc_start: 0.8350 (m-40) cc_final: 0.8143 (m-40) outliers start: 146 outliers final: 112 residues processed: 1185 average time/residue: 0.5783 time to fit residues: 1262.4490 Evaluate side-chains 1128 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1008 time to evaluate : 5.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 250 GLN Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 159 THR Chi-restraints excluded: chain P residue 83 ASP Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain P residue 177 THR Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 210 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 207 SER Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain T residue 158 VAL Chi-restraints excluded: chain T residue 210 LEU Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 94 GLU Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain U residue 146 SER Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 92 MET Chi-restraints excluded: chain W residue 15 LEU Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 170 LEU Chi-restraints excluded: chain Y residue 173 THR Chi-restraints excluded: chain Y residue 248 THR Chi-restraints excluded: chain Y residue 252 LEU Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain Z residue 244 GLN Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 115 ASP Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain a residue 261 ASN Chi-restraints excluded: chain a residue 263 THR Chi-restraints excluded: chain b residue 32 ILE Chi-restraints excluded: chain b residue 252 LEU Chi-restraints excluded: chain c residue 92 MET Chi-restraints excluded: chain d residue 32 ILE Chi-restraints excluded: chain d residue 105 ASN Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 265 GLN Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 88 LEU Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 117 GLU Chi-restraints excluded: chain e residue 171 THR Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain e residue 195 THR Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 265 GLN Chi-restraints excluded: chain e residue 270 LEU Chi-restraints excluded: chain f residue 158 VAL Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain g residue 232 VAL Chi-restraints excluded: chain g residue 268 LEU Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 255 GLN Chi-restraints excluded: chain h residue 265 GLN Chi-restraints excluded: chain h residue 266 THR Chi-restraints excluded: chain i residue 101 ASP Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain i residue 269 SER Chi-restraints excluded: chain k residue 2 LEU Chi-restraints excluded: chain k residue 5 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 589 optimal weight: 0.9980 chunk 948 optimal weight: 6.9990 chunk 579 optimal weight: 6.9990 chunk 450 optimal weight: 0.7980 chunk 659 optimal weight: 2.9990 chunk 995 optimal weight: 2.9990 chunk 916 optimal weight: 2.9990 chunk 792 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 612 optimal weight: 1.9990 chunk 485 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 262 GLN O 122 GLN Q 29 GLN ** Q 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 155 ASN ** S 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 262 GLN ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 29 GLN ** X 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 40 ASN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 54 GLN ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 255 GLN ** k 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 72816 Z= 0.177 Angle : 0.505 13.900 98753 Z= 0.272 Chirality : 0.035 0.324 12802 Planarity : 0.003 0.065 12617 Dihedral : 3.813 21.172 10064 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.61 % Allowed : 16.20 % Favored : 82.18 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.67 (0.09), residues: 9916 helix: 3.35 (0.06), residues: 7363 sheet: -2.13 (0.25), residues: 370 loop : -0.12 (0.14), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP Z 48 HIS 0.004 0.001 HIS Q 213 PHE 0.029 0.001 PHE W 216 ARG 0.010 0.001 ARG a 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 1186 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1057 time to evaluate : 6.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 239 GLU cc_start: 0.7116 (mp0) cc_final: 0.6845 (mp0) REVERT: E 210 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8009 (mp) REVERT: F 242 LYS cc_start: 0.8733 (mtpp) cc_final: 0.8508 (mtpt) REVERT: G 8 ASN cc_start: 0.8146 (p0) cc_final: 0.7780 (p0) REVERT: G 50 MET cc_start: 0.9125 (mtp) cc_final: 0.8866 (mtp) REVERT: G 232 VAL cc_start: 0.8576 (t) cc_final: 0.8295 (p) REVERT: H 242 LYS cc_start: 0.8725 (tppt) cc_final: 0.8434 (tppt) REVERT: I 76 ASP cc_start: 0.7457 (m-30) cc_final: 0.7256 (m-30) REVERT: I 97 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8107 (tt) REVERT: K 31 ARG cc_start: 0.8573 (ttm-80) cc_final: 0.8271 (ttm-80) REVERT: K 83 ASP cc_start: 0.7081 (m-30) cc_final: 0.6839 (m-30) REVERT: K 94 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: K 252 LEU cc_start: 0.8743 (mm) cc_final: 0.8083 (tt) REVERT: L 87 ASP cc_start: 0.8190 (m-30) cc_final: 0.7938 (m-30) REVERT: L 117 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7983 (mm-30) REVERT: L 219 LYS cc_start: 0.7759 (mttp) cc_final: 0.7272 (tppt) REVERT: O 94 GLU cc_start: 0.5845 (mm-30) cc_final: 0.5207 (tt0) REVERT: O 161 GLN cc_start: 0.8282 (mm-40) cc_final: 0.7510 (mm-40) REVERT: P 259 ILE cc_start: 0.8924 (mt) cc_final: 0.8577 (mp) REVERT: P 262 GLN cc_start: 0.8543 (mp10) cc_final: 0.8115 (mp10) REVERT: Q 94 GLU cc_start: 0.7916 (tp30) cc_final: 0.7526 (tp30) REVERT: Q 117 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7226 (mm-30) REVERT: R 94 GLU cc_start: 0.5662 (mm-30) cc_final: 0.4810 (mt-10) REVERT: S 122 GLN cc_start: 0.8790 (mt0) cc_final: 0.8011 (tp-100) REVERT: T 210 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8245 (mp) REVERT: U 24 GLU cc_start: 0.7992 (tp30) cc_final: 0.7751 (mm-30) REVERT: U 32 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.7106 (mp) REVERT: U 94 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7811 (mt-10) REVERT: U 151 GLU cc_start: 0.5635 (tp30) cc_final: 0.5313 (tm-30) REVERT: V 5 ILE cc_start: 0.8433 (tp) cc_final: 0.8037 (tp) REVERT: X 42 LYS cc_start: 0.5420 (tptt) cc_final: 0.4688 (tppt) REVERT: X 175 THR cc_start: 0.8785 (t) cc_final: 0.8473 (m) REVERT: Y 94 GLU cc_start: 0.7240 (mp0) cc_final: 0.6794 (tt0) REVERT: Y 133 ASN cc_start: 0.8202 (t0) cc_final: 0.7942 (t0) REVERT: Z 37 LYS cc_start: 0.7452 (mmtt) cc_final: 0.7043 (mptt) REVERT: Z 251 GLN cc_start: 0.8192 (mp10) cc_final: 0.7638 (mp10) REVERT: a 252 LEU cc_start: 0.8510 (mm) cc_final: 0.8231 (mt) REVERT: b 101 ASP cc_start: 0.8002 (t0) cc_final: 0.7722 (t70) REVERT: c 109 PHE cc_start: 0.7955 (t80) cc_final: 0.7754 (t80) REVERT: c 124 GLN cc_start: 0.7648 (tp-100) cc_final: 0.7356 (pt0) REVERT: e 88 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8204 (tt) REVERT: e 244 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8369 (mt0) REVERT: h 53 MET cc_start: 0.6744 (mmt) cc_final: 0.6094 (mmm) REVERT: h 255 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.7000 (mp10) REVERT: i 152 ASP cc_start: 0.7783 (m-30) cc_final: 0.7525 (p0) REVERT: i 185 MET cc_start: 0.8033 (tpp) cc_final: 0.7679 (tpp) REVERT: j 2 LEU cc_start: 0.8743 (mp) cc_final: 0.8164 (tt) REVERT: j 87 ASP cc_start: 0.8816 (m-30) cc_final: 0.8595 (m-30) REVERT: j 115 ASP cc_start: 0.8613 (t70) cc_final: 0.8053 (t0) REVERT: j 262 GLN cc_start: 0.7873 (mt0) cc_final: 0.7632 (tm-30) REVERT: k 94 GLU cc_start: 0.8952 (tp30) cc_final: 0.8714 (tp30) outliers start: 129 outliers final: 107 residues processed: 1142 average time/residue: 0.5741 time to fit residues: 1181.6788 Evaluate side-chains 1128 residues out of total 7992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1012 time to evaluate : 6.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 250 GLN Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 202 SER Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 201 SER Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 159 THR Chi-restraints excluded: chain P residue 83 ASP Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 210 LEU Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain T residue 158 VAL Chi-restraints excluded: chain T residue 210 LEU Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 94 GLU Chi-restraints excluded: chain U residue 118 SER Chi-restraints excluded: chain U residue 146 SER Chi-restraints excluded: chain U residue 177 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 92 MET Chi-restraints excluded: chain W residue 15 LEU Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 150 ASN Chi-restraints excluded: chain Y residue 170 LEU Chi-restraints excluded: chain Y residue 248 THR Chi-restraints excluded: chain Y residue 252 LEU Chi-restraints excluded: chain Z residue 104 LEU Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain Z residue 244 GLN Chi-restraints excluded: chain a residue 115 ASP Chi-restraints excluded: chain a residue 261 ASN Chi-restraints excluded: chain a residue 263 THR Chi-restraints excluded: chain b residue 32 ILE Chi-restraints excluded: chain b residue 252 LEU Chi-restraints excluded: chain c residue 92 MET Chi-restraints excluded: chain d residue 32 ILE Chi-restraints excluded: chain d residue 105 ASN Chi-restraints excluded: chain d residue 159 THR Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 252 LEU Chi-restraints excluded: chain d residue 265 GLN Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 88 LEU Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 117 GLU Chi-restraints excluded: chain e residue 171 THR Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain e residue 195 THR Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 244 GLN Chi-restraints excluded: chain e residue 265 GLN Chi-restraints excluded: chain e residue 270 LEU Chi-restraints excluded: chain f residue 158 VAL Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain g residue 232 VAL Chi-restraints excluded: chain g residue 268 LEU Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 255 GLN Chi-restraints excluded: chain h residue 265 GLN Chi-restraints excluded: chain h residue 266 THR Chi-restraints excluded: chain i residue 54 GLN Chi-restraints excluded: chain i residue 101 ASP Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain i residue 269 SER Chi-restraints excluded: chain k residue 2 LEU Chi-restraints excluded: chain k residue 5 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 629 optimal weight: 0.8980 chunk 844 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 chunk 730 optimal weight: 7.9990 chunk 117 optimal weight: 0.8980 chunk 220 optimal weight: 6.9990 chunk 793 optimal weight: 0.0000 chunk 332 optimal weight: 4.9990 chunk 815 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 GLN D 29 GLN ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 262 GLN O 251 GLN Q 29 GLN Q 54 GLN Q 155 ASN ** Q 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 255 GLN ** k 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.117333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.106301 restraints weight = 143350.537| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.05 r_work: 0.3524 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 72816 Z= 0.171 Angle : 0.504 13.007 98753 Z= 0.270 Chirality : 0.035 0.360 12802 Planarity : 0.003 0.096 12617 Dihedral : 3.778 20.478 10064 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.59 % Allowed : 16.39 % Favored : 82.02 % Cbeta Deviations : 0.01 % 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: 3.72 (0.09), residues: 9916 helix: 3.39 (0.06), residues: 7363 sheet: -2.07 (0.26), residues: 370 loop : -0.14 (0.14), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP T 48 HIS 0.003 0.001 HIS Q 213 PHE 0.029 0.001 PHE W 216 ARG 0.013 0.001 ARG a 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19977.56 seconds wall clock time: 367 minutes 30.26 seconds (22050.26 seconds total)