Starting phenix.real_space_refine on Sat Mar 23 20:09:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvr_41649/03_2024/8tvr_41649.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvr_41649/03_2024/8tvr_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvr_41649/03_2024/8tvr_41649.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvr_41649/03_2024/8tvr_41649.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvr_41649/03_2024/8tvr_41649.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvr_41649/03_2024/8tvr_41649.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Residue "A GLU 52": "OE1" <-> "OE2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "S GLU 63": "OE1" <-> "OE2" Residue "S TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 346": "OE1" <-> "OE2" Residue "S GLU 357": "OE1" <-> "OE2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "E GLU 52": "OE1" <-> "OE2" Residue "G GLU 137": "OE1" <-> "OE2" Residue "G PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 294": "OE1" <-> "OE2" Residue "G GLU 346": "OE1" <-> "OE2" Residue "I GLU 52": "OE1" <-> "OE2" Residue "J GLU 52": "OE1" <-> "OE2" Residue "K GLU 35": "OE1" <-> "OE2" Residue "K GLU 63": "OE1" <-> "OE2" Residue "K GLU 169": "OE1" <-> "OE2" Residue "K PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 19": "OE1" <-> "OE2" Residue "N GLU 19": "OE1" <-> "OE2" Residue "O GLU 63": "OE1" <-> "OE2" Residue "O ASP 88": "OD1" <-> "OD2" Residue "O GLU 169": "OE1" <-> "OE2" Residue "O PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 52": "OE1" <-> "OE2" Residue "Q TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 19": "OE1" <-> "OE2" Residue "T GLU 167": "OE1" <-> "OE2" Residue "T PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 294": "OE1" <-> "OE2" Residue "T GLU 346": "OE1" <-> "OE2" Residue "T GLU 357": "OE1" <-> "OE2" Residue "V GLU 52": "OE1" <-> "OE2" Residue "W GLU 52": "OE1" <-> "OE2" Residue "W GLU 54": "OE1" <-> "OE2" Residue "W GLU 117": "OE1" <-> "OE2" Residue "Y GLU 169": "OE1" <-> "OE2" Residue "Y TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 346": "OE1" <-> "OE2" Residue "Y GLU 357": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 20.14, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 15.41 Conformation dependent library (CDL) restraints added in 7.3 seconds 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: 5.34 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: 17.93 Time building geometry restraints manager: 16.49 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: 99.01 - 106.01: 844 106.01 - 113.00: 20921 113.00 - 120.00: 13244 120.00 - 127.00: 18046 127.00 - 133.99: 387 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 2.440 nonbonded pdb=" OD1 ASN F 53 " pdb=" OG SER F 57 " model vdw 2.197 2.440 nonbonded pdb=" NH2 ARG K 73 " pdb=" O ASP K 342 " model vdw 2.198 2.520 nonbonded pdb=" OD1 ASN R 53 " pdb=" OG SER R 57 " model vdw 2.199 2.440 nonbonded pdb=" NH2 ARG O 73 " pdb=" O ASP O 342 " model vdw 2.200 2.520 ... (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 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: 4.370 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: 0.040 Extract box with map and model: 18.990 Check model and map are aligned: 0.590 Set scattering table: 0.380 Process input model: 107.290 Find NCS groups from input model: 2.770 Set up NCS constraints: 0.360 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:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.990 ------------------------------------------------------------------------------- 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= 0.169 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.012 0.001 TRP G 161 HIS 0.003 0.001 HIS M 88 PHE 0.012 0.001 PHE Y 384 TYR 0.015 0.001 TYR S 80 ARG 0.003 0.000 ARG K 148 *********************** 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 fitting. rotamer outliers: 72 poor density : 509 time to evaluate : 4.499 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: 1.5394 time to fit residues: 1060.6646 Evaluate side-chains 541 residues out of total 4182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 489 time to evaluate : 3.753 ------------------------------------------------------------------------------- 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 405 optimal weight: 3.9990 chunk 363 optimal weight: 8.9990 chunk 201 optimal weight: 0.2980 chunk 124 optimal weight: 4.9990 chunk 245 optimal weight: 8.9990 chunk 194 optimal weight: 7.9990 chunk 376 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 228 optimal weight: 7.9990 chunk 280 optimal weight: 6.9990 chunk 435 optimal weight: 0.7980 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN D 45 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 ASN ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 267 GLN H 45 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 68 ASN L 45 ASN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 63 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** ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 ASN T 267 GLN V 45 ASN ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 99 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 39342 Z= 0.425 Angle : 0.690 7.915 53442 Z= 0.376 Chirality : 0.056 0.206 5934 Planarity : 0.006 0.067 6996 Dihedral : 7.084 88.904 5496 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.07 % Allowed : 13.85 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.11), residues: 4902 helix: -0.27 (0.34), residues: 264 sheet: -0.48 (0.12), residues: 1524 loop : -1.15 (0.10), residues: 3114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP G 326 HIS 0.006 0.002 HIS K 252 PHE 0.018 0.003 PHE Y 384 TYR 0.014 0.002 TYR T 80 ARG 0.006 0.001 ARG W 14 *********************** 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 670 residues out of total 4182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 500 time to evaluate : 4.658 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8884 (pttp) cc_final: 0.8521 (pttt) REVERT: S 54 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7422 (m-30) REVERT: S 241 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8515 (p) REVERT: S 357 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: S 395 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.6807 (tt0) REVERT: E 52 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7752 (tp30) REVERT: G 167 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7388 (pm20) REVERT: G 294 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8549 (mt-10) REVERT: G 395 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7378 (mm-30) REVERT: K 37 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7266 (pp) REVERT: O 37 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7324 (pp) REVERT: O 373 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8222 (mmmm) REVERT: P 24 LYS cc_start: 0.8769 (pttp) cc_final: 0.8425 (ptmm) REVERT: T 174 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7215 (mtt90) REVERT: T 395 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7408 (mm-30) REVERT: V 24 LYS cc_start: 0.8822 (pttp) cc_final: 0.8500 (pttt) REVERT: Y 12 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8176 (tpp) REVERT: Y 54 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7639 (m-30) REVERT: Y 138 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6599 (mp) REVERT: Y 182 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7279 (mm-30) REVERT: Y 241 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8531 (p) REVERT: Y 357 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8080 (mp0) REVERT: Y 404 GLN cc_start: 0.8136 (pm20) cc_final: 0.7769 (mp10) outliers start: 170 outliers final: 102 residues processed: 624 average time/residue: 1.5267 time to fit residues: 1149.1433 Evaluate side-chains 599 residues out of total 4182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 480 time to evaluate : 4.725 ------------------------------------------------------------------------------- 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 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 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 E residue 36 ILE Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 55 ASP 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 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 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 84 THR Chi-restraints excluded: chain K residue 37 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 240 LYS Chi-restraints excluded: chain K residue 241 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 395 GLU Chi-restraints excluded: chain K residue 409 LEU 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 84 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 174 ARG 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 55 ASP 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 174 ARG 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 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 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 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 242 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 362 optimal weight: 1.9990 chunk 296 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 436 optimal weight: 1.9990 chunk 471 optimal weight: 6.9990 chunk 388 optimal weight: 0.9980 chunk 433 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 350 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN S 267 GLN S 404 GLN D 45 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 68 ASN J 78 GLN K 267 GLN K 349 GLN L 45 ASN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN O 267 GLN O 349 GLN P 45 ASN ** P 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 45 ASN ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN Y 267 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 39342 Z= 0.250 Angle : 0.569 6.251 53442 Z= 0.312 Chirality : 0.051 0.194 5934 Planarity : 0.005 0.056 6996 Dihedral : 6.429 57.176 5479 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.73 % Allowed : 15.71 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.11), residues: 4902 helix: -0.16 (0.33), residues: 270 sheet: -0.41 (0.13), residues: 1476 loop : -1.10 (0.10), residues: 3156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 161 HIS 0.005 0.001 HIS Q 88 PHE 0.019 0.002 PHE O 384 TYR 0.012 0.002 TYR S 80 ARG 0.004 0.000 ARG O 148 *********************** 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 663 residues out of total 4182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 507 time to evaluate : 4.422 Fit side-chains REVERT: A 24 LYS cc_start: 0.8876 (pttp) cc_final: 0.8542 (pttp) REVERT: B 54 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7537 (tm-30) REVERT: B 68 ASN cc_start: 0.8841 (p0) cc_final: 0.8236 (p0) REVERT: S 241 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8524 (p) REVERT: S 395 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.6765 (tt0) REVERT: D 24 LYS cc_start: 0.9038 (pttp) cc_final: 0.8194 (pttp) REVERT: E 52 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7725 (tp30) REVERT: G 167 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7263 (pm20) REVERT: G 294 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8434 (mt-10) REVERT: G 387 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8008 (m-30) REVERT: G 395 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7342 (mm-30) REVERT: K 111 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8089 (mm-40) REVERT: O 111 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8110 (mm-40) REVERT: O 454 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7935 (mp) REVERT: T 174 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7373 (mtt90) REVERT: T 387 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8233 (m-30) REVERT: T 395 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7372 (mm-30) REVERT: V 24 LYS cc_start: 0.8812 (pttp) cc_final: 0.8526 (pttp) REVERT: W 68 ASN cc_start: 0.8816 (p0) cc_final: 0.8214 (p0) REVERT: Y 241 THR cc_start: 0.8771 (OUTLIER) cc_final: 0.8542 (p) REVERT: Y 404 GLN cc_start: 0.8100 (pm20) cc_final: 0.7748 (mp10) outliers start: 156 outliers final: 92 residues processed: 626 average time/residue: 1.4592 time to fit residues: 1105.8622 Evaluate side-chains 598 residues out of total 4182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 493 time to evaluate : 5.574 ------------------------------------------------------------------------------- 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 32 THR Chi-restraints excluded: chain S residue 137 GLU Chi-restraints excluded: chain S residue 196 ASP Chi-restraints excluded: chain S residue 241 THR Chi-restraints excluded: chain S residue 267 GLN 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 52 GLU Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 84 THR 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 387 ASP 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 I residue 98 SER 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 237 THR Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 267 GLN 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 454 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain M residue 98 SER 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 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 237 THR Chi-restraints excluded: chain O residue 241 THR Chi-restraints excluded: chain O residue 267 GLN 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 395 GLU 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 116 ILE Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain R residue 55 ASP 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 167 GLU Chi-restraints excluded: chain T residue 174 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 387 ASP 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 16 ILE 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 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 102 THR Chi-restraints excluded: chain Y residue 137 GLU Chi-restraints excluded: chain Y residue 196 ASP Chi-restraints excluded: chain Y residue 241 THR Chi-restraints excluded: chain Y residue 267 GLN 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 431 optimal weight: 4.9990 chunk 328 optimal weight: 9.9990 chunk 226 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 208 optimal weight: 7.9990 chunk 293 optimal weight: 0.8980 chunk 438 optimal weight: 0.0060 chunk 463 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 chunk 415 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 overall best weight: 2.3800 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN D 45 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 68 ASN K 267 GLN K 349 GLN L 45 ASN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN O 267 GLN O 349 GLN P 45 ASN ** P 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 45 ASN ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN Y 267 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 39342 Z= 0.344 Angle : 0.635 7.488 53442 Z= 0.347 Chirality : 0.054 0.198 5934 Planarity : 0.005 0.062 6996 Dihedral : 6.526 56.713 5464 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.59 % Allowed : 16.00 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.11), residues: 4902 helix: -0.19 (0.33), residues: 270 sheet: -0.49 (0.12), residues: 1506 loop : -1.20 (0.10), residues: 3126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP T 326 HIS 0.005 0.001 HIS I 88 PHE 0.019 0.002 PHE O 384 TYR 0.014 0.002 TYR O 80 ARG 0.004 0.001 ARG B 14 *********************** 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 684 residues out of total 4182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 492 time to evaluate : 4.877 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8878 (pttp) cc_final: 0.8505 (pttt) REVERT: S 54 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7729 (m-30) REVERT: S 245 ASP cc_start: 0.7412 (m-30) cc_final: 0.7111 (m-30) REVERT: S 294 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8246 (pt0) REVERT: S 395 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.6797 (tt0) REVERT: D 24 LYS cc_start: 0.9054 (pttp) cc_final: 0.8294 (pttp) REVERT: E 52 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7730 (tp30) REVERT: G 138 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6270 (mp) REVERT: G 167 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7358 (pm20) REVERT: G 294 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8509 (mt-10) REVERT: G 387 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8116 (m-30) REVERT: G 395 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7412 (mm-30) REVERT: I 108 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8246 (mtpt) REVERT: K 111 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8099 (mm-40) REVERT: K 137 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: M 108 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8284 (mtpt) REVERT: O 111 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8101 (mm-40) REVERT: O 137 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: O 373 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8274 (mmmm) REVERT: O 454 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8027 (mp) REVERT: T 138 LEU cc_start: 0.6715 (OUTLIER) cc_final: 0.6341 (mp) REVERT: T 148 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7248 (mmt90) REVERT: T 387 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8303 (m-30) REVERT: T 395 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7436 (mm-30) REVERT: V 24 LYS cc_start: 0.8816 (pttp) cc_final: 0.8474 (pttt) REVERT: Y 12 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8127 (tpp) REVERT: Y 54 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7915 (m-30) REVERT: Y 138 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6555 (mp) REVERT: Y 241 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8542 (p) REVERT: Y 245 ASP cc_start: 0.7607 (m-30) cc_final: 0.7262 (m-30) REVERT: Y 294 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8418 (pt0) REVERT: Y 404 GLN cc_start: 0.8088 (pm20) cc_final: 0.7820 (mp10) outliers start: 192 outliers final: 118 residues processed: 636 average time/residue: 1.4747 time to fit residues: 1137.5926 Evaluate side-chains 623 residues out of total 4182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 480 time to evaluate : 4.535 ------------------------------------------------------------------------------- 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 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 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 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 36 ILE Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 55 ASP 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 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 387 ASP 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 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 108 LYS 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 137 GLU Chi-restraints excluded: chain K residue 167 GLU 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 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 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 M residue 108 LYS 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 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 116 ARG Chi-restraints excluded: chain O residue 137 GLU Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain O residue 174 ARG 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 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 409 LEU Chi-restraints excluded: chain O residue 454 LEU Chi-restraints excluded: chain O residue 458 THR 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 55 ASP 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 148 ARG Chi-restraints excluded: chain T residue 167 GLU Chi-restraints excluded: chain T residue 174 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 387 ASP 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 1.9990 chunk 263 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 345 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 395 optimal weight: 1.9990 chunk 320 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 chunk 416 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN S 267 GLN D 45 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 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** ** L 63 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 ** both conformations clash, **PLEASE CHECK MANUALLY** V 45 ASN ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN Y 267 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 39342 Z= 0.290 Angle : 0.595 6.364 53442 Z= 0.326 Chirality : 0.052 0.208 5934 Planarity : 0.005 0.060 6996 Dihedral : 6.405 58.459 5464 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.66 % Allowed : 16.69 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.11), residues: 4902 helix: -0.18 (0.33), residues: 270 sheet: -0.48 (0.13), residues: 1476 loop : -1.16 (0.10), residues: 3156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 161 HIS 0.005 0.001 HIS M 88 PHE 0.019 0.002 PHE O 384 TYR 0.013 0.002 TYR O 80 ARG 0.004 0.000 ARG W 14 *********************** 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 696 residues out of total 4182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 501 time to evaluate : 4.200 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8861 (pttp) cc_final: 0.8484 (pttt) REVERT: S 54 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7687 (m-30) REVERT: S 138 LEU cc_start: 0.6677 (OUTLIER) cc_final: 0.6364 (mp) REVERT: S 267 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8223 (pp30) REVERT: S 294 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8294 (pt0) REVERT: S 357 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: S 395 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.6782 (tt0) REVERT: D 24 LYS cc_start: 0.8939 (pttp) cc_final: 0.8282 (pttp) REVERT: E 52 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7722 (tp30) REVERT: G 167 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7288 (pm20) REVERT: G 387 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8087 (m-30) REVERT: G 395 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7392 (mm-30) REVERT: J 24 LYS cc_start: 0.8637 (ptpt) cc_final: 0.8432 (ptpp) REVERT: K 111 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8081 (mm-40) REVERT: K 137 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: N 52 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7924 (tt0) REVERT: O 111 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8103 (mm-40) REVERT: O 137 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: O 373 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8264 (mmmm) REVERT: T 148 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7219 (mmt90) REVERT: T 387 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8261 (m-30) REVERT: T 395 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7420 (mm-30) REVERT: V 24 LYS cc_start: 0.8833 (pttp) cc_final: 0.8499 (pttt) REVERT: Y 12 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8128 (tpp) REVERT: Y 54 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7899 (m-30) REVERT: Y 138 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6427 (mp) REVERT: Y 241 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8531 (p) REVERT: Y 294 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8466 (pt0) REVERT: Y 357 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7998 (mp0) REVERT: Y 404 GLN cc_start: 0.8078 (pm20) cc_final: 0.7831 (mp10) outliers start: 195 outliers final: 123 residues processed: 647 average time/residue: 1.4498 time to fit residues: 1139.0045 Evaluate side-chains 633 residues out of total 4182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 485 time to evaluate : 4.165 ------------------------------------------------------------------------------- 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 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 32 THR Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 63 GLU 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 196 ASP Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 267 GLN 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 S residue 458 THR Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 55 ASP 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 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 387 ASP 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 5 THR 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 84 THR Chi-restraints excluded: chain J residue 106 VAL 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 137 GLU Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain K residue 227 SER 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 337 VAL Chi-restraints excluded: chain K residue 394 LEU Chi-restraints excluded: chain K residue 409 LEU 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 52 GLU Chi-restraints excluded: chain N residue 84 THR 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 137 GLU Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain O residue 174 ARG 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 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 458 THR Chi-restraints excluded: chain Q residue 116 ILE Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 55 ASP 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 148 ARG Chi-restraints excluded: chain T residue 167 GLU Chi-restraints excluded: chain T residue 174 ARG 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 387 ASP 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 41 VAL 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 55 ASP 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 63 GLU 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 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 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 156 optimal weight: 2.9990 chunk 417 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 272 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 464 optimal weight: 2.9990 chunk 385 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 38 optimal weight: 0.0470 chunk 153 optimal weight: 0.7980 chunk 243 optimal weight: 0.9980 overall best weight: 1.5682 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN ** S 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 68 ASN K 56 ASN K 349 GLN L 45 ASN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 63 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 ** both conformations clash, **PLEASE CHECK MANUALLY** V 45 ASN ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN Y 267 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0846 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= 0.247 Angle : 0.567 6.406 53442 Z= 0.310 Chirality : 0.051 0.184 5934 Planarity : 0.004 0.058 6996 Dihedral : 6.249 59.314 5464 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.71 % Allowed : 17.19 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.11), residues: 4902 helix: -0.12 (0.33), residues: 270 sheet: -0.45 (0.13), residues: 1476 loop : -1.13 (0.10), residues: 3156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 161 HIS 0.004 0.001 HIS M 88 PHE 0.018 0.002 PHE K 384 TYR 0.012 0.002 TYR O 80 ARG 0.006 0.000 ARG O 148 *********************** 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 710 residues out of total 4182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 513 time to evaluate : 4.529 Fit side-chains REVERT: A 24 LYS cc_start: 0.8847 (pttp) cc_final: 0.8470 (pttt) REVERT: B 54 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7513 (tm-30) REVERT: B 68 ASN cc_start: 0.8849 (p0) cc_final: 0.8215 (p0) REVERT: S 138 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6412 (mp) REVERT: S 294 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8283 (pt0) REVERT: S 357 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: S 395 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.6826 (tt0) REVERT: D 24 LYS cc_start: 0.8936 (pttp) cc_final: 0.8291 (pttp) REVERT: D 54 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6111 (tp30) REVERT: E 52 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7715 (tp30) REVERT: G 138 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.5966 (mp) REVERT: G 167 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7188 (pm20) REVERT: G 294 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8421 (pt0) REVERT: G 387 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8060 (m-30) REVERT: K 111 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8087 (mm-40) REVERT: K 137 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: K 138 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6445 (mp) REVERT: K 373 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8185 (mmtm) REVERT: N 52 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: O 111 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8112 (mm-40) REVERT: O 137 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: O 138 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6335 (mp) REVERT: O 373 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8239 (mmmm) REVERT: O 454 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.8019 (mp) REVERT: P 54 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.6146 (tp30) REVERT: T 138 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6334 (mp) REVERT: T 148 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7222 (mmt90) REVERT: T 387 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8292 (m-30) REVERT: V 24 LYS cc_start: 0.8793 (pttp) cc_final: 0.8453 (pttt) REVERT: W 68 ASN cc_start: 0.8821 (p0) cc_final: 0.8189 (p0) REVERT: Y 54 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7891 (m-30) REVERT: Y 138 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6456 (mp) REVERT: Y 241 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8540 (p) REVERT: Y 294 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8474 (pt0) REVERT: Y 357 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.8005 (mp0) REVERT: Y 404 GLN cc_start: 0.8098 (pm20) cc_final: 0.7876 (mp10) outliers start: 197 outliers final: 128 residues processed: 661 average time/residue: 1.4776 time to fit residues: 1184.5821 Evaluate side-chains 657 residues out of total 4182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 500 time to evaluate : 4.734 ------------------------------------------------------------------------------- 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 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 137 GLU Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain S residue 167 GLU Chi-restraints excluded: chain S residue 196 ASP Chi-restraints excluded: chain S residue 216 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 S residue 458 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 55 ASP 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 294 GLU Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 387 ASP Chi-restraints excluded: chain G residue 394 LEU Chi-restraints excluded: chain G residue 435 ASP Chi-restraints excluded: chain H residue 22 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 J residue 106 VAL 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 137 GLU Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain K residue 196 ASP Chi-restraints excluded: chain K residue 227 SER 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 288 MET Chi-restraints excluded: chain K residue 337 VAL Chi-restraints excluded: chain K residue 373 LYS Chi-restraints excluded: chain K residue 394 LEU Chi-restraints excluded: chain K residue 409 LEU 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 24 LYS Chi-restraints excluded: chain N residue 52 GLU Chi-restraints excluded: chain N residue 84 THR 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 137 GLU Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 167 GLU 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 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 454 LEU Chi-restraints excluded: chain O residue 458 THR Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain Q residue 116 ILE Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain R residue 55 ASP 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 137 GLU Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 148 ARG Chi-restraints excluded: chain T residue 167 GLU Chi-restraints excluded: chain T residue 174 ARG 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 387 ASP Chi-restraints excluded: chain T residue 394 LEU 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 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 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 267 GLN Chi-restraints excluded: chain Y residue 269 SER Chi-restraints excluded: chain Y residue 271 ILE 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 Chi-restraints excluded: chain Y residue 435 ASP Chi-restraints excluded: chain Y residue 458 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 339 optimal weight: 4.9990 chunk 262 optimal weight: 7.9990 chunk 390 optimal weight: 4.9990 chunk 259 optimal weight: 6.9990 chunk 462 optimal weight: 6.9990 chunk 289 optimal weight: 3.9990 chunk 282 optimal weight: 3.9990 chunk 213 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN C 76 ASN S 267 GLN S 404 GLN D 45 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 GLN J 68 ASN K 56 ASN K 349 GLN L 45 ASN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 63 GLN N 68 ASN O 56 ASN O 267 GLN O 349 GLN P 45 ASN ** P 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 267 GLN V 45 ASN ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 63 GLN X 68 ASN X 76 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 39342 Z= 0.588 Angle : 0.806 8.630 53442 Z= 0.438 Chirality : 0.061 0.269 5934 Planarity : 0.007 0.076 6996 Dihedral : 7.204 62.952 5464 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 5.60 % Allowed : 17.26 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.11), residues: 4902 helix: -0.49 (0.33), residues: 270 sheet: -0.75 (0.12), residues: 1536 loop : -1.38 (0.10), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP T 326 HIS 0.008 0.002 HIS O 252 PHE 0.021 0.003 PHE O 384 TYR 0.018 0.003 TYR O 420 ARG 0.009 0.001 ARG B 14 *********************** 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 734 residues out of total 4182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 500 time to evaluate : 4.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8913 (pttp) cc_final: 0.8529 (pttt) REVERT: S 12 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8159 (tpp) REVERT: S 138 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6637 (mp) REVERT: S 267 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8024 (pp30) REVERT: S 294 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8326 (pt0) REVERT: S 357 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: S 395 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.6930 (tt0) REVERT: D 24 LYS cc_start: 0.9079 (pttp) cc_final: 0.8326 (pttp) REVERT: D 54 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6235 (tp30) REVERT: E 52 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7701 (tp30) REVERT: G 138 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6345 (mp) REVERT: G 167 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7238 (pm20) REVERT: G 387 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8209 (m-30) REVERT: I 108 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8300 (mtpt) REVERT: J 110 ASP cc_start: 0.8172 (t0) cc_final: 0.7771 (t70) REVERT: K 111 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8109 (mm-40) REVERT: K 137 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: K 138 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6854 (mp) REVERT: K 373 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8266 (mmmm) REVERT: M 108 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8334 (mtpt) REVERT: N 52 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: N 110 ASP cc_start: 0.8178 (t0) cc_final: 0.7728 (t70) REVERT: O 14 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7780 (mttt) REVERT: O 111 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8130 (mm-40) REVERT: O 137 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7166 (mp0) REVERT: O 138 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6842 (mp) REVERT: O 245 ASP cc_start: 0.7577 (m-30) cc_final: 0.7314 (m-30) REVERT: O 373 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8379 (mmmm) REVERT: P 24 LYS cc_start: 0.8827 (pttp) cc_final: 0.8480 (ptmm) REVERT: P 54 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6279 (tp30) REVERT: T 63 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8411 (tt0) REVERT: T 138 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6521 (mp) REVERT: T 148 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7259 (mmt90) REVERT: T 387 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8451 (m-30) REVERT: V 24 LYS cc_start: 0.8864 (pttp) cc_final: 0.8530 (pttt) REVERT: W 37 ASP cc_start: 0.7898 (m-30) cc_final: 0.7669 (m-30) REVERT: Y 138 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6777 (mp) REVERT: Y 142 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7949 (ttt180) REVERT: Y 294 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8468 (pt0) REVERT: Y 357 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8049 (mp0) REVERT: Y 404 GLN cc_start: 0.8144 (pm20) cc_final: 0.7920 (mp10) outliers start: 234 outliers final: 135 residues processed: 684 average time/residue: 1.4620 time to fit residues: 1213.4360 Evaluate side-chains 660 residues out of total 4182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 493 time to evaluate : 4.504 ------------------------------------------------------------------------------- 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 62 THR 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 138 LEU Chi-restraints excluded: chain S residue 196 ASP Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 267 GLN 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 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 52 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 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 294 GLU Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 387 ASP Chi-restraints excluded: chain G residue 394 LEU 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 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 108 LYS 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 J residue 106 VAL 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 137 GLU 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 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 394 LEU Chi-restraints excluded: chain K residue 396 VAL Chi-restraints excluded: chain K residue 409 LEU 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 38 THR Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 108 LYS 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 52 GLU Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain O residue 14 LYS 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 137 GLU Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain O residue 174 ARG 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 267 GLN 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 439 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 63 GLU Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 148 ARG Chi-restraints excluded: chain T residue 167 GLU Chi-restraints excluded: chain T residue 174 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 387 ASP Chi-restraints excluded: chain T residue 394 LEU 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 38 THR Chi-restraints excluded: chain W residue 62 THR Chi-restraints excluded: chain W residue 108 LYS 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 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 196 ASP Chi-restraints excluded: chain Y residue 216 THR Chi-restraints excluded: chain Y residue 269 SER Chi-restraints excluded: chain Y residue 271 ILE 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 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 286 optimal weight: 2.9990 chunk 184 optimal weight: 0.7980 chunk 276 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 294 optimal weight: 1.9990 chunk 315 optimal weight: 0.8980 chunk 228 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 363 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** S 267 GLN D 45 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN G 5 GLN H 45 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 68 ASN K 267 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** T 5 GLN V 45 ASN ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 267 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.0853 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= 0.165 Angle : 0.517 5.897 53442 Z= 0.285 Chirality : 0.050 0.192 5934 Planarity : 0.004 0.050 6996 Dihedral : 6.095 57.567 5461 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.78 % Allowed : 19.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.11), residues: 4902 helix: 0.61 (0.35), residues: 228 sheet: -0.44 (0.13), residues: 1422 loop : -1.11 (0.10), residues: 3252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 161 HIS 0.003 0.001 HIS G 99 PHE 0.017 0.001 PHE K 384 TYR 0.010 0.001 TYR S 80 ARG 0.005 0.000 ARG O 148 *********************** 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 675 residues out of total 4182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 517 time to evaluate : 4.555 Fit side-chains REVERT: A 24 LYS cc_start: 0.8825 (pttp) cc_final: 0.8486 (pttp) REVERT: B 54 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7537 (tm-30) REVERT: B 68 ASN cc_start: 0.8796 (p0) cc_final: 0.8217 (p0) REVERT: S 267 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8033 (pp30) REVERT: S 294 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8325 (pt0) REVERT: D 24 LYS cc_start: 0.8922 (pttp) cc_final: 0.8279 (pttp) REVERT: D 54 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.6080 (tp30) REVERT: E 52 GLU cc_start: 0.7953 (tt0) cc_final: 0.7630 (tp30) REVERT: G 138 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5964 (mp) REVERT: G 167 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7278 (pm20) REVERT: G 180 ARG cc_start: 0.8257 (mmm160) cc_final: 0.7705 (mtt90) REVERT: G 294 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8395 (pt0) REVERT: G 387 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7942 (m-30) REVERT: J 107 LEU cc_start: 0.9093 (tt) cc_final: 0.8850 (tp) REVERT: K 180 ARG cc_start: 0.8268 (mmm-85) cc_final: 0.7915 (mtp85) REVERT: O 111 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8138 (mm-40) REVERT: O 373 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8234 (mmmm) REVERT: P 54 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6112 (tp30) REVERT: T 387 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8099 (m-30) REVERT: V 24 LYS cc_start: 0.8766 (pttp) cc_final: 0.8475 (pttp) REVERT: W 68 ASN cc_start: 0.8768 (p0) cc_final: 0.8190 (p0) REVERT: Y 267 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8274 (pp30) REVERT: Y 294 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8489 (pt0) REVERT: Y 404 GLN cc_start: 0.7995 (pm20) cc_final: 0.7728 (mp10) outliers start: 158 outliers final: 100 residues processed: 635 average time/residue: 1.4722 time to fit residues: 1140.3469 Evaluate side-chains 617 residues out of total 4182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 505 time to evaluate : 4.415 ------------------------------------------------------------------------------- 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 62 THR Chi-restraints excluded: chain C residue 20 SER 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 137 GLU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 267 GLN Chi-restraints excluded: chain S residue 271 ILE 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 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 F residue 120 LYS 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 255 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 360 VAL Chi-restraints excluded: chain G residue 387 ASP Chi-restraints excluded: chain G residue 394 LEU 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 J residue 20 SER Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 106 VAL 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 167 GLU Chi-restraints excluded: chain K residue 227 SER 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 267 GLN 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 K residue 409 LEU Chi-restraints excluded: chain M residue 98 SER 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 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 237 THR Chi-restraints excluded: chain O residue 240 LYS Chi-restraints excluded: chain O residue 241 THR 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 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 84 THR Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 167 GLU 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 387 ASP Chi-restraints excluded: chain T residue 394 LEU Chi-restraints excluded: chain T residue 435 ASP Chi-restraints excluded: chain T residue 458 THR 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 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 102 THR Chi-restraints excluded: chain Y residue 199 VAL Chi-restraints excluded: chain Y residue 216 THR Chi-restraints excluded: chain Y residue 267 GLN Chi-restraints excluded: chain Y residue 269 SER 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 420 optimal weight: 5.9990 chunk 443 optimal weight: 9.9990 chunk 404 optimal weight: 6.9990 chunk 431 optimal weight: 10.0000 chunk 259 optimal weight: 7.9990 chunk 187 optimal weight: 4.9990 chunk 338 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 389 optimal weight: 3.9990 chunk 407 optimal weight: 7.9990 chunk 429 optimal weight: 3.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN S 267 GLN D 45 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 68 ASN K 267 GLN L 45 ASN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN O 267 GLN P 45 ASN ** P 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 45 ASN ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN ** Y 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 267 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 39342 Z= 0.509 Angle : 0.758 9.101 53442 Z= 0.412 Chirality : 0.059 0.254 5934 Planarity : 0.006 0.071 6996 Dihedral : 6.917 61.446 5453 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.95 % Allowed : 19.30 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.11), residues: 4902 helix: -0.38 (0.33), residues: 270 sheet: -0.71 (0.12), residues: 1530 loop : -1.31 (0.10), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP T 326 HIS 0.008 0.002 HIS M 88 PHE 0.021 0.003 PHE O 384 TYR 0.017 0.003 TYR J 32 ARG 0.007 0.001 ARG W 14 *********************** 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 671 residues out of total 4182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 506 time to evaluate : 4.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8905 (pttp) cc_final: 0.8517 (pttt) REVERT: A 121 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7408 (ptpt) REVERT: S 138 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6519 (mp) REVERT: S 267 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8025 (pp30) REVERT: S 294 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8342 (pt0) REVERT: S 357 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7869 (mp0) REVERT: D 24 LYS cc_start: 0.9095 (pttp) cc_final: 0.8344 (pttp) REVERT: D 54 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6191 (tp30) REVERT: E 52 GLU cc_start: 0.7995 (tt0) cc_final: 0.7727 (tp30) REVERT: E 99 GLN cc_start: 0.8985 (tt0) cc_final: 0.8746 (tt0) REVERT: G 138 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6329 (mp) REVERT: G 167 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7222 (pm20) REVERT: G 294 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8563 (pt0) REVERT: G 387 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8184 (m-30) REVERT: G 395 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7268 (mm-30) REVERT: K 8 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7376 (ptp) REVERT: K 111 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8119 (mm-40) REVERT: K 137 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: K 245 ASP cc_start: 0.7590 (m-30) cc_final: 0.7324 (m-30) REVERT: K 373 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8235 (mmmm) REVERT: M 116 ILE cc_start: 0.7877 (mp) cc_final: 0.7617 (mt) REVERT: O 111 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8132 (mm-40) REVERT: O 137 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: O 138 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6688 (mp) REVERT: O 245 ASP cc_start: 0.7556 (m-30) cc_final: 0.7302 (m-30) REVERT: O 373 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8364 (mmmm) REVERT: P 24 LYS cc_start: 0.8836 (pttp) cc_final: 0.8496 (ptmm) REVERT: P 54 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.6231 (tp30) REVERT: Q 99 GLN cc_start: 0.8981 (tt0) cc_final: 0.8667 (tt0) REVERT: T 138 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6534 (mp) REVERT: T 387 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8413 (m-30) REVERT: T 395 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7306 (mm-30) REVERT: V 24 LYS cc_start: 0.8890 (pttp) cc_final: 0.8553 (pttt) REVERT: Y 138 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6606 (mp) REVERT: Y 267 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8222 (pp30) REVERT: Y 294 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8473 (pt0) REVERT: Y 357 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8066 (mp0) REVERT: Y 404 GLN cc_start: 0.8124 (pm20) cc_final: 0.7827 (mp10) outliers start: 165 outliers final: 114 residues processed: 638 average time/residue: 1.4852 time to fit residues: 1146.3741 Evaluate side-chains 641 residues out of total 4182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 501 time to evaluate : 4.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain C residue 20 SER 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 102 THR 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 216 THR Chi-restraints excluded: chain S residue 267 GLN 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 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 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 294 GLU Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 387 ASP 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 G residue 458 THR 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 J residue 16 ILE Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 106 VAL 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 137 GLU Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain K residue 227 SER 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 337 VAL Chi-restraints excluded: chain K residue 373 LYS Chi-restraints excluded: chain K residue 394 LEU Chi-restraints excluded: chain K residue 409 LEU 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 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 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 137 GLU Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain O residue 174 ARG 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 267 GLN 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 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 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 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 387 ASP 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 T residue 458 THR 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 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 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 267 GLN 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 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 283 optimal weight: 1.9990 chunk 455 optimal weight: 1.9990 chunk 278 optimal weight: 0.0970 chunk 216 optimal weight: 2.9990 chunk 316 optimal weight: 0.9990 chunk 478 optimal weight: 0.9990 chunk 440 optimal weight: 5.9990 chunk 380 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 294 optimal weight: 0.6980 chunk 233 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** S 267 GLN D 45 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** V 45 ASN ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 267 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 39342 Z= 0.162 Angle : 0.514 5.749 53442 Z= 0.283 Chirality : 0.050 0.201 5934 Planarity : 0.004 0.056 6996 Dihedral : 5.932 57.754 5453 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.04 % Allowed : 20.28 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.11), residues: 4902 helix: 0.70 (0.36), residues: 228 sheet: -0.40 (0.13), residues: 1362 loop : -1.06 (0.10), residues: 3312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 161 HIS 0.003 0.001 HIS T 99 PHE 0.016 0.001 PHE K 384 TYR 0.011 0.001 TYR L 114 ARG 0.004 0.000 ARG O 148 ********************** 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 644 residues out of total 4182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 517 time to evaluate : 4.327 Fit side-chains REVERT: A 24 LYS cc_start: 0.8824 (pttp) cc_final: 0.8477 (pttp) REVERT: A 121 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7393 (ptpt) REVERT: B 68 ASN cc_start: 0.8781 (p0) cc_final: 0.8210 (p0) REVERT: B 108 LYS cc_start: 0.8804 (mmtp) cc_final: 0.8561 (mptm) REVERT: S 267 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7917 (pp30) REVERT: S 294 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8328 (pt0) REVERT: S 357 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: D 24 LYS cc_start: 0.8923 (pttp) cc_final: 0.8276 (pttp) REVERT: D 54 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.6153 (tp30) REVERT: E 52 GLU cc_start: 0.7923 (tt0) cc_final: 0.7685 (tp30) REVERT: G 138 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.5986 (mp) REVERT: G 167 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7232 (pm20) REVERT: G 180 ARG cc_start: 0.8280 (mmm160) cc_final: 0.7719 (mtt90) REVERT: G 294 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8386 (pt0) REVERT: G 387 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7929 (m-30) REVERT: G 395 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7035 (mm-30) REVERT: J 107 LEU cc_start: 0.9076 (tt) cc_final: 0.8873 (tp) REVERT: K 111 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8131 (mm-40) REVERT: K 180 ARG cc_start: 0.8261 (mmm-85) cc_final: 0.7921 (mtp85) REVERT: M 54 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7207 (tm-30) REVERT: N 52 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: O 12 MET cc_start: 0.8610 (tpt) cc_final: 0.7676 (tpt) REVERT: O 111 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8138 (mm-40) REVERT: O 373 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8234 (mmmm) REVERT: P 54 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.6200 (tp30) REVERT: Q 99 GLN cc_start: 0.8895 (tt0) cc_final: 0.8660 (tt0) REVERT: T 167 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: V 24 LYS cc_start: 0.8795 (pttp) cc_final: 0.8514 (pttp) REVERT: W 68 ASN cc_start: 0.8752 (p0) cc_final: 0.8183 (p0) REVERT: W 108 LYS cc_start: 0.8798 (mmtp) cc_final: 0.8568 (mptm) REVERT: Y 245 ASP cc_start: 0.7343 (m-30) cc_final: 0.7036 (m-30) REVERT: Y 267 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8257 (pp30) REVERT: Y 294 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8480 (pt0) REVERT: Y 357 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8057 (mp0) outliers start: 127 outliers final: 93 residues processed: 610 average time/residue: 1.5123 time to fit residues: 1120.5217 Evaluate side-chains 618 residues out of total 4182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 508 time to evaluate : 4.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain C residue 20 SER 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 102 THR Chi-restraints excluded: chain S residue 137 GLU Chi-restraints excluded: chain S residue 167 GLU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 267 GLN 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 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 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 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 294 GLU Chi-restraints excluded: chain G residue 360 VAL Chi-restraints excluded: chain G residue 387 ASP Chi-restraints excluded: chain G residue 395 GLU 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 98 SER 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 J residue 106 VAL 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 394 LEU Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain N residue 52 GLU 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 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 458 THR Chi-restraints excluded: chain P residue 54 GLU 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 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 435 ASP Chi-restraints excluded: chain T residue 458 THR Chi-restraints excluded: chain V residue 62 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 102 THR Chi-restraints excluded: chain Y residue 199 VAL Chi-restraints excluded: chain Y residue 216 THR Chi-restraints excluded: chain Y residue 267 GLN 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 Chi-restraints excluded: chain Y residue 435 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 0.7980 chunk 405 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 351 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 381 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 391 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN C 113 GLN S 267 GLN S 404 GLN D 45 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 267 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** ** P 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 45 ASN ** V 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN ** Y 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 267 GLN Y 404 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.123661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.113253 restraints weight = 42624.123| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 0.58 r_work: 0.3022 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 39342 Z= 0.464 Angle : 0.731 9.020 53442 Z= 0.397 Chirality : 0.057 0.240 5934 Planarity : 0.006 0.074 6996 Dihedral : 6.820 59.695 5453 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.80 % Allowed : 19.56 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.11), residues: 4902 helix: -0.31 (0.33), residues: 270 sheet: -0.69 (0.12), residues: 1530 loop : -1.27 (0.10), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP G 326 HIS 0.007 0.002 HIS M 88 PHE 0.021 0.003 PHE T 410 TYR 0.018 0.003 TYR E 93 ARG 0.007 0.001 ARG W 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16125.51 seconds wall clock time: 287 minutes 51.79 seconds (17271.79 seconds total)