Starting phenix.real_space_refine on Tue Aug 26 14:27:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tvr_41649/08_2025/8tvr_41649.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tvr_41649/08_2025/8tvr_41649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tvr_41649/08_2025/8tvr_41649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tvr_41649/08_2025/8tvr_41649.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tvr_41649/08_2025/8tvr_41649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tvr_41649/08_2025/8tvr_41649.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 24390 2.51 5 N 6540 2.21 5 O 7476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38532 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "B" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "C" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "S" Number of atoms: 3683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3683 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 17, 'TRANS': 453} Chain: "D" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "E" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "F" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "G" Number of atoms: 3683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3683 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 17, 'TRANS': 453} Chain: "H" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "I" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "J" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "K" Number of atoms: 3683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3683 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 17, 'TRANS': 453} Chain: "L" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "M" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "N" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "O" Number of atoms: 3683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3683 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 17, 'TRANS': 453} Chain: "P" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "Q" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "R" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "T" Number of atoms: 3683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3683 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 17, 'TRANS': 453} Chain: "V" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "W" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "X" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "Y" Number of atoms: 3683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3683 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 17, 'TRANS': 453} Time building chain proxies: 8.03, per 1000 atoms: 0.21 Number of scatterers: 38532 At special positions: 0 Unit cell: (208.681, 194.692, 121.245, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 7476 8.00 N 6540 7.00 C 24390 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: 2.78 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9120 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 114 sheets defined 7.7% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 110 through 122 removed outlier: 3.686A pdb=" N ILE A 116 " --> pdb=" O ASP A 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 110 removed outlier: 3.554A pdb=" N ASP B 110 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 122 removed outlier: 4.332A pdb=" N GLU B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 122 removed outlier: 3.641A pdb=" N GLU C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 226 through 229 Processing helix chain 'S' and resid 252 through 256 Processing helix chain 'S' and resid 273 through 282 Processing helix chain 'S' and resid 318 through 320 No H-bonds generated for 'chain 'S' and resid 318 through 320' Processing helix chain 'D' and resid 110 through 122 removed outlier: 3.594A pdb=" N ILE D 116 " --> pdb=" O ASP D 112 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS D 120 " --> pdb=" O ILE D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 110 removed outlier: 3.617A pdb=" N ASP E 110 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 122 removed outlier: 4.247A pdb=" N GLU E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 122 removed outlier: 3.660A pdb=" N GLU F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 229 Processing helix chain 'G' and resid 252 through 256 Processing helix chain 'G' and resid 273 through 282 Processing helix chain 'H' and resid 42 through 46 Processing helix chain 'H' and resid 110 through 122 removed outlier: 3.774A pdb=" N ILE H 116 " --> pdb=" O ASP H 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 46 Processing helix chain 'I' and resid 105 through 110 removed outlier: 3.655A pdb=" N ASP I 110 " --> pdb=" O LEU I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 122 removed outlier: 4.304A pdb=" N GLU I 117 " --> pdb=" O GLN I 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 122 removed outlier: 3.579A pdb=" N GLU J 117 " --> pdb=" O GLN J 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 229 removed outlier: 3.603A pdb=" N MET K 229 " --> pdb=" O PRO K 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 226 through 229' Processing helix chain 'K' and resid 252 through 256 Processing helix chain 'K' and resid 273 through 282 Processing helix chain 'L' and resid 42 through 46 Processing helix chain 'L' and resid 110 through 122 removed outlier: 3.775A pdb=" N ILE L 116 " --> pdb=" O ASP L 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 110 removed outlier: 3.654A pdb=" N ASP M 110 " --> pdb=" O LEU M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 122 removed outlier: 4.274A pdb=" N GLU M 117 " --> pdb=" O GLN M 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 113 through 122 removed outlier: 3.577A pdb=" N GLU N 117 " --> pdb=" O GLN N 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 229 removed outlier: 3.555A pdb=" N MET O 229 " --> pdb=" O PRO O 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 226 through 229' Processing helix chain 'O' and resid 252 through 256 Processing helix chain 'O' and resid 273 through 282 Processing helix chain 'P' and resid 110 through 122 removed outlier: 3.588A pdb=" N ILE P 116 " --> pdb=" O ASP P 112 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS P 120 " --> pdb=" O ILE P 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 110 removed outlier: 3.613A pdb=" N ASP Q 110 " --> pdb=" O LEU Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 113 through 120 removed outlier: 4.253A pdb=" N GLU Q 117 " --> pdb=" O GLN Q 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 122 removed outlier: 3.671A pdb=" N GLU R 117 " --> pdb=" O GLN R 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 226 through 229 Processing helix chain 'T' and resid 252 through 256 Processing helix chain 'T' and resid 273 through 282 Processing helix chain 'V' and resid 42 through 46 Processing helix chain 'V' and resid 110 through 122 removed outlier: 3.676A pdb=" N ILE V 116 " --> pdb=" O ASP V 112 " (cutoff:3.500A) Processing helix chain 'W' and resid 42 through 46 Processing helix chain 'W' and resid 105 through 110 removed outlier: 3.550A pdb=" N ASP W 110 " --> pdb=" O LEU W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 122 removed outlier: 4.257A pdb=" N GLU W 117 " --> pdb=" O GLN W 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 122 removed outlier: 3.689A pdb=" N GLU X 117 " --> pdb=" O GLN X 113 " (cutoff:3.500A) Processing helix chain 'Y' and resid 226 through 229 Processing helix chain 'Y' and resid 252 through 256 Processing helix chain 'Y' and resid 273 through 282 Processing helix chain 'Y' and resid 318 through 320 No H-bonds generated for 'chain 'Y' and resid 318 through 320' Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 9 removed outlier: 3.590A pdb=" N VAL A 8 " --> pdb=" O THR B 84 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS B 81 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL B 49 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.799A pdb=" N MET A 90 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TYR A 102 " --> pdb=" O MET A 90 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE A 92 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 61 removed outlier: 4.458A pdb=" N VAL A 49 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS A 81 " --> pdb=" O GLU A 52 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 8 " --> pdb=" O THR A 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 8 through 9 removed outlier: 4.425A pdb=" N LYS C 81 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL C 49 " --> pdb=" O ILE C 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 74 removed outlier: 4.131A pdb=" N ILE B 66 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY B 29 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N MET B 90 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR B 102 " --> pdb=" O MET B 90 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE B 92 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 73 through 74 removed outlier: 4.312A pdb=" N ILE C 66 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N HIS C 88 " --> pdb=" O ASN C 105 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASN C 105 " --> pdb=" O HIS C 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 3 through 5 Processing sheet with id=AA8, first strand: chain 'S' and resid 3 through 5 removed outlier: 7.055A pdb=" N LEU S 464 " --> pdb=" O SER S 398 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER S 398 " --> pdb=" O LEU S 464 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLY S 466 " --> pdb=" O VAL S 396 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL S 396 " --> pdb=" O GLY S 466 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN S 468 " --> pdb=" O LEU S 394 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU S 394 " --> pdb=" O GLN S 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 13 through 15 removed outlier: 3.620A pdb=" N ASP S 20 " --> pdb=" O ASP S 15 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 51 through 54 removed outlier: 6.713A pdb=" N VAL S 360 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 59 through 65 removed outlier: 3.580A pdb=" N GLY S 61 " --> pdb=" O VAL S 74 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU S 79 " --> pdb=" O VAL S 86 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER S 84 " --> pdb=" O LYS S 81 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 96 through 99 Processing sheet with id=AB4, first strand: chain 'S' and resid 141 through 147 removed outlier: 6.651A pdb=" N SER S 154 " --> pdb=" O ARG S 142 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE S 144 " --> pdb=" O ALA S 152 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA S 152 " --> pdb=" O ILE S 144 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ARG S 146 " --> pdb=" O ARG S 150 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG S 150 " --> pdb=" O ARG S 146 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N SER S 160 " --> pdb=" O LYS S 155 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 190 through 193 Processing sheet with id=AB6, first strand: chain 'S' and resid 240 through 242 removed outlier: 4.989A pdb=" N TYR S 247 " --> pdb=" O ILE S 263 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 292 through 298 removed outlier: 4.108A pdb=" N VAL S 312 " --> pdb=" O LEU S 329 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLN S 325 " --> pdb=" O ASP S 316 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP S 336 " --> pdb=" O THR S 331 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 340 through 346 removed outlier: 3.673A pdb=" N VAL S 341 " --> pdb=" O GLY S 353 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE S 343 " --> pdb=" O THR S 351 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR S 351 " --> pdb=" O PHE S 343 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR S 345 " --> pdb=" O GLN S 349 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN S 349 " --> pdb=" O TYR S 345 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 375 through 377 removed outlier: 4.285A pdb=" N ILE S 457 " --> pdb=" O ARG S 408 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ARG S 408 " --> pdb=" O ILE S 457 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 384 through 385 removed outlier: 3.567A pdb=" N PHE S 384 " --> pdb=" O ILE S 450 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE S 450 " --> pdb=" O PHE S 384 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 8 through 9 removed outlier: 3.587A pdb=" N VAL D 8 " --> pdb=" O THR E 84 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LYS E 81 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VAL E 49 " --> pdb=" O ILE E 61 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 65 through 66 removed outlier: 6.830A pdb=" N MET D 90 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR D 102 " --> pdb=" O MET D 90 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE D 92 " --> pdb=" O VAL D 100 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 58 through 61 removed outlier: 4.509A pdb=" N VAL D 49 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS D 81 " --> pdb=" O GLU D 52 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 8 through 9 removed outlier: 4.587A pdb=" N VAL F 49 " --> pdb=" O ILE F 61 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 73 through 74 removed outlier: 4.122A pdb=" N ILE E 66 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY E 29 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N MET E 90 " --> pdb=" O TYR E 102 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TYR E 102 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE E 92 " --> pdb=" O VAL E 100 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 78 through 79 removed outlier: 4.409A pdb=" N ILE F 66 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N MET F 90 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ALA F 104 " --> pdb=" O MET F 90 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE F 92 " --> pdb=" O TYR F 102 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N TYR F 102 " --> pdb=" O ILE F 92 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 3 through 5 Processing sheet with id=AC9, first strand: chain 'G' and resid 3 through 5 removed outlier: 4.291A pdb=" N CYS G 467 " --> pdb=" O GLU G 395 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU G 395 " --> pdb=" O CYS G 467 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE G 469 " --> pdb=" O ASP G 393 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASP G 393 " --> pdb=" O ILE G 469 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS G 441 " --> pdb=" O ASP G 393 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU G 395 " --> pdb=" O LEU G 439 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU G 439 " --> pdb=" O GLU G 395 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 13 through 15 removed outlier: 3.600A pdb=" N ASP G 20 " --> pdb=" O ASP G 15 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 51 through 54 removed outlier: 6.779A pdb=" N VAL G 360 " --> pdb=" O ARG G 52 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 59 through 65 removed outlier: 3.653A pdb=" N GLY G 61 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU G 79 " --> pdb=" O VAL G 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER G 84 " --> pdb=" O LYS G 81 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 96 through 99 Processing sheet with id=AD5, first strand: chain 'G' and resid 141 through 147 removed outlier: 6.603A pdb=" N SER G 154 " --> pdb=" O ARG G 142 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE G 144 " --> pdb=" O ALA G 152 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA G 152 " --> pdb=" O ILE G 144 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG G 146 " --> pdb=" O ARG G 150 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG G 150 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N SER G 160 " --> pdb=" O LYS G 155 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 190 through 193 Processing sheet with id=AD7, first strand: chain 'G' and resid 240 through 242 removed outlier: 5.011A pdb=" N TYR G 247 " --> pdb=" O ILE G 263 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 292 through 298 removed outlier: 4.083A pdb=" N VAL G 312 " --> pdb=" O LEU G 329 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLN G 325 " --> pdb=" O ASP G 316 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP G 336 " --> pdb=" O THR G 331 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 340 through 346 removed outlier: 3.571A pdb=" N VAL G 341 " --> pdb=" O GLY G 353 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE G 343 " --> pdb=" O THR G 351 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR G 351 " --> pdb=" O PHE G 343 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TYR G 345 " --> pdb=" O GLN G 349 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN G 349 " --> pdb=" O TYR G 345 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 375 through 377 removed outlier: 4.228A pdb=" N ILE G 457 " --> pdb=" O ARG G 408 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ARG G 408 " --> pdb=" O ILE G 457 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 384 through 385 removed outlier: 3.634A pdb=" N PHE G 384 " --> pdb=" O ILE G 450 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE G 450 " --> pdb=" O PHE G 384 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 8 through 9 removed outlier: 3.558A pdb=" N VAL H 8 " --> pdb=" O THR I 84 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS I 81 " --> pdb=" O GLU I 52 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL I 49 " --> pdb=" O ILE I 61 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.823A pdb=" N MET H 90 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR H 102 " --> pdb=" O MET H 90 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE H 92 " --> pdb=" O VAL H 100 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 58 through 61 removed outlier: 4.499A pdb=" N VAL H 49 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS H 81 " --> pdb=" O GLU H 52 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 8 through 9 removed outlier: 4.436A pdb=" N LYS J 81 " --> pdb=" O GLU J 52 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL J 49 " --> pdb=" O ILE J 61 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 73 through 74 removed outlier: 4.141A pdb=" N ILE I 66 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY I 29 " --> pdb=" O ILE I 67 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N MET I 90 " --> pdb=" O TYR I 102 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR I 102 " --> pdb=" O MET I 90 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE I 92 " --> pdb=" O VAL I 100 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 78 through 79 removed outlier: 4.295A pdb=" N ILE J 66 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N HIS J 88 " --> pdb=" O ASN J 105 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN J 105 " --> pdb=" O HIS J 88 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 3 through 5 Processing sheet with id=AF1, first strand: chain 'K' and resid 3 through 5 removed outlier: 6.929A pdb=" N LEU K 464 " --> pdb=" O SER K 398 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER K 398 " --> pdb=" O LEU K 464 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLY K 466 " --> pdb=" O VAL K 396 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL K 396 " --> pdb=" O GLY K 466 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN K 468 " --> pdb=" O LEU K 394 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU K 394 " --> pdb=" O GLN K 468 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 13 through 15 removed outlier: 3.662A pdb=" N ASP K 20 " --> pdb=" O ASP K 15 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 51 through 54 removed outlier: 6.747A pdb=" N VAL K 360 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 59 through 65 removed outlier: 3.619A pdb=" N GLY K 61 " --> pdb=" O VAL K 74 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU K 79 " --> pdb=" O VAL K 86 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER K 84 " --> pdb=" O LYS K 81 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 96 through 99 Processing sheet with id=AF6, first strand: chain 'K' and resid 141 through 147 removed outlier: 4.037A pdb=" N ASP K 143 " --> pdb=" O SER K 154 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N SER K 160 " --> pdb=" O LYS K 155 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 190 through 193 Processing sheet with id=AF8, first strand: chain 'K' and resid 240 through 242 removed outlier: 4.984A pdb=" N TYR K 247 " --> pdb=" O ILE K 263 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 292 through 298 removed outlier: 4.289A pdb=" N GLN K 325 " --> pdb=" O ASP K 316 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 340 through 346 removed outlier: 3.528A pdb=" N VAL K 341 " --> pdb=" O GLY K 353 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE K 343 " --> pdb=" O THR K 351 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR K 351 " --> pdb=" O PHE K 343 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TYR K 345 " --> pdb=" O GLN K 349 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLN K 349 " --> pdb=" O TYR K 345 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 375 through 378 removed outlier: 4.269A pdb=" N ILE K 457 " --> pdb=" O ARG K 408 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ARG K 408 " --> pdb=" O ILE K 457 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 384 through 385 Processing sheet with id=AG4, first strand: chain 'L' and resid 8 through 9 removed outlier: 3.563A pdb=" N VAL L 8 " --> pdb=" O THR M 84 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS M 81 " --> pdb=" O GLU M 52 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL M 49 " --> pdb=" O ILE M 61 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 65 through 67 removed outlier: 6.817A pdb=" N MET L 90 " --> pdb=" O TYR L 102 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR L 102 " --> pdb=" O MET L 90 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE L 92 " --> pdb=" O VAL L 100 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 58 through 61 removed outlier: 4.496A pdb=" N VAL L 49 " --> pdb=" O ILE L 61 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS L 81 " --> pdb=" O GLU L 52 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 8 through 9 removed outlier: 4.429A pdb=" N LYS N 81 " --> pdb=" O GLU N 52 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL N 49 " --> pdb=" O ILE N 61 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 73 through 74 removed outlier: 4.138A pdb=" N ILE M 66 " --> pdb=" O VAL M 74 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY M 29 " --> pdb=" O ILE M 67 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N MET M 90 " --> pdb=" O TYR M 102 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR M 102 " --> pdb=" O MET M 90 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE M 92 " --> pdb=" O VAL M 100 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 78 through 79 removed outlier: 4.293A pdb=" N ILE N 66 " --> pdb=" O VAL N 74 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS N 88 " --> pdb=" O ASN N 105 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN N 105 " --> pdb=" O HIS N 88 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'O' and resid 3 through 5 Processing sheet with id=AH2, first strand: chain 'O' and resid 3 through 5 removed outlier: 6.931A pdb=" N LEU O 464 " --> pdb=" O SER O 398 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER O 398 " --> pdb=" O LEU O 464 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY O 466 " --> pdb=" O VAL O 396 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL O 396 " --> pdb=" O GLY O 466 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN O 468 " --> pdb=" O LEU O 394 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU O 394 " --> pdb=" O GLN O 468 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'O' and resid 13 through 15 removed outlier: 3.662A pdb=" N ASP O 20 " --> pdb=" O ASP O 15 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'O' and resid 51 through 54 removed outlier: 6.735A pdb=" N VAL O 360 " --> pdb=" O ARG O 52 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 59 through 65 removed outlier: 3.617A pdb=" N GLY O 61 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU O 79 " --> pdb=" O VAL O 86 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER O 84 " --> pdb=" O LYS O 81 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 96 through 99 Processing sheet with id=AH7, first strand: chain 'O' and resid 141 through 147 removed outlier: 4.050A pdb=" N ASP O 143 " --> pdb=" O SER O 154 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N SER O 160 " --> pdb=" O LYS O 155 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'O' and resid 190 through 193 Processing sheet with id=AH9, first strand: chain 'O' and resid 240 through 242 removed outlier: 5.004A pdb=" N TYR O 247 " --> pdb=" O ILE O 263 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'O' and resid 292 through 298 removed outlier: 4.286A pdb=" N GLN O 325 " --> pdb=" O ASP O 316 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'O' and resid 340 through 346 removed outlier: 3.532A pdb=" N VAL O 341 " --> pdb=" O GLY O 353 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE O 343 " --> pdb=" O THR O 351 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR O 351 " --> pdb=" O PHE O 343 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR O 345 " --> pdb=" O GLN O 349 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLN O 349 " --> pdb=" O TYR O 345 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'O' and resid 375 through 378 removed outlier: 4.210A pdb=" N ILE O 457 " --> pdb=" O ARG O 408 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ARG O 408 " --> pdb=" O ILE O 457 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'O' and resid 384 through 385 removed outlier: 3.509A pdb=" N ILE O 450 " --> pdb=" O PHE O 384 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'P' and resid 8 through 9 removed outlier: 3.586A pdb=" N VAL P 8 " --> pdb=" O THR Q 84 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS Q 81 " --> pdb=" O GLU Q 52 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL Q 49 " --> pdb=" O ILE Q 61 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'P' and resid 65 through 66 removed outlier: 6.826A pdb=" N MET P 90 " --> pdb=" O TYR P 102 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR P 102 " --> pdb=" O MET P 90 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE P 92 " --> pdb=" O VAL P 100 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'P' and resid 58 through 61 removed outlier: 4.515A pdb=" N VAL P 49 " --> pdb=" O ILE P 61 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS P 81 " --> pdb=" O GLU P 52 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'Q' and resid 8 through 9 removed outlier: 4.584A pdb=" N VAL R 49 " --> pdb=" O ILE R 61 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'Q' and resid 73 through 74 removed outlier: 4.125A pdb=" N ILE Q 66 " --> pdb=" O VAL Q 74 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY Q 29 " --> pdb=" O ILE Q 67 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N MET Q 90 " --> pdb=" O TYR Q 102 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR Q 102 " --> pdb=" O MET Q 90 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE Q 92 " --> pdb=" O VAL Q 100 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'R' and resid 78 through 79 removed outlier: 4.410A pdb=" N ILE R 66 " --> pdb=" O VAL R 74 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N HIS R 88 " --> pdb=" O ASN R 105 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN R 105 " --> pdb=" O HIS R 88 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'T' and resid 3 through 5 Processing sheet with id=AJ3, first strand: chain 'T' and resid 3 through 5 removed outlier: 4.294A pdb=" N CYS T 467 " --> pdb=" O GLU T 395 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLU T 395 " --> pdb=" O CYS T 467 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE T 469 " --> pdb=" O ASP T 393 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASP T 393 " --> pdb=" O ILE T 469 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LYS T 441 " --> pdb=" O ASP T 393 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU T 395 " --> pdb=" O LEU T 439 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU T 439 " --> pdb=" O GLU T 395 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'T' and resid 13 through 15 removed outlier: 3.594A pdb=" N ASP T 20 " --> pdb=" O ASP T 15 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'T' and resid 51 through 54 removed outlier: 6.779A pdb=" N VAL T 360 " --> pdb=" O ARG T 52 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'T' and resid 59 through 65 removed outlier: 3.672A pdb=" N GLY T 61 " --> pdb=" O VAL T 74 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU T 79 " --> pdb=" O VAL T 86 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER T 84 " --> pdb=" O LYS T 81 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'T' and resid 96 through 99 Processing sheet with id=AJ8, first strand: chain 'T' and resid 141 through 147 removed outlier: 6.592A pdb=" N SER T 154 " --> pdb=" O ARG T 142 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE T 144 " --> pdb=" O ALA T 152 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA T 152 " --> pdb=" O ILE T 144 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG T 146 " --> pdb=" O ARG T 150 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG T 150 " --> pdb=" O ARG T 146 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N SER T 160 " --> pdb=" O LYS T 155 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'T' and resid 190 through 193 Processing sheet with id=AK1, first strand: chain 'T' and resid 240 through 242 removed outlier: 5.008A pdb=" N TYR T 247 " --> pdb=" O ILE T 263 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'T' and resid 292 through 298 removed outlier: 4.091A pdb=" N VAL T 312 " --> pdb=" O LEU T 329 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLN T 325 " --> pdb=" O ASP T 316 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP T 336 " --> pdb=" O THR T 331 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'T' and resid 340 through 346 removed outlier: 3.577A pdb=" N VAL T 341 " --> pdb=" O GLY T 353 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE T 343 " --> pdb=" O THR T 351 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR T 351 " --> pdb=" O PHE T 343 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TYR T 345 " --> pdb=" O GLN T 349 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN T 349 " --> pdb=" O TYR T 345 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'T' and resid 375 through 377 removed outlier: 4.225A pdb=" N ILE T 457 " --> pdb=" O ARG T 408 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ARG T 408 " --> pdb=" O ILE T 457 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'T' and resid 384 through 385 removed outlier: 3.640A pdb=" N PHE T 384 " --> pdb=" O ILE T 450 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE T 450 " --> pdb=" O PHE T 384 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'V' and resid 8 through 9 removed outlier: 3.587A pdb=" N VAL V 8 " --> pdb=" O THR W 84 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS W 81 " --> pdb=" O GLU W 52 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL W 49 " --> pdb=" O ILE W 61 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'V' and resid 65 through 66 removed outlier: 6.802A pdb=" N MET V 90 " --> pdb=" O TYR V 102 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR V 102 " --> pdb=" O MET V 90 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE V 92 " --> pdb=" O VAL V 100 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'V' and resid 58 through 61 removed outlier: 4.460A pdb=" N VAL V 49 " --> pdb=" O ILE V 61 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS V 81 " --> pdb=" O GLU V 52 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL X 8 " --> pdb=" O THR V 84 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'W' and resid 8 through 9 removed outlier: 4.396A pdb=" N LYS X 81 " --> pdb=" O GLU X 52 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL X 49 " --> pdb=" O ILE X 61 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'W' and resid 73 through 74 removed outlier: 4.132A pdb=" N ILE W 66 " --> pdb=" O VAL W 74 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY W 29 " --> pdb=" O ILE W 67 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N MET W 90 " --> pdb=" O TYR W 102 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR W 102 " --> pdb=" O MET W 90 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE W 92 " --> pdb=" O VAL W 100 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'X' and resid 73 through 74 removed outlier: 4.312A pdb=" N ILE X 66 " --> pdb=" O VAL X 74 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N HIS X 88 " --> pdb=" O ASN X 105 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN X 105 " --> pdb=" O HIS X 88 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'Y' and resid 3 through 5 Processing sheet with id=AL4, first strand: chain 'Y' and resid 3 through 5 removed outlier: 7.045A pdb=" N LEU Y 464 " --> pdb=" O SER Y 398 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER Y 398 " --> pdb=" O LEU Y 464 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLY Y 466 " --> pdb=" O VAL Y 396 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL Y 396 " --> pdb=" O GLY Y 466 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLN Y 468 " --> pdb=" O LEU Y 394 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU Y 394 " --> pdb=" O GLN Y 468 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'Y' and resid 11 through 15 removed outlier: 3.616A pdb=" N ASP Y 20 " --> pdb=" O ASP Y 15 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'Y' and resid 51 through 54 removed outlier: 6.714A pdb=" N VAL Y 360 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'Y' and resid 59 through 65 removed outlier: 3.579A pdb=" N GLY Y 61 " --> pdb=" O VAL Y 74 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU Y 79 " --> pdb=" O VAL Y 86 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER Y 84 " --> pdb=" O LYS Y 81 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'Y' and resid 96 through 99 Processing sheet with id=AL9, first strand: chain 'Y' and resid 141 through 147 removed outlier: 6.632A pdb=" N SER Y 154 " --> pdb=" O ARG Y 142 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE Y 144 " --> pdb=" O ALA Y 152 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ALA Y 152 " --> pdb=" O ILE Y 144 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG Y 146 " --> pdb=" O ARG Y 150 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ARG Y 150 " --> pdb=" O ARG Y 146 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER Y 160 " --> pdb=" O LYS Y 155 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'Y' and resid 190 through 193 Processing sheet with id=AM2, first strand: chain 'Y' and resid 240 through 242 removed outlier: 5.000A pdb=" N TYR Y 247 " --> pdb=" O ILE Y 263 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'Y' and resid 292 through 298 removed outlier: 4.100A pdb=" N VAL Y 312 " --> pdb=" O LEU Y 329 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLN Y 325 " --> pdb=" O ASP Y 316 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP Y 336 " --> pdb=" O THR Y 331 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'Y' and resid 340 through 346 removed outlier: 3.677A pdb=" N VAL Y 341 " --> pdb=" O GLY Y 353 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE Y 343 " --> pdb=" O THR Y 351 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR Y 351 " --> pdb=" O PHE Y 343 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR Y 345 " --> pdb=" O GLN Y 349 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN Y 349 " --> pdb=" O TYR Y 345 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'Y' and resid 375 through 378 removed outlier: 4.235A pdb=" N ILE Y 457 " --> pdb=" O ARG Y 408 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ARG Y 408 " --> pdb=" O ILE Y 457 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'Y' and resid 384 through 385 removed outlier: 3.613A pdb=" N PHE Y 384 " --> pdb=" O ILE Y 450 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE Y 450 " --> pdb=" O PHE Y 384 " (cutoff:3.500A) 1093 hydrogen bonds defined for protein. 2712 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: 10.02 Time building geometry restraints manager: 3.65 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: 7970 1.33 - 1.45: 9254 1.45 - 1.57: 21908 1.57 - 1.69: 0 1.69 - 1.81: 210 Bond restraints: 39342 Sorted by residual: bond pdb=" C PRO G 185 " pdb=" O PRO G 185 " ideal model delta sigma weight residual 1.238 1.208 0.030 1.37e-02 5.33e+03 4.94e+00 bond pdb=" N SER C 57 " pdb=" CA SER C 57 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.28e+00 bond pdb=" N SER X 57 " pdb=" CA SER X 57 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 4.16e+00 bond pdb=" N SER N 57 " pdb=" CA SER N 57 " ideal model delta sigma weight residual 1.458 1.483 -0.025 1.30e-02 5.92e+03 3.65e+00 bond pdb=" N SER J 57 " pdb=" CA SER J 57 " ideal model delta sigma weight residual 1.458 1.482 -0.024 1.30e-02 5.92e+03 3.39e+00 ... (remaining 39337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 52633 1.76 - 3.52: 734 3.52 - 5.28: 61 5.28 - 7.04: 11 7.04 - 8.80: 3 Bond angle restraints: 53442 Sorted by residual: angle pdb=" C ALA Y 181 " pdb=" N GLU Y 182 " pdb=" CA GLU Y 182 " ideal model delta sigma weight residual 121.54 128.39 -6.85 1.91e+00 2.74e-01 1.28e+01 angle pdb=" C GLU S 286 " pdb=" N GLU S 287 " pdb=" CA GLU S 287 " ideal model delta sigma weight residual 121.54 127.88 -6.34 1.91e+00 2.74e-01 1.10e+01 angle pdb=" C GLU G 286 " pdb=" N GLU G 287 " pdb=" CA GLU G 287 " ideal model delta sigma weight residual 121.54 127.84 -6.30 1.91e+00 2.74e-01 1.09e+01 angle pdb=" C GLU T 286 " pdb=" N GLU T 287 " pdb=" CA GLU T 287 " ideal model delta sigma weight residual 121.54 127.83 -6.29 1.91e+00 2.74e-01 1.08e+01 angle pdb=" C GLU Y 286 " pdb=" N GLU Y 287 " pdb=" CA GLU Y 287 " ideal model delta sigma weight residual 121.54 127.78 -6.24 1.91e+00 2.74e-01 1.07e+01 ... (remaining 53437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 20684 17.83 - 35.65: 2090 35.65 - 53.48: 591 53.48 - 71.30: 101 71.30 - 89.13: 48 Dihedral angle restraints: 23514 sinusoidal: 9180 harmonic: 14334 Sorted by residual: dihedral pdb=" CA THR O 458 " pdb=" C THR O 458 " pdb=" N LYS O 459 " pdb=" CA LYS O 459 " ideal model delta harmonic sigma weight residual 180.00 160.78 19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ALA Y 285 " pdb=" C ALA Y 285 " pdb=" N GLU Y 286 " pdb=" CA GLU Y 286 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ALA S 285 " pdb=" C ALA S 285 " pdb=" N GLU S 286 " pdb=" CA GLU S 286 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 23511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3700 0.038 - 0.075: 1343 0.075 - 0.113: 722 0.113 - 0.150: 161 0.150 - 0.188: 8 Chirality restraints: 5934 Sorted by residual: chirality pdb=" CB ILE O 188 " pdb=" CA ILE O 188 " pdb=" CG1 ILE O 188 " pdb=" CG2 ILE O 188 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CB ILE S 188 " pdb=" CA ILE S 188 " pdb=" CG1 ILE S 188 " pdb=" CG2 ILE S 188 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CB ILE Y 188 " pdb=" CA ILE Y 188 " pdb=" CG1 ILE Y 188 " pdb=" CG2 ILE Y 188 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.02e-01 ... (remaining 5931 not shown) Planarity restraints: 6996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN K 184 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO K 185 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO K 185 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO K 185 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN O 184 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO O 185 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO O 185 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO O 185 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 184 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" C GLN G 184 " 0.028 2.00e-02 2.50e+03 pdb=" O GLN G 184 " -0.010 2.00e-02 2.50e+03 pdb=" N PRO G 185 " -0.009 2.00e-02 2.50e+03 ... (remaining 6993 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2534 2.74 - 3.28: 36430 3.28 - 3.82: 65330 3.82 - 4.36: 85229 4.36 - 4.90: 144912 Nonbonded interactions: 334435 Sorted by model distance: nonbonded pdb=" OD2 ASP E 112 " pdb=" OG SER E 115 " model vdw 2.196 3.040 nonbonded pdb=" OD1 ASN F 53 " pdb=" OG SER F 57 " model vdw 2.197 3.040 nonbonded pdb=" NH2 ARG K 73 " pdb=" O ASP K 342 " model vdw 2.198 3.120 nonbonded pdb=" OD1 ASN R 53 " pdb=" OG SER R 57 " model vdw 2.199 3.040 nonbonded pdb=" NH2 ARG O 73 " pdb=" O ASP O 342 " model vdw 2.200 3.120 ... (remaining 334430 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 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'S' selection = chain 'T' selection = chain 'Y' } 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: 7.570 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: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 33.870 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 0.030 39342 Z= 0.124 Angle : 0.534 8.803 53442 Z= 0.298 Chirality : 0.050 0.188 5934 Planarity : 0.004 0.043 6996 Dihedral : 16.183 89.129 14394 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.72 % Allowed : 11.86 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.11), residues: 4902 helix: 0.20 (0.35), residues: 228 sheet: -0.50 (0.12), residues: 1548 loop : -0.97 (0.11), residues: 3126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 148 TYR 0.015 0.001 TYR S 80 PHE 0.012 0.001 PHE Y 384 TRP 0.012 0.001 TRP G 161 HIS 0.003 0.001 HIS M 88 Details of bonding type rmsd covalent geometry : bond 0.00256 (39342) covalent geometry : angle 0.53442 (53442) hydrogen bonds : bond 0.12446 ( 1081) hydrogen bonds : angle 6.87445 ( 2712) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 4182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 509 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8884 (pttp) cc_final: 0.8468 (pttt) REVERT: B 54 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7464 (tm-30) REVERT: C 28 ASN cc_start: 0.8512 (m110) cc_final: 0.8236 (m-40) REVERT: S 267 GLN cc_start: 0.7931 (pt0) cc_final: 0.7695 (pp30) REVERT: S 357 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: E 52 GLU cc_start: 0.7966 (tt0) cc_final: 0.7634 (tp30) REVERT: G 245 ASP cc_start: 0.7159 (m-30) cc_final: 0.6817 (m-30) REVERT: G 294 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8422 (pt0) REVERT: K 390 ARG cc_start: 0.6598 (tpt-90) cc_final: 0.6289 (tpt-90) REVERT: T 245 ASP cc_start: 0.7180 (m-30) cc_final: 0.6779 (m-30) REVERT: X 28 ASN cc_start: 0.8484 (m110) cc_final: 0.8207 (m-40) REVERT: Y 267 GLN cc_start: 0.8158 (pt0) cc_final: 0.7917 (pp30) REVERT: Y 357 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: Y 404 GLN cc_start: 0.8035 (pm20) cc_final: 0.7621 (mp10) outliers start: 72 outliers final: 49 residues processed: 573 average time/residue: 0.6396 time to fit residues: 440.3923 Evaluate side-chains 541 residues out of total 4182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 489 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 196 ASP Chi-restraints excluded: chain S residue 227 SER Chi-restraints excluded: chain S residue 269 SER Chi-restraints excluded: chain S residue 357 GLU Chi-restraints excluded: chain S residue 360 VAL Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 294 GLU Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 227 SER Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 269 SER Chi-restraints excluded: chain K residue 337 VAL Chi-restraints excluded: chain K residue 394 LEU Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 241 THR Chi-restraints excluded: chain O residue 269 SER Chi-restraints excluded: chain O residue 271 ILE Chi-restraints excluded: chain O residue 337 VAL Chi-restraints excluded: chain O residue 394 LEU Chi-restraints excluded: chain O residue 458 THR Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 174 ARG Chi-restraints excluded: chain T residue 271 ILE Chi-restraints excluded: chain T residue 337 VAL Chi-restraints excluded: chain T residue 360 VAL Chi-restraints excluded: chain W residue 62 THR Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain Y residue 54 ASP Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 196 ASP Chi-restraints excluded: chain Y residue 227 SER Chi-restraints excluded: chain Y residue 269 SER Chi-restraints excluded: chain Y residue 357 GLU Chi-restraints excluded: chain Y residue 360 VAL Chi-restraints excluded: chain Y residue 395 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 470 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 GLN B 99 GLN D 45 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN E 42 ASN G 184 GLN G 231 GLN H 45 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 GLN J 68 ASN J 78 GLN L 45 ASN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 63 GLN N 68 ASN N 78 GLN O 231 GLN P 45 ASN ** P 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 GLN Q 42 ASN T 231 GLN V 45 ASN ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 99 GLN Y 225 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.123366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.112618 restraints weight = 42804.599| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 0.61 r_work: 0.3004 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 39342 Z= 0.351 Angle : 0.785 8.630 53442 Z= 0.429 Chirality : 0.060 0.235 5934 Planarity : 0.007 0.079 6996 Dihedral : 7.522 88.187 5496 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.47 % Allowed : 13.53 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.11), residues: 4902 helix: -0.47 (0.33), residues: 264 sheet: -0.52 (0.12), residues: 1512 loop : -1.22 (0.10), residues: 3126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG W 14 TYR 0.016 0.003 TYR N 102 PHE 0.020 0.003 PHE O 384 TRP 0.018 0.003 TRP G 326 HIS 0.008 0.002 HIS O 252 Details of bonding type rmsd covalent geometry : bond 0.00843 (39342) covalent geometry : angle 0.78532 (53442) hydrogen bonds : bond 0.04809 ( 1081) hydrogen bonds : angle 6.45787 ( 2712) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 4182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 495 time to evaluate : 0.973 Fit side-chains REVERT: A 24 LYS cc_start: 0.8939 (pttp) cc_final: 0.8509 (pttt) REVERT: B 54 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7439 (tm-30) REVERT: S 12 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8204 (tpp) REVERT: S 241 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8538 (p) REVERT: S 357 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: S 395 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7007 (tt0) REVERT: G 167 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7659 (pm20) REVERT: G 294 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8432 (pt0) REVERT: G 395 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7414 (mm-30) REVERT: I 108 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8458 (mtpt) REVERT: K 37 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7228 (pp) REVERT: M 108 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8374 (mtpt) REVERT: M 112 ASP cc_start: 0.8770 (t0) cc_final: 0.8530 (t0) REVERT: O 37 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7280 (pp) REVERT: O 373 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8293 (mmmm) REVERT: O 407 ASP cc_start: 0.7976 (m-30) cc_final: 0.7758 (m-30) REVERT: P 24 LYS cc_start: 0.8754 (pttp) cc_final: 0.8403 (ptmm) REVERT: Q 119 ASP cc_start: 0.8416 (m-30) cc_final: 0.8086 (m-30) REVERT: T 37 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7580 (pp) REVERT: T 180 ARG cc_start: 0.8295 (ttt90) cc_final: 0.8090 (ttt180) REVERT: T 395 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7442 (mm-30) REVERT: Y 12 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8207 (tpp) REVERT: Y 54 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8028 (m-30) REVERT: Y 138 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7084 (mp) REVERT: Y 167 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7126 (pm20) REVERT: Y 174 ARG cc_start: 0.8263 (mtt90) cc_final: 0.7863 (mtt90) REVERT: Y 241 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8533 (p) REVERT: Y 288 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.8044 (ttm) REVERT: Y 357 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: Y 404 GLN cc_start: 0.8169 (pm20) cc_final: 0.7877 (mp10) outliers start: 187 outliers final: 108 residues processed: 628 average time/residue: 0.6255 time to fit residues: 472.7181 Evaluate side-chains 610 residues out of total 4182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 481 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain S residue 12 MET Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain S residue 137 GLU Chi-restraints excluded: chain S residue 196 ASP Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 241 THR Chi-restraints excluded: chain S residue 269 SER Chi-restraints excluded: chain S residue 271 ILE Chi-restraints excluded: chain S residue 294 GLU Chi-restraints excluded: chain S residue 357 GLU Chi-restraints excluded: chain S residue 360 VAL Chi-restraints excluded: chain S residue 395 GLU Chi-restraints excluded: chain S residue 435 ASP Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 294 GLU Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 394 LEU Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 435 ASP Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 121 LYS Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain K residue 196 ASP Chi-restraints excluded: chain K residue 240 LYS Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 269 SER Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain K residue 337 VAL Chi-restraints excluded: chain K residue 394 LEU Chi-restraints excluded: chain K residue 395 GLU Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 121 LYS Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 108 LYS Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain N residue 16 ILE Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain O residue 196 ASP Chi-restraints excluded: chain O residue 240 LYS Chi-restraints excluded: chain O residue 241 THR Chi-restraints excluded: chain O residue 269 SER Chi-restraints excluded: chain O residue 271 ILE Chi-restraints excluded: chain O residue 288 MET Chi-restraints excluded: chain O residue 337 VAL Chi-restraints excluded: chain O residue 373 LYS Chi-restraints excluded: chain O residue 395 GLU Chi-restraints excluded: chain O residue 409 LEU Chi-restraints excluded: chain O residue 458 THR Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 167 GLU Chi-restraints excluded: chain T residue 196 ASP Chi-restraints excluded: chain T residue 237 THR Chi-restraints excluded: chain T residue 269 SER Chi-restraints excluded: chain T residue 271 ILE Chi-restraints excluded: chain T residue 337 VAL Chi-restraints excluded: chain T residue 360 VAL Chi-restraints excluded: chain T residue 394 LEU Chi-restraints excluded: chain T residue 395 GLU Chi-restraints excluded: chain T residue 435 ASP Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain W residue 62 THR Chi-restraints excluded: chain X residue 20 SER Chi-restraints excluded: chain X residue 24 LYS Chi-restraints excluded: chain X residue 36 ILE Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain Y residue 12 MET Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 54 ASP Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 137 GLU Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 167 GLU Chi-restraints excluded: chain Y residue 196 ASP Chi-restraints excluded: chain Y residue 216 THR Chi-restraints excluded: chain Y residue 241 THR Chi-restraints excluded: chain Y residue 269 SER Chi-restraints excluded: chain Y residue 271 ILE Chi-restraints excluded: chain Y residue 288 MET Chi-restraints excluded: chain Y residue 294 GLU Chi-restraints excluded: chain Y residue 357 GLU Chi-restraints excluded: chain Y residue 360 VAL Chi-restraints excluded: chain Y residue 395 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 213 optimal weight: 0.6980 chunk 254 optimal weight: 0.0970 chunk 331 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 chunk 455 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 459 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 338 optimal weight: 1.9990 chunk 394 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN S 225 GLN S 267 GLN S 404 GLN D 45 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN G 5 GLN G 184 GLN H 45 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 68 ASN K 349 GLN L 45 ASN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN O 349 GLN P 45 ASN ** P 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 GLN R 76 ASN V 45 ASN ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 225 GLN Y 267 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.128806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.118460 restraints weight = 42064.958| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 0.60 r_work: 0.3092 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 39342 Z= 0.135 Angle : 0.546 6.011 53442 Z= 0.301 Chirality : 0.050 0.185 5934 Planarity : 0.004 0.053 6996 Dihedral : 6.332 58.018 5478 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.30 % Allowed : 15.69 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.11), residues: 4902 helix: -0.35 (0.33), residues: 264 sheet: -0.44 (0.13), residues: 1410 loop : -1.03 (0.10), residues: 3228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 148 TYR 0.012 0.001 TYR F 114 PHE 0.018 0.002 PHE K 384 TRP 0.012 0.002 TRP G 161 HIS 0.004 0.001 HIS I 88 Details of bonding type rmsd covalent geometry : bond 0.00303 (39342) covalent geometry : angle 0.54599 (53442) hydrogen bonds : bond 0.03568 ( 1081) hydrogen bonds : angle 5.94840 ( 2712) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 4182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 517 time to evaluate : 1.322 Fit side-chains REVERT: A 24 LYS cc_start: 0.8913 (pttp) cc_final: 0.8512 (pttp) REVERT: S 54 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7904 (m-30) REVERT: S 357 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7992 (mp0) REVERT: D 24 LYS cc_start: 0.8990 (pttp) cc_final: 0.8099 (pttp) REVERT: E 119 ASP cc_start: 0.8653 (m-30) cc_final: 0.8448 (m-30) REVERT: G 167 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7465 (pm20) REVERT: G 395 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7264 (mm-30) REVERT: H 90 MET cc_start: 0.8879 (ttm) cc_final: 0.8626 (ttm) REVERT: J 24 LYS cc_start: 0.8842 (ptpp) cc_final: 0.8567 (ptpp) REVERT: K 180 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.7875 (mtp85) REVERT: K 288 MET cc_start: 0.8079 (ttm) cc_final: 0.7663 (tpt) REVERT: L 90 MET cc_start: 0.8755 (ttm) cc_final: 0.8544 (ttm) REVERT: N 24 LYS cc_start: 0.8858 (ptpp) cc_final: 0.8592 (ptpp) REVERT: O 159 ASP cc_start: 0.6753 (t0) cc_final: 0.6541 (t0) REVERT: O 288 MET cc_start: 0.8115 (ttm) cc_final: 0.7703 (tpt) REVERT: O 407 ASP cc_start: 0.7684 (m-30) cc_final: 0.7469 (m-30) REVERT: O 454 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7845 (mp) REVERT: Q 119 ASP cc_start: 0.8676 (m-30) cc_final: 0.8304 (m-30) REVERT: T 167 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: T 395 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7246 (mm-30) REVERT: Y 167 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7144 (pm20) REVERT: Y 357 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7969 (mp0) REVERT: Y 404 GLN cc_start: 0.8037 (pm20) cc_final: 0.7789 (mp10) outliers start: 138 outliers final: 75 residues processed: 620 average time/residue: 0.6522 time to fit residues: 486.7712 Evaluate side-chains 580 residues out of total 4182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 496 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 137 GLU Chi-restraints excluded: chain S residue 267 GLN Chi-restraints excluded: chain S residue 357 GLU Chi-restraints excluded: chain S residue 360 VAL Chi-restraints excluded: chain S residue 435 ASP Chi-restraints excluded: chain S residue 458 THR Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 394 LEU Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 435 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain K residue 227 SER Chi-restraints excluded: chain K residue 240 LYS Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 269 SER Chi-restraints excluded: chain K residue 337 VAL Chi-restraints excluded: chain K residue 454 LEU Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain O residue 240 LYS Chi-restraints excluded: chain O residue 241 THR Chi-restraints excluded: chain O residue 269 SER Chi-restraints excluded: chain O residue 271 ILE Chi-restraints excluded: chain O residue 337 VAL Chi-restraints excluded: chain O residue 394 LEU Chi-restraints excluded: chain O residue 409 LEU Chi-restraints excluded: chain O residue 454 LEU Chi-restraints excluded: chain O residue 458 THR Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain T residue 167 GLU Chi-restraints excluded: chain T residue 237 THR Chi-restraints excluded: chain T residue 269 SER Chi-restraints excluded: chain T residue 271 ILE Chi-restraints excluded: chain T residue 337 VAL Chi-restraints excluded: chain T residue 360 VAL Chi-restraints excluded: chain T residue 394 LEU Chi-restraints excluded: chain T residue 395 GLU Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 116 ILE Chi-restraints excluded: chain W residue 62 THR Chi-restraints excluded: chain X residue 20 SER Chi-restraints excluded: chain X residue 24 LYS Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 167 GLU Chi-restraints excluded: chain Y residue 267 GLN Chi-restraints excluded: chain Y residue 357 GLU Chi-restraints excluded: chain Y residue 360 VAL Chi-restraints excluded: chain Y residue 395 GLU Chi-restraints excluded: chain Y residue 435 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 303 optimal weight: 5.9990 chunk 471 optimal weight: 4.9990 chunk 367 optimal weight: 5.9990 chunk 337 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 318 optimal weight: 4.9990 chunk 422 optimal weight: 8.9990 chunk 308 optimal weight: 6.9990 chunk 177 optimal weight: 0.8980 chunk 301 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN S 225 GLN D 45 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN G 184 GLN H 45 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 68 ASN L 45 ASN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN P 45 ASN ** P 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN V 45 ASN ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN Y 225 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.126690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.116433 restraints weight = 42172.265| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 0.56 r_work: 0.3074 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 39342 Z= 0.182 Angle : 0.595 6.854 53442 Z= 0.326 Chirality : 0.052 0.202 5934 Planarity : 0.005 0.059 6996 Dihedral : 6.245 52.533 5463 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.92 % Allowed : 16.04 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.11), residues: 4902 helix: -0.20 (0.33), residues: 270 sheet: -0.52 (0.12), residues: 1536 loop : -1.12 (0.10), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 101 TYR 0.011 0.002 TYR O 80 PHE 0.018 0.002 PHE O 384 TRP 0.012 0.002 TRP K 161 HIS 0.005 0.001 HIS M 88 Details of bonding type rmsd covalent geometry : bond 0.00424 (39342) covalent geometry : angle 0.59497 (53442) hydrogen bonds : bond 0.03782 ( 1081) hydrogen bonds : angle 5.98973 ( 2712) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 4182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 494 time to evaluate : 1.337 Fit side-chains REVERT: A 24 LYS cc_start: 0.8910 (pttp) cc_final: 0.8475 (pttt) REVERT: S 54 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7940 (m-30) REVERT: S 294 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8325 (mt-10) REVERT: S 395 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.6852 (tt0) REVERT: D 14 ARG cc_start: 0.9291 (ttm170) cc_final: 0.8985 (tpp-160) REVERT: D 24 LYS cc_start: 0.9011 (pttp) cc_final: 0.8205 (pttp) REVERT: E 52 GLU cc_start: 0.8279 (tt0) cc_final: 0.7837 (tp30) REVERT: E 119 ASP cc_start: 0.8695 (m-30) cc_final: 0.8323 (m-30) REVERT: G 14 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7853 (mtmt) REVERT: G 138 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6715 (mp) REVERT: G 167 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7415 (pm20) REVERT: G 395 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7302 (mm-30) REVERT: H 90 MET cc_start: 0.8855 (ttm) cc_final: 0.8590 (ttm) REVERT: K 111 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8138 (mm-40) REVERT: K 180 ARG cc_start: 0.8358 (mmm-85) cc_final: 0.7902 (mtp85) REVERT: O 8 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.7341 (ptp) REVERT: O 111 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8117 (mm-40) REVERT: O 373 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8126 (mmmm) REVERT: O 407 ASP cc_start: 0.7674 (m-30) cc_final: 0.7422 (m-30) REVERT: O 454 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7910 (mp) REVERT: P 14 ARG cc_start: 0.9287 (ttm170) cc_final: 0.8991 (tpp-160) REVERT: Q 119 ASP cc_start: 0.8677 (m-30) cc_final: 0.8244 (m-30) REVERT: T 14 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7860 (mtmt) REVERT: T 167 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: T 395 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7274 (mm-30) REVERT: Y 137 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: Y 138 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6943 (mp) REVERT: Y 167 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7098 (pm20) REVERT: Y 174 ARG cc_start: 0.8145 (mtt90) cc_final: 0.7893 (mtt90) REVERT: Y 180 ARG cc_start: 0.8222 (ttt180) cc_final: 0.8003 (ttt180) REVERT: Y 294 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8284 (mt-10) REVERT: Y 404 GLN cc_start: 0.8084 (pm20) cc_final: 0.7836 (mp10) outliers start: 164 outliers final: 97 residues processed: 617 average time/residue: 0.6219 time to fit residues: 464.3404 Evaluate side-chains 594 residues out of total 4182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 478 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 137 GLU Chi-restraints excluded: chain S residue 196 ASP Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 294 GLU Chi-restraints excluded: chain S residue 360 VAL Chi-restraints excluded: chain S residue 395 GLU Chi-restraints excluded: chain S residue 435 ASP Chi-restraints excluded: chain S residue 458 THR Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 435 ASP Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 111 GLN Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain K residue 227 SER Chi-restraints excluded: chain K residue 240 LYS Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 269 SER Chi-restraints excluded: chain K residue 337 VAL Chi-restraints excluded: chain K residue 454 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain O residue 8 MET Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 111 GLN Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain O residue 240 LYS Chi-restraints excluded: chain O residue 241 THR Chi-restraints excluded: chain O residue 269 SER Chi-restraints excluded: chain O residue 271 ILE Chi-restraints excluded: chain O residue 337 VAL Chi-restraints excluded: chain O residue 373 LYS Chi-restraints excluded: chain O residue 394 LEU Chi-restraints excluded: chain O residue 409 LEU Chi-restraints excluded: chain O residue 454 LEU Chi-restraints excluded: chain O residue 458 THR Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain T residue 14 LYS Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 167 GLU Chi-restraints excluded: chain T residue 196 ASP Chi-restraints excluded: chain T residue 237 THR Chi-restraints excluded: chain T residue 269 SER Chi-restraints excluded: chain T residue 271 ILE Chi-restraints excluded: chain T residue 337 VAL Chi-restraints excluded: chain T residue 360 VAL Chi-restraints excluded: chain T residue 395 GLU Chi-restraints excluded: chain T residue 435 ASP Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 116 ILE Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 62 THR Chi-restraints excluded: chain X residue 20 SER Chi-restraints excluded: chain X residue 24 LYS Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 137 GLU Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 167 GLU Chi-restraints excluded: chain Y residue 216 THR Chi-restraints excluded: chain Y residue 294 GLU Chi-restraints excluded: chain Y residue 360 VAL Chi-restraints excluded: chain Y residue 395 GLU Chi-restraints excluded: chain Y residue 435 ASP Chi-restraints excluded: chain Y residue 458 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 55 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 227 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 452 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 246 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 350 optimal weight: 2.9990 chunk 367 optimal weight: 4.9990 chunk 327 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN S 404 GLN D 45 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN F 76 ASN H 45 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 68 ASN K 56 ASN L 45 ASN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN O 56 ASN P 45 ASN ** P 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 GLN R 76 ASN V 45 ASN ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN Y 225 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.122948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.112250 restraints weight = 42597.881| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 0.59 r_work: 0.3017 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 39342 Z= 0.335 Angle : 0.771 7.927 53442 Z= 0.421 Chirality : 0.059 0.233 5934 Planarity : 0.006 0.077 6996 Dihedral : 6.988 60.864 5456 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 5.05 % Allowed : 16.16 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.11), residues: 4902 helix: -0.39 (0.33), residues: 264 sheet: -0.62 (0.12), residues: 1512 loop : -1.32 (0.10), residues: 3126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 14 TYR 0.017 0.003 TYR I 50 PHE 0.021 0.003 PHE O 384 TRP 0.017 0.003 TRP G 326 HIS 0.008 0.002 HIS O 252 Details of bonding type rmsd covalent geometry : bond 0.00801 (39342) covalent geometry : angle 0.77076 (53442) hydrogen bonds : bond 0.04606 ( 1081) hydrogen bonds : angle 6.38609 ( 2712) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 4182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 500 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8942 (pttp) cc_final: 0.8505 (pttt) REVERT: B 54 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7561 (tm-30) REVERT: S 54 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8132 (m-30) REVERT: S 138 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7115 (mp) REVERT: S 167 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7239 (pm20) REVERT: S 294 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8188 (pt0) REVERT: S 395 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7012 (tt0) REVERT: D 24 LYS cc_start: 0.9044 (pttp) cc_final: 0.8237 (pttp) REVERT: D 54 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6076 (tp30) REVERT: E 119 ASP cc_start: 0.8720 (m-30) cc_final: 0.8273 (m-30) REVERT: G 138 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6935 (mp) REVERT: G 167 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7470 (pm20) REVERT: G 395 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7599 (mm-30) REVERT: J 52 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: J 110 ASP cc_start: 0.8279 (t0) cc_final: 0.7611 (t70) REVERT: K 111 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8186 (mm-40) REVERT: K 373 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8284 (mmtm) REVERT: N 110 ASP cc_start: 0.8287 (t0) cc_final: 0.7615 (t70) REVERT: O 8 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7381 (ptp) REVERT: O 12 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.7685 (tpt) REVERT: O 111 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8152 (mm-40) REVERT: O 138 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7174 (mp) REVERT: O 373 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8202 (mmmm) REVERT: P 24 LYS cc_start: 0.8758 (pttp) cc_final: 0.8419 (ptmm) REVERT: P 54 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.6011 (tp30) REVERT: Q 119 ASP cc_start: 0.8547 (m-30) cc_final: 0.8166 (m-30) REVERT: T 138 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6784 (mp) REVERT: T 167 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: T 395 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7570 (mm-30) REVERT: V 24 LYS cc_start: 0.8949 (pttp) cc_final: 0.8501 (pttt) REVERT: Y 54 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8108 (m-30) REVERT: Y 137 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: Y 138 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7043 (mp) REVERT: Y 142 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7815 (ttt180) REVERT: Y 167 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7112 (pm20) REVERT: Y 294 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8193 (pt0) REVERT: Y 404 GLN cc_start: 0.8160 (pm20) cc_final: 0.7926 (mp10) outliers start: 211 outliers final: 124 residues processed: 658 average time/residue: 0.6266 time to fit residues: 499.5395 Evaluate side-chains 642 residues out of total 4182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 491 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 137 GLU Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain S residue 167 GLU Chi-restraints excluded: chain S residue 174 ARG Chi-restraints excluded: chain S residue 196 ASP Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 294 GLU Chi-restraints excluded: chain S residue 360 VAL Chi-restraints excluded: chain S residue 395 GLU Chi-restraints excluded: chain S residue 435 ASP Chi-restraints excluded: chain S residue 458 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 435 ASP Chi-restraints excluded: chain G residue 458 THR Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 24 LYS Chi-restraints excluded: chain J residue 52 GLU Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 101 ARG Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 111 GLN Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain K residue 196 ASP Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 240 LYS Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 255 THR Chi-restraints excluded: chain K residue 269 SER Chi-restraints excluded: chain K residue 271 ILE Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain K residue 337 VAL Chi-restraints excluded: chain K residue 373 LYS Chi-restraints excluded: chain K residue 454 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain N residue 24 LYS Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain O residue 8 MET Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain O residue 111 GLN Chi-restraints excluded: chain O residue 116 ARG Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain O residue 196 ASP Chi-restraints excluded: chain O residue 237 THR Chi-restraints excluded: chain O residue 240 LYS Chi-restraints excluded: chain O residue 241 THR Chi-restraints excluded: chain O residue 255 THR Chi-restraints excluded: chain O residue 269 SER Chi-restraints excluded: chain O residue 271 ILE Chi-restraints excluded: chain O residue 288 MET Chi-restraints excluded: chain O residue 337 VAL Chi-restraints excluded: chain O residue 373 LYS Chi-restraints excluded: chain O residue 394 LEU Chi-restraints excluded: chain O residue 396 VAL Chi-restraints excluded: chain O residue 409 LEU Chi-restraints excluded: chain O residue 458 THR Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 167 GLU Chi-restraints excluded: chain T residue 196 ASP Chi-restraints excluded: chain T residue 237 THR Chi-restraints excluded: chain T residue 255 THR Chi-restraints excluded: chain T residue 269 SER Chi-restraints excluded: chain T residue 271 ILE Chi-restraints excluded: chain T residue 337 VAL Chi-restraints excluded: chain T residue 360 VAL Chi-restraints excluded: chain T residue 395 GLU Chi-restraints excluded: chain T residue 435 ASP Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 62 THR Chi-restraints excluded: chain X residue 20 SER Chi-restraints excluded: chain X residue 24 LYS Chi-restraints excluded: chain X residue 36 ILE Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain X residue 86 GLN Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 54 ASP Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 137 GLU Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 142 ARG Chi-restraints excluded: chain Y residue 167 GLU Chi-restraints excluded: chain Y residue 199 VAL Chi-restraints excluded: chain Y residue 216 THR Chi-restraints excluded: chain Y residue 294 GLU Chi-restraints excluded: chain Y residue 360 VAL Chi-restraints excluded: chain Y residue 395 GLU Chi-restraints excluded: chain Y residue 435 ASP Chi-restraints excluded: chain Y residue 458 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 378 optimal weight: 0.9980 chunk 190 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 238 optimal weight: 0.0470 chunk 340 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 152 optimal weight: 0.9990 chunk 277 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 251 optimal weight: 3.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 GLN C 68 ASN S 225 GLN D 45 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN F 76 ASN H 45 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 68 ASN K 349 GLN L 45 ASN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN O 349 GLN P 45 ASN ** P 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 GLN R 76 ASN V 45 ASN ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 ASN X 86 GLN Y 225 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.130524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.120261 restraints weight = 42129.898| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 0.58 r_work: 0.3133 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 39342 Z= 0.104 Angle : 0.508 5.649 53442 Z= 0.280 Chirality : 0.049 0.191 5934 Planarity : 0.004 0.055 6996 Dihedral : 5.714 51.595 5456 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.16 % Allowed : 18.72 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.11), residues: 4902 helix: 0.59 (0.35), residues: 228 sheet: -0.41 (0.13), residues: 1416 loop : -1.01 (0.10), residues: 3258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 180 TYR 0.009 0.001 TYR T 80 PHE 0.017 0.001 PHE K 384 TRP 0.013 0.001 TRP O 161 HIS 0.003 0.001 HIS N 58 Details of bonding type rmsd covalent geometry : bond 0.00223 (39342) covalent geometry : angle 0.50810 (53442) hydrogen bonds : bond 0.03210 ( 1081) hydrogen bonds : angle 5.75391 ( 2712) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 4182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 531 time to evaluate : 1.110 Fit side-chains REVERT: A 24 LYS cc_start: 0.8878 (pttp) cc_final: 0.8498 (pttp) REVERT: B 54 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7436 (tm-30) REVERT: S 294 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: D 24 LYS cc_start: 0.8890 (pttp) cc_final: 0.8222 (pttp) REVERT: E 52 GLU cc_start: 0.8207 (tt0) cc_final: 0.7771 (tp30) REVERT: G 180 ARG cc_start: 0.8092 (mmm-85) cc_final: 0.7507 (mtt90) REVERT: J 107 LEU cc_start: 0.8887 (tt) cc_final: 0.8662 (tp) REVERT: K 180 ARG cc_start: 0.8256 (mmm-85) cc_final: 0.7771 (mtp85) REVERT: K 288 MET cc_start: 0.7999 (ttm) cc_final: 0.7626 (tpt) REVERT: L 90 MET cc_start: 0.8864 (ttm) cc_final: 0.8640 (ttm) REVERT: N 107 LEU cc_start: 0.8903 (tt) cc_final: 0.8689 (tp) REVERT: O 180 ARG cc_start: 0.8192 (mtp180) cc_final: 0.7600 (ttt180) REVERT: O 288 MET cc_start: 0.8009 (ttm) cc_final: 0.7648 (tpt) REVERT: P 24 LYS cc_start: 0.8638 (pttp) cc_final: 0.8334 (pttp) REVERT: Q 119 ASP cc_start: 0.8644 (m-30) cc_final: 0.8366 (m-30) REVERT: T 167 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: T 180 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7926 (mmm-85) REVERT: V 24 LYS cc_start: 0.8890 (pttp) cc_final: 0.8503 (pttp) REVERT: V 121 LYS cc_start: 0.7303 (pttt) cc_final: 0.7021 (ttpt) REVERT: X 28 ASN cc_start: 0.8509 (m110) cc_final: 0.8194 (m-40) REVERT: Y 54 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7843 (m-30) REVERT: Y 294 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8044 (mt-10) REVERT: Y 404 GLN cc_start: 0.7914 (pm20) cc_final: 0.7707 (mp10) outliers start: 132 outliers final: 80 residues processed: 625 average time/residue: 0.6043 time to fit residues: 458.7999 Evaluate side-chains 593 residues out of total 4182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 508 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 294 GLU Chi-restraints excluded: chain S residue 360 VAL Chi-restraints excluded: chain S residue 435 ASP Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 394 LEU Chi-restraints excluded: chain G residue 435 ASP Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain K residue 240 LYS Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 269 SER Chi-restraints excluded: chain K residue 394 LEU Chi-restraints excluded: chain K residue 454 LEU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain O residue 240 LYS Chi-restraints excluded: chain O residue 241 THR Chi-restraints excluded: chain O residue 269 SER Chi-restraints excluded: chain O residue 394 LEU Chi-restraints excluded: chain O residue 409 LEU Chi-restraints excluded: chain O residue 454 LEU Chi-restraints excluded: chain O residue 458 THR Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 167 GLU Chi-restraints excluded: chain T residue 180 ARG Chi-restraints excluded: chain T residue 237 THR Chi-restraints excluded: chain T residue 269 SER Chi-restraints excluded: chain T residue 271 ILE Chi-restraints excluded: chain T residue 337 VAL Chi-restraints excluded: chain T residue 360 VAL Chi-restraints excluded: chain T residue 394 LEU Chi-restraints excluded: chain T residue 458 THR Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 62 THR Chi-restraints excluded: chain X residue 24 LYS Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 54 ASP Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 137 GLU Chi-restraints excluded: chain Y residue 199 VAL Chi-restraints excluded: chain Y residue 294 GLU Chi-restraints excluded: chain Y residue 360 VAL Chi-restraints excluded: chain Y residue 395 GLU Chi-restraints excluded: chain Y residue 435 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 35 optimal weight: 3.9990 chunk 253 optimal weight: 0.4980 chunk 314 optimal weight: 3.9990 chunk 400 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 376 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 252 optimal weight: 0.9980 chunk 474 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN S 225 GLN S 404 GLN D 45 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN H 45 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 68 ASN J 78 GLN L 45 ASN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN P 45 ASN ** P 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN V 45 ASN ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN Y 225 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.127759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.117507 restraints weight = 42201.023| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 0.60 r_work: 0.3091 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 39342 Z= 0.157 Angle : 0.568 6.597 53442 Z= 0.312 Chirality : 0.051 0.200 5934 Planarity : 0.004 0.062 6996 Dihedral : 5.901 51.399 5452 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.09 % Allowed : 18.29 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.11), residues: 4902 helix: -0.31 (0.33), residues: 264 sheet: -0.45 (0.13), residues: 1476 loop : -1.05 (0.10), residues: 3162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.011 0.001 TYR Y 80 PHE 0.016 0.002 PHE K 384 TRP 0.012 0.002 TRP K 161 HIS 0.004 0.001 HIS Q 88 Details of bonding type rmsd covalent geometry : bond 0.00363 (39342) covalent geometry : angle 0.56755 (53442) hydrogen bonds : bond 0.03583 ( 1081) hydrogen bonds : angle 5.83190 ( 2712) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 4182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 507 time to evaluate : 1.205 Fit side-chains REVERT: A 24 LYS cc_start: 0.8887 (pttp) cc_final: 0.8442 (pttt) REVERT: B 121 LYS cc_start: 0.8299 (ttpt) cc_final: 0.8029 (ptmt) REVERT: S 54 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.8009 (m-30) REVERT: S 138 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6785 (mp) REVERT: S 294 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8170 (mt-10) REVERT: S 395 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.6493 (tp30) REVERT: D 24 LYS cc_start: 0.8907 (pttp) cc_final: 0.8224 (pttp) REVERT: E 52 GLU cc_start: 0.8281 (tt0) cc_final: 0.7844 (tp30) REVERT: E 119 ASP cc_start: 0.8744 (m-30) cc_final: 0.8356 (m-30) REVERT: F 24 LYS cc_start: 0.8514 (ptpt) cc_final: 0.8187 (ptpt) REVERT: G 159 ASP cc_start: 0.6677 (t0) cc_final: 0.6464 (t0) REVERT: G 395 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7419 (mm-30) REVERT: J 107 LEU cc_start: 0.8951 (tt) cc_final: 0.8740 (tp) REVERT: K 8 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7622 (mtp) REVERT: K 111 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8146 (mm-40) REVERT: K 138 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6726 (mp) REVERT: K 180 ARG cc_start: 0.8280 (mmm-85) cc_final: 0.7834 (mtp85) REVERT: N 107 LEU cc_start: 0.8941 (tt) cc_final: 0.8735 (tp) REVERT: O 8 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7380 (ptp) REVERT: O 12 MET cc_start: 0.8614 (tpt) cc_final: 0.7655 (tpt) REVERT: O 373 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8101 (mmmm) REVERT: Q 119 ASP cc_start: 0.8656 (m-30) cc_final: 0.8367 (m-30) REVERT: T 138 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6572 (mp) REVERT: T 167 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: T 180 ARG cc_start: 0.8312 (ttt180) cc_final: 0.7977 (mmm-85) REVERT: T 395 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7412 (mm-30) REVERT: V 24 LYS cc_start: 0.8923 (pttp) cc_final: 0.8484 (pttt) REVERT: V 121 LYS cc_start: 0.7563 (pttt) cc_final: 0.7260 (ttpt) REVERT: W 121 LYS cc_start: 0.8329 (ttpt) cc_final: 0.8051 (ptmt) REVERT: Y 54 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7956 (m-30) REVERT: Y 137 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: Y 138 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6876 (mp) REVERT: Y 142 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8350 (ttt90) REVERT: Y 167 GLU cc_start: 0.7283 (pm20) cc_final: 0.7067 (pm20) REVERT: Y 294 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8083 (pt0) REVERT: Y 404 GLN cc_start: 0.8054 (pm20) cc_final: 0.7809 (mp10) outliers start: 171 outliers final: 102 residues processed: 644 average time/residue: 0.6357 time to fit residues: 498.2378 Evaluate side-chains 622 residues out of total 4182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 502 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 137 GLU Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 294 GLU Chi-restraints excluded: chain S residue 360 VAL Chi-restraints excluded: chain S residue 395 GLU Chi-restraints excluded: chain S residue 435 ASP Chi-restraints excluded: chain S residue 458 THR Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 435 ASP Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 8 MET Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 111 GLN Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain K residue 227 SER Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 337 VAL Chi-restraints excluded: chain K residue 394 LEU Chi-restraints excluded: chain K residue 396 VAL Chi-restraints excluded: chain K residue 454 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain O residue 8 MET Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain O residue 241 THR Chi-restraints excluded: chain O residue 255 THR Chi-restraints excluded: chain O residue 337 VAL Chi-restraints excluded: chain O residue 373 LYS Chi-restraints excluded: chain O residue 394 LEU Chi-restraints excluded: chain O residue 396 VAL Chi-restraints excluded: chain O residue 409 LEU Chi-restraints excluded: chain O residue 458 THR Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 167 GLU Chi-restraints excluded: chain T residue 196 ASP Chi-restraints excluded: chain T residue 237 THR Chi-restraints excluded: chain T residue 269 SER Chi-restraints excluded: chain T residue 271 ILE Chi-restraints excluded: chain T residue 337 VAL Chi-restraints excluded: chain T residue 360 VAL Chi-restraints excluded: chain T residue 395 GLU Chi-restraints excluded: chain T residue 435 ASP Chi-restraints excluded: chain T residue 458 THR Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 62 THR Chi-restraints excluded: chain X residue 20 SER Chi-restraints excluded: chain X residue 24 LYS Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 54 ASP Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 137 GLU Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 142 ARG Chi-restraints excluded: chain Y residue 199 VAL Chi-restraints excluded: chain Y residue 216 THR Chi-restraints excluded: chain Y residue 294 GLU Chi-restraints excluded: chain Y residue 360 VAL Chi-restraints excluded: chain Y residue 395 GLU Chi-restraints excluded: chain Y residue 435 ASP Chi-restraints excluded: chain Y residue 458 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 8.9990 chunk 327 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 chunk 266 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 88 optimal weight: 0.0970 chunk 354 optimal weight: 6.9990 chunk 312 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 101 optimal weight: 0.1980 chunk 356 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN S 225 GLN S 404 GLN D 45 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN H 45 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 68 ASN L 45 ASN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN O 56 ASN P 45 ASN ** P 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN V 45 ASN ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN Y 225 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.127797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.117550 restraints weight = 42065.458| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 0.59 r_work: 0.3087 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 39342 Z= 0.158 Angle : 0.571 6.502 53442 Z= 0.313 Chirality : 0.051 0.206 5934 Planarity : 0.004 0.064 6996 Dihedral : 5.926 50.823 5450 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.09 % Allowed : 18.32 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.11), residues: 4902 helix: -0.33 (0.32), residues: 264 sheet: -0.48 (0.13), residues: 1476 loop : -1.05 (0.10), residues: 3162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 180 TYR 0.014 0.001 TYR N 32 PHE 0.017 0.002 PHE K 384 TRP 0.012 0.002 TRP S 161 HIS 0.004 0.001 HIS Q 88 Details of bonding type rmsd covalent geometry : bond 0.00365 (39342) covalent geometry : angle 0.57071 (53442) hydrogen bonds : bond 0.03596 ( 1081) hydrogen bonds : angle 5.83803 ( 2712) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 4182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 500 time to evaluate : 1.591 Fit side-chains REVERT: A 24 LYS cc_start: 0.8880 (pttp) cc_final: 0.8433 (pttt) REVERT: B 121 LYS cc_start: 0.8292 (ttpt) cc_final: 0.8028 (ptmt) REVERT: S 54 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7967 (m-30) REVERT: S 138 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6767 (mp) REVERT: S 294 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8236 (mt-10) REVERT: S 395 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.6496 (tp30) REVERT: S 458 THR cc_start: 0.8103 (OUTLIER) cc_final: 0.7841 (t) REVERT: D 24 LYS cc_start: 0.8939 (pttp) cc_final: 0.8249 (pttp) REVERT: E 52 GLU cc_start: 0.8264 (tt0) cc_final: 0.7832 (tp30) REVERT: E 119 ASP cc_start: 0.8744 (m-30) cc_final: 0.8347 (m-30) REVERT: F 24 LYS cc_start: 0.8572 (ptpt) cc_final: 0.8225 (ptpt) REVERT: G 138 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6409 (mp) REVERT: J 107 LEU cc_start: 0.8948 (tt) cc_final: 0.8722 (tp) REVERT: K 8 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7624 (mtp) REVERT: K 111 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8133 (mm-40) REVERT: K 138 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6748 (mp) REVERT: K 180 ARG cc_start: 0.8286 (mmm-85) cc_final: 0.7843 (mtp85) REVERT: K 288 MET cc_start: 0.7791 (ttm) cc_final: 0.7403 (tpt) REVERT: N 107 LEU cc_start: 0.8954 (tt) cc_final: 0.8727 (tp) REVERT: O 8 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7355 (ptp) REVERT: O 111 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8133 (mm-40) REVERT: O 288 MET cc_start: 0.7795 (ttm) cc_final: 0.7425 (tpt) REVERT: O 373 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8076 (mmmm) REVERT: Q 119 ASP cc_start: 0.8649 (m-30) cc_final: 0.8358 (m-30) REVERT: T 138 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6555 (mp) REVERT: T 167 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: T 169 GLU cc_start: 0.8293 (pt0) cc_final: 0.8091 (pt0) REVERT: T 180 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7941 (mmm-85) REVERT: T 435 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.8032 (m-30) REVERT: T 454 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7722 (mp) REVERT: V 24 LYS cc_start: 0.8914 (pttp) cc_final: 0.8474 (pttt) REVERT: V 121 LYS cc_start: 0.7530 (pttt) cc_final: 0.7229 (ttpt) REVERT: Y 54 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7965 (m-30) REVERT: Y 137 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: Y 138 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6793 (mp) REVERT: Y 142 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8348 (ttt90) REVERT: Y 294 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8138 (pt0) REVERT: Y 404 GLN cc_start: 0.8046 (pm20) cc_final: 0.7815 (mp10) outliers start: 171 outliers final: 118 residues processed: 637 average time/residue: 0.6594 time to fit residues: 511.8690 Evaluate side-chains 629 residues out of total 4182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 489 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 137 GLU Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain S residue 196 ASP Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 227 SER Chi-restraints excluded: chain S residue 294 GLU Chi-restraints excluded: chain S residue 360 VAL Chi-restraints excluded: chain S residue 395 GLU Chi-restraints excluded: chain S residue 435 ASP Chi-restraints excluded: chain S residue 458 THR Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 435 ASP Chi-restraints excluded: chain G residue 458 THR Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 24 LYS Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 8 MET Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 111 GLN Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain K residue 227 SER Chi-restraints excluded: chain K residue 240 LYS Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 271 ILE Chi-restraints excluded: chain K residue 337 VAL Chi-restraints excluded: chain K residue 394 LEU Chi-restraints excluded: chain K residue 396 VAL Chi-restraints excluded: chain K residue 454 LEU Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain N residue 24 LYS Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain O residue 8 MET Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 111 GLN Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain O residue 196 ASP Chi-restraints excluded: chain O residue 240 LYS Chi-restraints excluded: chain O residue 241 THR Chi-restraints excluded: chain O residue 255 THR Chi-restraints excluded: chain O residue 337 VAL Chi-restraints excluded: chain O residue 373 LYS Chi-restraints excluded: chain O residue 394 LEU Chi-restraints excluded: chain O residue 396 VAL Chi-restraints excluded: chain O residue 409 LEU Chi-restraints excluded: chain O residue 454 LEU Chi-restraints excluded: chain O residue 458 THR Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 167 GLU Chi-restraints excluded: chain T residue 180 ARG Chi-restraints excluded: chain T residue 196 ASP Chi-restraints excluded: chain T residue 237 THR Chi-restraints excluded: chain T residue 255 THR Chi-restraints excluded: chain T residue 269 SER Chi-restraints excluded: chain T residue 271 ILE Chi-restraints excluded: chain T residue 337 VAL Chi-restraints excluded: chain T residue 360 VAL Chi-restraints excluded: chain T residue 435 ASP Chi-restraints excluded: chain T residue 454 LEU Chi-restraints excluded: chain T residue 458 THR Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 62 THR Chi-restraints excluded: chain X residue 20 SER Chi-restraints excluded: chain X residue 24 LYS Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 54 ASP Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 137 GLU Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 142 ARG Chi-restraints excluded: chain Y residue 199 VAL Chi-restraints excluded: chain Y residue 216 THR Chi-restraints excluded: chain Y residue 294 GLU Chi-restraints excluded: chain Y residue 360 VAL Chi-restraints excluded: chain Y residue 395 GLU Chi-restraints excluded: chain Y residue 435 ASP Chi-restraints excluded: chain Y residue 458 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 344 optimal weight: 2.9990 chunk 471 optimal weight: 0.0060 chunk 6 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 459 optimal weight: 3.9990 chunk 447 optimal weight: 0.7980 chunk 203 optimal weight: 8.9990 chunk 137 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 348 optimal weight: 4.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN S 225 GLN S 404 GLN D 45 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN H 45 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 68 ASN L 45 ASN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN O 56 ASN P 45 ASN ** P 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN V 45 ASN ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN Y 225 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.129188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.119016 restraints weight = 42092.510| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 0.60 r_work: 0.3109 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 39342 Z= 0.138 Angle : 0.548 6.236 53442 Z= 0.301 Chirality : 0.051 0.187 5934 Planarity : 0.004 0.062 6996 Dihedral : 5.752 49.510 5450 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.61 % Allowed : 18.96 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.11), residues: 4902 helix: -0.26 (0.33), residues: 264 sheet: -0.45 (0.13), residues: 1476 loop : -1.01 (0.10), residues: 3162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 180 TYR 0.012 0.001 TYR N 32 PHE 0.016 0.002 PHE K 384 TRP 0.012 0.002 TRP S 161 HIS 0.004 0.001 HIS Q 88 Details of bonding type rmsd covalent geometry : bond 0.00314 (39342) covalent geometry : angle 0.54776 (53442) hydrogen bonds : bond 0.03448 ( 1081) hydrogen bonds : angle 5.74811 ( 2712) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 4182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 502 time to evaluate : 1.445 Fit side-chains REVERT: A 16 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8442 (tp) REVERT: A 24 LYS cc_start: 0.8879 (pttp) cc_final: 0.8431 (pttt) REVERT: B 121 LYS cc_start: 0.8262 (ttpt) cc_final: 0.8023 (ptmt) REVERT: S 54 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7942 (m-30) REVERT: S 294 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: S 458 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7787 (t) REVERT: D 24 LYS cc_start: 0.8936 (pttp) cc_final: 0.8257 (pttp) REVERT: D 32 TYR cc_start: 0.8396 (m-80) cc_final: 0.8181 (m-80) REVERT: E 52 GLU cc_start: 0.8247 (tt0) cc_final: 0.7820 (tp30) REVERT: E 119 ASP cc_start: 0.8706 (m-30) cc_final: 0.8410 (m-30) REVERT: F 24 LYS cc_start: 0.8524 (ptpt) cc_final: 0.8320 (ptpt) REVERT: G 138 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6387 (mp) REVERT: J 107 LEU cc_start: 0.8918 (tt) cc_final: 0.8679 (tp) REVERT: K 8 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7599 (mtp) REVERT: K 12 MET cc_start: 0.8571 (tpt) cc_final: 0.7589 (tpt) REVERT: K 111 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8142 (mm-40) REVERT: K 138 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6666 (mp) REVERT: K 180 ARG cc_start: 0.8254 (mmm-85) cc_final: 0.7801 (mtp85) REVERT: K 288 MET cc_start: 0.7778 (ttm) cc_final: 0.7385 (tpt) REVERT: N 107 LEU cc_start: 0.8934 (tt) cc_final: 0.8619 (tp) REVERT: O 12 MET cc_start: 0.8564 (tpt) cc_final: 0.7588 (tpt) REVERT: O 111 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8139 (mm-40) REVERT: O 288 MET cc_start: 0.7778 (ttm) cc_final: 0.7399 (tpt) REVERT: O 373 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8068 (mmmm) REVERT: P 54 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.5889 (tp30) REVERT: Q 119 ASP cc_start: 0.8617 (m-30) cc_final: 0.8360 (m-30) REVERT: R 24 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8158 (mttt) REVERT: T 138 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6527 (mp) REVERT: T 167 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: T 169 GLU cc_start: 0.8355 (pt0) cc_final: 0.8131 (pt0) REVERT: T 180 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7934 (mmm-85) REVERT: T 454 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7734 (mp) REVERT: V 24 LYS cc_start: 0.8882 (pttp) cc_final: 0.8443 (pttt) REVERT: V 121 LYS cc_start: 0.7612 (pttt) cc_final: 0.7293 (ttpt) REVERT: W 121 LYS cc_start: 0.8297 (ttpt) cc_final: 0.8039 (ptmt) REVERT: Y 54 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7930 (m-30) REVERT: Y 137 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: Y 138 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6723 (mp) REVERT: Y 142 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8341 (ttt90) REVERT: Y 294 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8087 (mt-10) REVERT: Y 404 GLN cc_start: 0.8023 (pm20) cc_final: 0.7791 (mp10) outliers start: 151 outliers final: 113 residues processed: 619 average time/residue: 0.6318 time to fit residues: 475.1487 Evaluate side-chains 633 residues out of total 4182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 499 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 137 GLU Chi-restraints excluded: chain S residue 196 ASP Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 227 SER Chi-restraints excluded: chain S residue 294 GLU Chi-restraints excluded: chain S residue 360 VAL Chi-restraints excluded: chain S residue 435 ASP Chi-restraints excluded: chain S residue 458 THR Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 435 ASP Chi-restraints excluded: chain G residue 458 THR Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 24 LYS Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 8 MET Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 111 GLN Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain K residue 227 SER Chi-restraints excluded: chain K residue 240 LYS Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 337 VAL Chi-restraints excluded: chain K residue 394 LEU Chi-restraints excluded: chain K residue 454 LEU Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain N residue 24 LYS Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 111 GLN Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain O residue 240 LYS Chi-restraints excluded: chain O residue 241 THR Chi-restraints excluded: chain O residue 255 THR Chi-restraints excluded: chain O residue 337 VAL Chi-restraints excluded: chain O residue 373 LYS Chi-restraints excluded: chain O residue 394 LEU Chi-restraints excluded: chain O residue 396 VAL Chi-restraints excluded: chain O residue 409 LEU Chi-restraints excluded: chain O residue 454 LEU Chi-restraints excluded: chain O residue 458 THR Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 167 GLU Chi-restraints excluded: chain T residue 180 ARG Chi-restraints excluded: chain T residue 196 ASP Chi-restraints excluded: chain T residue 237 THR Chi-restraints excluded: chain T residue 255 THR Chi-restraints excluded: chain T residue 269 SER Chi-restraints excluded: chain T residue 271 ILE Chi-restraints excluded: chain T residue 337 VAL Chi-restraints excluded: chain T residue 360 VAL Chi-restraints excluded: chain T residue 394 LEU Chi-restraints excluded: chain T residue 454 LEU Chi-restraints excluded: chain T residue 458 THR Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 62 THR Chi-restraints excluded: chain X residue 20 SER Chi-restraints excluded: chain X residue 24 LYS Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 54 ASP Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 137 GLU Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 142 ARG Chi-restraints excluded: chain Y residue 199 VAL Chi-restraints excluded: chain Y residue 216 THR Chi-restraints excluded: chain Y residue 294 GLU Chi-restraints excluded: chain Y residue 360 VAL Chi-restraints excluded: chain Y residue 395 GLU Chi-restraints excluded: chain Y residue 435 ASP Chi-restraints excluded: chain Y residue 458 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 168 optimal weight: 9.9990 chunk 222 optimal weight: 0.8980 chunk 302 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 399 optimal weight: 4.9990 chunk 384 optimal weight: 2.9990 chunk 435 optimal weight: 4.9990 chunk 233 optimal weight: 0.2980 chunk 316 optimal weight: 3.9990 chunk 337 optimal weight: 3.9990 chunk 479 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN C 113 GLN S 404 GLN D 45 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN H 45 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 68 ASN K 56 ASN L 45 ASN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN N 78 GLN P 45 ASN ** P 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN V 45 ASN ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN Y 225 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.125813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.115539 restraints weight = 42331.193| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 0.57 r_work: 0.3065 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 39342 Z= 0.217 Angle : 0.645 7.603 53442 Z= 0.353 Chirality : 0.054 0.215 5934 Planarity : 0.005 0.068 6996 Dihedral : 6.261 53.709 5450 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.56 % Allowed : 19.23 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.11), residues: 4902 helix: -0.25 (0.33), residues: 270 sheet: -0.56 (0.12), residues: 1536 loop : -1.14 (0.11), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 180 TYR 0.015 0.002 TYR I 50 PHE 0.017 0.002 PHE S 384 TRP 0.014 0.002 TRP S 161 HIS 0.005 0.001 HIS M 88 Details of bonding type rmsd covalent geometry : bond 0.00512 (39342) covalent geometry : angle 0.64532 (53442) hydrogen bonds : bond 0.03966 ( 1081) hydrogen bonds : angle 6.00987 ( 2712) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 4182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 483 time to evaluate : 1.449 Fit side-chains REVERT: A 24 LYS cc_start: 0.8908 (pttp) cc_final: 0.8453 (pttt) REVERT: S 54 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.8052 (m-30) REVERT: S 138 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6916 (mp) REVERT: S 294 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8129 (pt0) REVERT: S 395 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.6845 (tt0) REVERT: D 24 LYS cc_start: 0.8961 (pttp) cc_final: 0.8261 (pttp) REVERT: D 32 TYR cc_start: 0.8402 (m-80) cc_final: 0.8176 (m-80) REVERT: D 54 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6029 (tp30) REVERT: E 52 GLU cc_start: 0.8250 (tt0) cc_final: 0.7823 (tp30) REVERT: E 119 ASP cc_start: 0.8753 (m-30) cc_final: 0.8338 (m-30) REVERT: F 76 ASN cc_start: 0.8524 (m-40) cc_final: 0.8240 (m-40) REVERT: G 138 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6792 (mp) REVERT: J 107 LEU cc_start: 0.8990 (tt) cc_final: 0.8783 (tp) REVERT: K 8 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7355 (ptp) REVERT: K 111 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8111 (mm-40) REVERT: K 138 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6978 (mp) REVERT: K 288 MET cc_start: 0.7836 (ttm) cc_final: 0.7461 (tpt) REVERT: N 107 LEU cc_start: 0.9013 (tt) cc_final: 0.8777 (tp) REVERT: O 8 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7385 (ptp) REVERT: O 111 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8090 (mm-40) REVERT: O 288 MET cc_start: 0.7823 (ttm) cc_final: 0.7466 (tpt) REVERT: P 54 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.5919 (tp30) REVERT: Q 119 ASP cc_start: 0.8690 (m-30) cc_final: 0.8357 (m-30) REVERT: R 24 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8278 (mttt) REVERT: T 138 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6760 (mp) REVERT: T 167 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: T 169 GLU cc_start: 0.8424 (pt0) cc_final: 0.8096 (pt0) REVERT: T 180 ARG cc_start: 0.8309 (ttt180) cc_final: 0.8084 (mmm-85) REVERT: T 435 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8074 (m-30) REVERT: V 24 LYS cc_start: 0.8915 (pttp) cc_final: 0.8460 (pttt) REVERT: Y 54 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.8036 (m-30) REVERT: Y 137 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7717 (mp0) REVERT: Y 138 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6935 (mp) REVERT: Y 142 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8328 (ttt90) REVERT: Y 167 GLU cc_start: 0.7389 (pm20) cc_final: 0.7149 (pm20) REVERT: Y 294 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8290 (pt0) REVERT: Y 404 GLN cc_start: 0.8038 (pm20) cc_final: 0.7818 (mp10) outliers start: 149 outliers final: 109 residues processed: 602 average time/residue: 0.6139 time to fit residues: 447.0706 Evaluate side-chains 608 residues out of total 4182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 478 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 137 GLU Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 294 GLU Chi-restraints excluded: chain S residue 360 VAL Chi-restraints excluded: chain S residue 395 GLU Chi-restraints excluded: chain S residue 435 ASP Chi-restraints excluded: chain S residue 458 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 435 ASP Chi-restraints excluded: chain G residue 458 THR Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 24 LYS Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 8 MET Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 111 GLN Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain K residue 227 SER Chi-restraints excluded: chain K residue 240 LYS Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 271 ILE Chi-restraints excluded: chain K residue 337 VAL Chi-restraints excluded: chain K residue 394 LEU Chi-restraints excluded: chain K residue 396 VAL Chi-restraints excluded: chain K residue 454 LEU Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain N residue 16 ILE Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain N residue 24 LYS Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain O residue 8 MET Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain O residue 111 GLN Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain O residue 196 ASP Chi-restraints excluded: chain O residue 241 THR Chi-restraints excluded: chain O residue 255 THR Chi-restraints excluded: chain O residue 337 VAL Chi-restraints excluded: chain O residue 394 LEU Chi-restraints excluded: chain O residue 396 VAL Chi-restraints excluded: chain O residue 409 LEU Chi-restraints excluded: chain O residue 458 THR Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 167 GLU Chi-restraints excluded: chain T residue 196 ASP Chi-restraints excluded: chain T residue 255 THR Chi-restraints excluded: chain T residue 269 SER Chi-restraints excluded: chain T residue 271 ILE Chi-restraints excluded: chain T residue 337 VAL Chi-restraints excluded: chain T residue 360 VAL Chi-restraints excluded: chain T residue 435 ASP Chi-restraints excluded: chain T residue 458 THR Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 62 THR Chi-restraints excluded: chain X residue 20 SER Chi-restraints excluded: chain X residue 24 LYS Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 54 ASP Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 137 GLU Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 142 ARG Chi-restraints excluded: chain Y residue 216 THR Chi-restraints excluded: chain Y residue 294 GLU Chi-restraints excluded: chain Y residue 360 VAL Chi-restraints excluded: chain Y residue 395 GLU Chi-restraints excluded: chain Y residue 435 ASP Chi-restraints excluded: chain Y residue 458 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 200 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 398 optimal weight: 0.2980 chunk 121 optimal weight: 0.3980 chunk 166 optimal weight: 7.9990 chunk 239 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 357 optimal weight: 2.9990 chunk 296 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 225 GLN S 404 GLN D 45 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 68 ASN L 45 ASN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN P 45 ASN ** P 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN V 45 ASN ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 225 GLN Y 267 GLN Y 349 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.127352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.117005 restraints weight = 42105.145| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 0.59 r_work: 0.3077 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 39342 Z= 0.178 Angle : 0.599 6.460 53442 Z= 0.329 Chirality : 0.052 0.193 5934 Planarity : 0.005 0.067 6996 Dihedral : 6.092 53.278 5447 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.63 % Allowed : 19.25 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.11), residues: 4902 helix: -0.23 (0.32), residues: 270 sheet: -0.53 (0.13), residues: 1476 loop : -1.09 (0.10), residues: 3156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 180 TYR 0.014 0.002 TYR J 32 PHE 0.017 0.002 PHE K 384 TRP 0.012 0.002 TRP G 161 HIS 0.005 0.001 HIS Q 88 Details of bonding type rmsd covalent geometry : bond 0.00415 (39342) covalent geometry : angle 0.59878 (53442) hydrogen bonds : bond 0.03736 ( 1081) hydrogen bonds : angle 5.94262 ( 2712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12365.88 seconds wall clock time: 211 minutes 24.20 seconds (12684.20 seconds total)