Starting phenix.real_space_refine on Sat Mar 7 05:13:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sg7_25106/03_2026/7sg7_25106.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sg7_25106/03_2026/7sg7_25106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sg7_25106/03_2026/7sg7_25106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sg7_25106/03_2026/7sg7_25106.map" model { file = "/net/cci-nas-00/data/ceres_data/7sg7_25106/03_2026/7sg7_25106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sg7_25106/03_2026/7sg7_25106.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 132 5.16 5 C 24696 2.51 5 N 6486 2.21 5 O 7488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38802 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 938 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 8, 'TRANS': 111} Chain: "B" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 915 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "C" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 8, 'TRANS': 112} Chain: "T" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 17, 'TRANS': 453} Chain: "D" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 938 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 8, 'TRANS': 111} Chain: "I" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 915 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "N" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 8, 'TRANS': 112} Chain: "S" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 17, 'TRANS': 453} Chain: "E" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 938 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 8, 'TRANS': 111} Chain: "J" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 915 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "O" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 8, 'TRANS': 112} Chain: "U" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 17, 'TRANS': 453} Chain: "F" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 938 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 8, 'TRANS': 111} Chain: "K" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 915 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "P" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 8, 'TRANS': 112} Chain: "V" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 17, 'TRANS': 453} Chain: "G" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 938 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 8, 'TRANS': 111} Chain: "L" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 915 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 8, 'TRANS': 112} Chain: "W" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 17, 'TRANS': 453} Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 938 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 8, 'TRANS': 111} Chain: "M" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 915 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "R" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 8, 'TRANS': 112} Chain: "X" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 17, 'TRANS': 453} Time building chain proxies: 8.69, per 1000 atoms: 0.22 Number of scatterers: 38802 At special positions: 0 Unit cell: (200.838, 207.57, 126.786, 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 132 16.00 O 7488 8.00 N 6486 7.00 C 24696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.5 seconds 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9096 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 123 sheets defined 9.0% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.524A pdb=" N TYR A 109 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP A 110 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 122 removed outlier: 3.723A pdb=" N ASP A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 123 Proline residue: B 116 - end of helix removed outlier: 3.636A pdb=" N ALA B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 46 removed outlier: 3.507A pdb=" N GLN C 46 " --> pdb=" O PRO C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 123 removed outlier: 3.835A pdb=" N ASP C 117 " --> pdb=" O GLN C 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 'T' and resid 318 through 320 No H-bonds generated for 'chain 'T' and resid 318 through 320' Processing helix chain 'D' and resid 105 through 110 removed outlier: 3.525A pdb=" N TYR D 109 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP D 110 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 122 removed outlier: 3.792A pdb=" N ASP D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 57 removed outlier: 4.071A pdb=" N SER I 57 " --> pdb=" O GLU I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 123 Proline residue: I 116 - end of helix Processing helix chain 'N' and resid 42 through 46 Processing helix chain 'N' and resid 54 through 56 No H-bonds generated for 'chain 'N' and resid 54 through 56' Processing helix chain 'N' and resid 113 through 124 removed outlier: 3.674A pdb=" N ASP N 117 " --> pdb=" O GLN N 113 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE N 119 " --> pdb=" O GLY N 115 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU N 120 " --> pdb=" O PRO N 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 226 through 229 Processing helix chain 'S' and resid 252 through 256 removed outlier: 3.541A pdb=" N GLY S 256 " --> pdb=" O PRO S 253 " (cutoff:3.500A) Processing helix chain 'S' and resid 273 through 282 removed outlier: 3.532A pdb=" N LYS S 278 " --> pdb=" O ALA S 274 " (cutoff:3.500A) Processing helix chain 'S' and resid 318 through 320 No H-bonds generated for 'chain 'S' and resid 318 through 320' Processing helix chain 'E' and resid 105 through 110 removed outlier: 3.509A pdb=" N TYR E 109 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP E 110 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 122 removed outlier: 3.757A pdb=" N ASP E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 57 removed outlier: 4.020A pdb=" N SER J 57 " --> pdb=" O GLU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 123 Proline residue: J 116 - end of helix removed outlier: 3.519A pdb=" N ALA J 123 " --> pdb=" O ILE J 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 46 removed outlier: 3.524A pdb=" N GLN O 46 " --> pdb=" O PRO O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 123 removed outlier: 3.598A pdb=" N ASP O 117 " --> pdb=" O GLN O 113 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE O 119 " --> pdb=" O GLY O 115 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU O 120 " --> pdb=" O PRO O 116 " (cutoff:3.500A) Processing helix chain 'U' and resid 226 through 229 Processing helix chain 'U' and resid 252 through 256 removed outlier: 3.575A pdb=" N GLY U 256 " --> pdb=" O PRO U 253 " (cutoff:3.500A) Processing helix chain 'U' and resid 273 through 282 removed outlier: 3.517A pdb=" N LYS U 278 " --> pdb=" O ALA U 274 " (cutoff:3.500A) Processing helix chain 'U' and resid 318 through 320 No H-bonds generated for 'chain 'U' and resid 318 through 320' Processing helix chain 'F' and resid 105 through 110 removed outlier: 3.562A pdb=" N TYR F 109 " --> pdb=" O VAL F 106 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP F 110 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 122 removed outlier: 3.720A pdb=" N ASP F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 57 removed outlier: 4.068A pdb=" N SER K 57 " --> pdb=" O GLU K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 123 Proline residue: K 116 - end of helix Processing helix chain 'P' and resid 42 through 46 removed outlier: 3.517A pdb=" N GLN P 46 " --> pdb=" O PRO P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 113 through 124 removed outlier: 3.991A pdb=" N ASP P 117 " --> pdb=" O GLN P 113 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU P 118 " --> pdb=" O PHE P 114 " (cutoff:3.500A) Processing helix chain 'V' and resid 226 through 229 Processing helix chain 'V' and resid 252 through 256 removed outlier: 3.514A pdb=" N GLY V 256 " --> pdb=" O PRO V 253 " (cutoff:3.500A) Processing helix chain 'V' and resid 273 through 282 Processing helix chain 'V' and resid 286 through 291 removed outlier: 4.168A pdb=" N ASP V 290 " --> pdb=" O GLU V 287 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY V 291 " --> pdb=" O LEU V 288 " (cutoff:3.500A) Processing helix chain 'V' and resid 318 through 320 No H-bonds generated for 'chain 'V' and resid 318 through 320' Processing helix chain 'G' and resid 105 through 110 removed outlier: 3.535A pdb=" N TYR G 109 " --> pdb=" O VAL G 106 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP G 110 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 122 removed outlier: 3.820A pdb=" N ASP G 117 " --> pdb=" O GLN G 113 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 57 removed outlier: 4.015A pdb=" N SER L 57 " --> pdb=" O GLU L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 123 Proline residue: L 116 - end of helix Processing helix chain 'Q' and resid 42 through 46 removed outlier: 3.521A pdb=" N GLN Q 46 " --> pdb=" O PRO Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 113 through 124 removed outlier: 3.895A pdb=" N ASP Q 117 " --> pdb=" O GLN Q 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 226 through 229 Processing helix chain 'W' and resid 252 through 256 removed outlier: 3.565A pdb=" N GLY W 256 " --> pdb=" O PRO W 253 " (cutoff:3.500A) Processing helix chain 'W' and resid 273 through 282 removed outlier: 3.511A pdb=" N LYS W 278 " --> pdb=" O ALA W 274 " (cutoff:3.500A) Processing helix chain 'W' and resid 318 through 320 No H-bonds generated for 'chain 'W' and resid 318 through 320' Processing helix chain 'H' and resid 105 through 110 removed outlier: 3.532A pdb=" N TYR H 109 " --> pdb=" O VAL H 106 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP H 110 " --> pdb=" O LEU H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 122 removed outlier: 3.675A pdb=" N ASP H 117 " --> pdb=" O GLN H 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 57 removed outlier: 4.087A pdb=" N SER M 57 " --> pdb=" O GLU M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 123 Proline residue: M 116 - end of helix Processing helix chain 'R' and resid 42 through 46 Processing helix chain 'R' and resid 54 through 56 No H-bonds generated for 'chain 'R' and resid 54 through 56' Processing helix chain 'R' and resid 113 through 124 removed outlier: 3.827A pdb=" N ASP R 117 " --> pdb=" O GLN R 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 226 through 229 Processing helix chain 'X' and resid 252 through 256 removed outlier: 3.502A pdb=" N GLY X 256 " --> pdb=" O PRO X 253 " (cutoff:3.500A) Processing helix chain 'X' and resid 273 through 282 removed outlier: 3.536A pdb=" N LYS X 278 " --> pdb=" O ALA X 274 " (cutoff:3.500A) Processing helix chain 'X' and resid 318 through 320 No H-bonds generated for 'chain 'X' and resid 318 through 320' Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 9 removed outlier: 4.362A pdb=" N LYS C 108 " --> pdb=" O VAL A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79 removed outlier: 4.303A pdb=" N VAL A 66 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 89 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N MET A 90 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR A 102 " --> pdb=" O MET A 90 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL A 92 " --> pdb=" O GLN A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 74 removed outlier: 4.079A pdb=" N VAL B 66 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE B 101 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 61 removed outlier: 4.780A pdb=" N VAL B 49 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS B 81 " --> pdb=" O GLU B 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 30 through 31 removed outlier: 4.680A pdb=" N VAL C 66 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 58 through 61 removed outlier: 3.558A pdb=" N VAL C 59 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL C 49 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'T' and resid 3 through 5 Processing sheet with id=AA9, first strand: chain 'T' and resid 3 through 5 removed outlier: 6.929A pdb=" N LEU T 464 " --> pdb=" O SER T 398 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER T 398 " --> pdb=" O LEU T 464 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N GLY T 466 " --> pdb=" O VAL T 396 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL T 396 " --> pdb=" O GLY T 466 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLN T 468 " --> pdb=" O LEU T 394 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU T 394 " --> pdb=" O GLN T 468 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LYS T 441 " --> pdb=" O ASP T 393 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU T 395 " --> pdb=" O LEU T 439 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU T 439 " --> pdb=" O GLU T 395 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'T' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'T' and resid 51 through 54 removed outlier: 6.818A pdb=" N THR T 360 " --> pdb=" O ARG T 52 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 59 through 65 removed outlier: 3.555A pdb=" N GLY T 61 " --> pdb=" O VAL T 74 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU T 79 " --> pdb=" O VAL T 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 96 through 99 removed outlier: 3.596A pdb=" N SER T 96 " --> pdb=" O GLY T 107 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 141 through 147 removed outlier: 4.434A pdb=" N ASP T 143 " --> pdb=" O SER T 154 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N SER T 160 " --> pdb=" O LYS T 155 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'T' and resid 190 through 193 removed outlier: 3.503A pdb=" N GLU T 207 " --> pdb=" O CYS T 200 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'T' and resid 240 through 242 removed outlier: 5.124A pdb=" N TYR T 247 " --> pdb=" O ILE T 263 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'T' and resid 294 through 296 Processing sheet with id=AB9, first strand: chain 'T' and resid 341 through 345 removed outlier: 3.538A pdb=" N ILE T 341 " --> pdb=" O GLY T 353 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE T 343 " --> pdb=" O THR T 351 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR T 351 " --> pdb=" O PHE T 343 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'T' and resid 375 through 378 removed outlier: 3.515A pdb=" N THR T 458 " --> pdb=" O GLN T 375 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 384 through 385 removed outlier: 3.539A pdb=" N VAL T 450 " --> pdb=" O PHE T 384 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 8 through 9 removed outlier: 4.376A pdb=" N LYS N 108 " --> pdb=" O VAL D 9 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 78 through 79 removed outlier: 4.320A pdb=" N VAL D 66 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER D 89 " --> pdb=" O GLY D 34 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET D 90 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR D 102 " --> pdb=" O MET D 90 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL D 92 " --> pdb=" O GLN D 100 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 58 through 60 Processing sheet with id=AC6, first strand: chain 'I' and resid 73 through 74 removed outlier: 4.117A pdb=" N VAL I 66 " --> pdb=" O VAL I 74 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 59 through 61 removed outlier: 4.713A pdb=" N VAL I 49 " --> pdb=" O VAL I 61 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 30 through 31 Processing sheet with id=AC9, first strand: chain 'N' and resid 58 through 61 removed outlier: 4.761A pdb=" N VAL N 49 " --> pdb=" O VAL N 61 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 74 through 75 Processing sheet with id=AD2, first strand: chain 'S' and resid 3 through 5 Processing sheet with id=AD3, first strand: chain 'S' and resid 3 through 5 removed outlier: 6.907A pdb=" N LEU S 464 " --> pdb=" O SER S 398 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER S 398 " --> pdb=" O LEU S 464 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLY S 466 " --> pdb=" O VAL S 396 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL S 396 " --> pdb=" O GLY S 466 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN S 468 " --> pdb=" O LEU S 394 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU S 394 " --> pdb=" O GLN S 468 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LYS S 441 " --> pdb=" O ASP S 393 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLU S 395 " --> pdb=" O LEU S 439 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU S 439 " --> pdb=" O GLU S 395 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 11 through 14 Processing sheet with id=AD5, first strand: chain 'S' and resid 51 through 54 removed outlier: 6.833A pdb=" N THR S 360 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 59 through 65 removed outlier: 3.638A pdb=" N GLY S 61 " --> pdb=" O VAL S 74 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU S 79 " --> pdb=" O VAL S 86 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'S' and resid 96 through 99 removed outlier: 3.936A pdb=" N SER S 96 " --> pdb=" O GLY S 107 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'S' and resid 141 through 143 removed outlier: 6.976A pdb=" N SER S 154 " --> pdb=" O ARG S 142 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 190 through 193 Processing sheet with id=AE1, first strand: chain 'S' and resid 240 through 242 removed outlier: 5.212A pdb=" N TYR S 247 " --> pdb=" O ILE S 263 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 295 through 296 removed outlier: 3.553A pdb=" N LEU S 296 " --> pdb=" O LEU S 303 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 344 through 346 Processing sheet with id=AE4, first strand: chain 'S' and resid 384 through 385 Processing sheet with id=AE5, first strand: chain 'S' and resid 408 through 411 Processing sheet with id=AE6, first strand: chain 'E' and resid 8 through 9 removed outlier: 4.367A pdb=" N LYS O 108 " --> pdb=" O VAL E 9 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 78 through 79 removed outlier: 4.330A pdb=" N VAL E 66 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY E 29 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N MET E 90 " --> pdb=" O TYR E 102 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR E 102 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL E 92 " --> pdb=" O GLN E 100 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 58 through 61 removed outlier: 4.851A pdb=" N VAL E 49 " --> pdb=" O VAL E 61 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 73 through 74 removed outlier: 4.154A pdb=" N VAL J 66 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 59 through 61 removed outlier: 4.502A pdb=" N VAL J 49 " --> pdb=" O VAL J 61 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 30 through 31 removed outlier: 4.660A pdb=" N VAL O 66 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR O 72 " --> pdb=" O ASN O 68 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 58 through 61 removed outlier: 4.810A pdb=" N VAL O 49 " --> pdb=" O VAL O 61 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'U' and resid 3 through 5 Processing sheet with id=AF5, first strand: chain 'U' and resid 3 through 5 removed outlier: 6.925A pdb=" N LEU U 464 " --> pdb=" O SER U 398 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER U 398 " --> pdb=" O LEU U 464 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N GLY U 466 " --> pdb=" O VAL U 396 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N VAL U 396 " --> pdb=" O GLY U 466 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLN U 468 " --> pdb=" O LEU U 394 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU U 394 " --> pdb=" O GLN U 468 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS U 441 " --> pdb=" O ASP U 393 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLU U 395 " --> pdb=" O LEU U 439 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU U 439 " --> pdb=" O GLU U 395 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U' and resid 11 through 15 removed outlier: 3.634A pdb=" N ASP U 20 " --> pdb=" O ASP U 15 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'U' and resid 51 through 54 removed outlier: 6.783A pdb=" N THR U 360 " --> pdb=" O ARG U 52 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'U' and resid 59 through 65 removed outlier: 3.569A pdb=" N GLY U 61 " --> pdb=" O VAL U 74 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU U 79 " --> pdb=" O VAL U 86 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'U' and resid 96 through 99 removed outlier: 3.621A pdb=" N SER U 96 " --> pdb=" O GLY U 107 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'U' and resid 141 through 143 removed outlier: 6.967A pdb=" N SER U 154 " --> pdb=" O ARG U 142 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'U' and resid 146 through 147 Processing sheet with id=AG3, first strand: chain 'U' and resid 188 through 193 Processing sheet with id=AG4, first strand: chain 'U' and resid 240 through 242 removed outlier: 5.184A pdb=" N TYR U 247 " --> pdb=" O ILE U 263 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'U' and resid 294 through 296 removed outlier: 3.540A pdb=" N LEU U 296 " --> pdb=" O LEU U 303 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'U' and resid 344 through 346 Processing sheet with id=AG7, first strand: chain 'U' and resid 384 through 385 Processing sheet with id=AG8, first strand: chain 'U' and resid 410 through 411 Processing sheet with id=AG9, first strand: chain 'F' and resid 78 through 79 removed outlier: 4.290A pdb=" N VAL F 66 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET F 90 " --> pdb=" O TYR F 102 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR F 102 " --> pdb=" O MET F 90 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL F 92 " --> pdb=" O GLN F 100 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 58 through 60 Processing sheet with id=AH2, first strand: chain 'K' and resid 73 through 74 removed outlier: 4.086A pdb=" N VAL K 66 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 59 through 61 removed outlier: 4.601A pdb=" N VAL K 49 " --> pdb=" O VAL K 61 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'P' and resid 30 through 31 removed outlier: 4.680A pdb=" N VAL P 66 " --> pdb=" O VAL P 74 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR P 72 " --> pdb=" O ASN P 68 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'P' and resid 58 through 61 removed outlier: 3.541A pdb=" N VAL P 59 " --> pdb=" O VAL P 51 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL P 49 " --> pdb=" O VAL P 61 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'V' and resid 3 through 5 Processing sheet with id=AH7, first strand: chain 'V' and resid 3 through 5 removed outlier: 6.929A pdb=" N LEU V 464 " --> pdb=" O SER V 398 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER V 398 " --> pdb=" O LEU V 464 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLY V 466 " --> pdb=" O VAL V 396 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N VAL V 396 " --> pdb=" O GLY V 466 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN V 468 " --> pdb=" O LEU V 394 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU V 394 " --> pdb=" O GLN V 468 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS V 441 " --> pdb=" O ASP V 393 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU V 395 " --> pdb=" O LEU V 439 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU V 439 " --> pdb=" O GLU V 395 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'V' and resid 11 through 12 Processing sheet with id=AH9, first strand: chain 'V' and resid 51 through 54 removed outlier: 6.820A pdb=" N THR V 360 " --> pdb=" O ARG V 52 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'V' and resid 59 through 65 removed outlier: 3.555A pdb=" N GLY V 61 " --> pdb=" O VAL V 74 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU V 79 " --> pdb=" O VAL V 86 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'V' and resid 96 through 99 removed outlier: 3.623A pdb=" N SER V 96 " --> pdb=" O GLY V 107 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'V' and resid 141 through 143 removed outlier: 6.977A pdb=" N SER V 154 " --> pdb=" O ARG V 142 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'V' and resid 160 through 161 Processing sheet with id=AI5, first strand: chain 'V' and resid 190 through 193 Processing sheet with id=AI6, first strand: chain 'V' and resid 240 through 242 removed outlier: 5.124A pdb=" N TYR V 247 " --> pdb=" O ILE V 263 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'V' and resid 294 through 296 Processing sheet with id=AI8, first strand: chain 'V' and resid 343 through 346 Processing sheet with id=AI9, first strand: chain 'V' and resid 384 through 385 Processing sheet with id=AJ1, first strand: chain 'V' and resid 424 through 425 Processing sheet with id=AJ2, first strand: chain 'G' and resid 78 through 79 removed outlier: 4.302A pdb=" N VAL G 66 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY G 29 " --> pdb=" O ILE G 67 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N MET G 90 " --> pdb=" O TYR G 102 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR G 102 " --> pdb=" O MET G 90 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL G 92 " --> pdb=" O GLN G 100 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'G' and resid 58 through 61 removed outlier: 4.854A pdb=" N VAL G 49 " --> pdb=" O VAL G 61 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'L' and resid 73 through 74 removed outlier: 4.099A pdb=" N VAL L 66 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'L' and resid 59 through 61 removed outlier: 4.526A pdb=" N VAL L 49 " --> pdb=" O VAL L 61 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'Q' and resid 30 through 31 removed outlier: 4.662A pdb=" N VAL Q 66 " --> pdb=" O VAL Q 74 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR Q 72 " --> pdb=" O ASN Q 68 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'Q' and resid 58 through 61 removed outlier: 4.821A pdb=" N VAL Q 49 " --> pdb=" O VAL Q 61 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'W' and resid 3 through 5 Processing sheet with id=AJ9, first strand: chain 'W' and resid 3 through 5 removed outlier: 6.926A pdb=" N LEU W 464 " --> pdb=" O SER W 398 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER W 398 " --> pdb=" O LEU W 464 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLY W 466 " --> pdb=" O VAL W 396 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N VAL W 396 " --> pdb=" O GLY W 466 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN W 468 " --> pdb=" O LEU W 394 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU W 394 " --> pdb=" O GLN W 468 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS W 441 " --> pdb=" O ASP W 393 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLU W 395 " --> pdb=" O LEU W 439 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU W 439 " --> pdb=" O GLU W 395 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'W' and resid 11 through 14 Processing sheet with id=AK2, first strand: chain 'W' and resid 51 through 54 removed outlier: 6.781A pdb=" N THR W 360 " --> pdb=" O ARG W 52 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'W' and resid 59 through 65 removed outlier: 3.546A pdb=" N GLY W 61 " --> pdb=" O VAL W 74 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU W 79 " --> pdb=" O VAL W 86 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'W' and resid 96 through 99 removed outlier: 3.696A pdb=" N SER W 96 " --> pdb=" O GLY W 107 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'W' and resid 141 through 143 removed outlier: 6.970A pdb=" N SER W 154 " --> pdb=" O ARG W 142 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'W' and resid 146 through 147 Processing sheet with id=AK7, first strand: chain 'W' and resid 190 through 193 Processing sheet with id=AK8, first strand: chain 'W' and resid 240 through 242 removed outlier: 5.207A pdb=" N TYR W 247 " --> pdb=" O ILE W 263 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'W' and resid 294 through 296 Processing sheet with id=AL1, first strand: chain 'W' and resid 343 through 346 Processing sheet with id=AL2, first strand: chain 'W' and resid 375 through 378 removed outlier: 3.566A pdb=" N GLN W 375 " --> pdb=" O THR W 458 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR W 458 " --> pdb=" O GLN W 375 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'W' and resid 384 through 385 Processing sheet with id=AL4, first strand: chain 'W' and resid 410 through 411 Processing sheet with id=AL5, first strand: chain 'H' and resid 78 through 79 removed outlier: 4.310A pdb=" N VAL H 66 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N MET H 90 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR H 102 " --> pdb=" O MET H 90 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL H 92 " --> pdb=" O GLN H 100 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'H' and resid 58 through 60 Processing sheet with id=AL7, first strand: chain 'M' and resid 73 through 74 removed outlier: 4.091A pdb=" N VAL M 66 " --> pdb=" O VAL M 74 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'M' and resid 59 through 61 removed outlier: 4.712A pdb=" N VAL M 49 " --> pdb=" O VAL M 61 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'R' and resid 30 through 31 Processing sheet with id=AM1, first strand: chain 'R' and resid 58 through 61 removed outlier: 4.765A pdb=" N VAL R 49 " --> pdb=" O VAL R 61 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'R' and resid 74 through 75 Processing sheet with id=AM3, first strand: chain 'X' and resid 3 through 5 Processing sheet with id=AM4, first strand: chain 'X' and resid 3 through 5 removed outlier: 6.905A pdb=" N LEU X 464 " --> pdb=" O SER X 398 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER X 398 " --> pdb=" O LEU X 464 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLY X 466 " --> pdb=" O VAL X 396 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL X 396 " --> pdb=" O GLY X 466 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLN X 468 " --> pdb=" O LEU X 394 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU X 394 " --> pdb=" O GLN X 468 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS X 441 " --> pdb=" O ASP X 393 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU X 395 " --> pdb=" O LEU X 439 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU X 439 " --> pdb=" O GLU X 395 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'X' and resid 11 through 14 Processing sheet with id=AM6, first strand: chain 'X' and resid 51 through 54 removed outlier: 6.835A pdb=" N THR X 360 " --> pdb=" O ARG X 52 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'X' and resid 59 through 65 removed outlier: 3.633A pdb=" N GLY X 61 " --> pdb=" O VAL X 74 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU X 79 " --> pdb=" O VAL X 86 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'X' and resid 96 through 99 removed outlier: 3.544A pdb=" N SER X 96 " --> pdb=" O GLY X 107 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'X' and resid 141 through 143 removed outlier: 6.973A pdb=" N SER X 154 " --> pdb=" O ARG X 142 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'X' and resid 188 through 193 Processing sheet with id=AN2, first strand: chain 'X' and resid 240 through 242 removed outlier: 5.218A pdb=" N TYR X 247 " --> pdb=" O ILE X 263 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'X' and resid 295 through 296 removed outlier: 3.535A pdb=" N LEU X 296 " --> pdb=" O LEU X 303 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'X' and resid 344 through 345 Processing sheet with id=AN5, first strand: chain 'X' and resid 384 through 385 Processing sheet with id=AN6, first strand: chain 'X' and resid 410 through 411 906 hydrogen bonds defined for protein. 2163 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: 8.41 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 6606 1.30 - 1.43: 10524 1.43 - 1.56: 22331 1.56 - 1.68: 1 1.68 - 1.81: 228 Bond restraints: 39690 Sorted by residual: bond pdb=" C PRO W 382 " pdb=" O PRO W 382 " ideal model delta sigma weight residual 1.235 1.178 0.057 1.30e-02 5.92e+03 1.91e+01 bond pdb=" C PRO U 382 " pdb=" O PRO U 382 " ideal model delta sigma weight residual 1.235 1.179 0.056 1.30e-02 5.92e+03 1.86e+01 bond pdb=" C PRO V 382 " pdb=" O PRO V 382 " ideal model delta sigma weight residual 1.233 1.190 0.043 1.23e-02 6.61e+03 1.20e+01 bond pdb=" C PRO T 382 " pdb=" O PRO T 382 " ideal model delta sigma weight residual 1.233 1.192 0.041 1.21e-02 6.83e+03 1.14e+01 bond pdb=" N ILE T 144 " pdb=" CA ILE T 144 " ideal model delta sigma weight residual 1.456 1.495 -0.038 1.14e-02 7.69e+03 1.12e+01 ... (remaining 39685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 53034 2.35 - 4.69: 799 4.69 - 7.04: 78 7.04 - 9.39: 9 9.39 - 11.74: 2 Bond angle restraints: 53922 Sorted by residual: angle pdb=" N ASP T 130 " pdb=" CA ASP T 130 " pdb=" C ASP T 130 " ideal model delta sigma weight residual 113.16 104.21 8.95 1.24e+00 6.50e-01 5.20e+01 angle pdb=" C ASN R 7 " pdb=" CA ASN R 7 " pdb=" CB ASN R 7 " ideal model delta sigma weight residual 117.23 109.83 7.40 1.36e+00 5.41e-01 2.96e+01 angle pdb=" C GLY T 372 " pdb=" N LEU T 373 " pdb=" CA LEU T 373 " ideal model delta sigma weight residual 122.93 115.21 7.72 1.45e+00 4.76e-01 2.84e+01 angle pdb=" C ILE T 426 " pdb=" N GLU T 427 " pdb=" CA GLU T 427 " ideal model delta sigma weight residual 122.19 133.93 -11.74 2.30e+00 1.89e-01 2.60e+01 angle pdb=" C ILE V 426 " pdb=" N GLU V 427 " pdb=" CA GLU V 427 " ideal model delta sigma weight residual 122.19 133.83 -11.64 2.30e+00 1.89e-01 2.56e+01 ... (remaining 53917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 21341 17.80 - 35.61: 1727 35.61 - 53.41: 308 53.41 - 71.21: 91 71.21 - 89.01: 53 Dihedral angle restraints: 23520 sinusoidal: 9174 harmonic: 14346 Sorted by residual: dihedral pdb=" CA GLY I 87 " pdb=" C GLY I 87 " pdb=" N HIS I 88 " pdb=" CA HIS I 88 " ideal model delta harmonic sigma weight residual -180.00 -156.85 -23.15 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA GLY K 87 " pdb=" C GLY K 87 " pdb=" N HIS K 88 " pdb=" CA HIS K 88 " ideal model delta harmonic sigma weight residual -180.00 -156.99 -23.01 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA GLY M 87 " pdb=" C GLY M 87 " pdb=" N HIS M 88 " pdb=" CA HIS M 88 " ideal model delta harmonic sigma weight residual -180.00 -158.05 -21.95 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 23517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4513 0.059 - 0.118: 1165 0.118 - 0.176: 154 0.176 - 0.235: 27 0.235 - 0.294: 9 Chirality restraints: 5868 Sorted by residual: chirality pdb=" CA GLU W 376 " pdb=" N GLU W 376 " pdb=" C GLU W 376 " pdb=" CB GLU W 376 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA ILE S 426 " pdb=" N ILE S 426 " pdb=" C ILE S 426 " pdb=" CB ILE S 426 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA THR G 6 " pdb=" N THR G 6 " pdb=" C THR G 6 " pdb=" CB THR G 6 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 5865 not shown) Planarity restraints: 7104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN W 374 " 0.021 2.00e-02 2.50e+03 4.31e-02 1.85e+01 pdb=" C GLN W 374 " -0.074 2.00e-02 2.50e+03 pdb=" O GLN W 374 " 0.029 2.00e-02 2.50e+03 pdb=" N GLN W 375 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU U 379 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.33e+01 pdb=" C LEU U 379 " -0.063 2.00e-02 2.50e+03 pdb=" O LEU U 379 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE U 380 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG T 150 " 0.017 2.00e-02 2.50e+03 3.61e-02 1.31e+01 pdb=" C ARG T 150 " -0.062 2.00e-02 2.50e+03 pdb=" O ARG T 150 " 0.024 2.00e-02 2.50e+03 pdb=" N TYR T 151 " 0.022 2.00e-02 2.50e+03 ... (remaining 7101 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 500 2.65 - 3.22: 33799 3.22 - 3.78: 54077 3.78 - 4.34: 79163 4.34 - 4.90: 135688 Nonbonded interactions: 303227 Sorted by model distance: nonbonded pdb=" OD1 ASP N 94 " pdb=" N ALA N 95 " model vdw 2.092 3.120 nonbonded pdb=" O ALA Q 27 " pdb=" ND2 ASN Q 28 " model vdw 2.124 3.120 nonbonded pdb=" OD2 ASP W 186 " pdb=" OG SER W 203 " model vdw 2.128 3.040 nonbonded pdb=" OD1 ASP L 94 " pdb=" N ALA L 95 " model vdw 2.130 3.120 nonbonded pdb=" OD1 ASP K 94 " pdb=" N ALA K 95 " model vdw 2.136 3.120 ... (remaining 303222 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 123) selection = chain 'B' selection = (chain 'C' and resid 7 through 123) selection = (chain 'D' and resid 7 through 123) selection = (chain 'E' and resid 7 through 123) selection = (chain 'F' and resid 7 through 123) selection = (chain 'G' and resid 7 through 123) selection = (chain 'H' and resid 7 through 123) selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = (chain 'N' and resid 7 through 123) selection = (chain 'O' and resid 7 through 123) selection = (chain 'P' and resid 7 through 123) selection = (chain 'Q' and resid 7 through 123) selection = (chain 'R' and resid 7 through 123) } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 8.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 32.960 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 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:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 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 : 0.004 0.071 39690 Z= 0.207 Angle : 0.652 11.736 53922 Z= 0.388 Chirality : 0.053 0.294 5868 Planarity : 0.004 0.086 7104 Dihedral : 14.503 89.015 14424 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.69 % Allowed : 0.72 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.11), residues: 4926 helix: -0.68 (0.32), residues: 252 sheet: -1.20 (0.14), residues: 1368 loop : -1.51 (0.10), residues: 3306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 21 TYR 0.011 0.001 TYR T 136 PHE 0.024 0.001 PHE P 101 TRP 0.025 0.002 TRP T 161 HIS 0.005 0.001 HIS T 377 Details of bonding type rmsd covalent geometry : bond 0.00368 (39690) covalent geometry : angle 0.65186 (53922) hydrogen bonds : bond 0.24951 ( 894) hydrogen bonds : angle 9.02021 ( 2163) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 4176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 590 time to evaluate : 1.524 Fit side-chains REVERT: A 94 ASP cc_start: 0.7951 (t0) cc_final: 0.7600 (t0) REVERT: A 98 SER cc_start: 0.8218 (m) cc_final: 0.7974 (m) REVERT: B 14 SER cc_start: 0.9305 (p) cc_final: 0.9025 (p) REVERT: B 39 ASP cc_start: 0.8873 (t70) cc_final: 0.8523 (t0) REVERT: B 85 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7995 (tm-30) REVERT: B 117 ASP cc_start: 0.8910 (t0) cc_final: 0.8596 (t0) REVERT: T 138 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8208 (mt) REVERT: T 153 TRP cc_start: 0.8279 (OUTLIER) cc_final: 0.7068 (p-90) REVERT: I 39 ASP cc_start: 0.8954 (t0) cc_final: 0.8723 (t0) REVERT: I 94 ASP cc_start: 0.8398 (t0) cc_final: 0.8096 (t0) REVERT: N 7 ASN cc_start: 0.8576 (m110) cc_final: 0.8284 (m110) REVERT: S 430 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8414 (tt0) REVERT: E 94 ASP cc_start: 0.8092 (t0) cc_final: 0.7811 (t0) REVERT: J 24 LYS cc_start: 0.8639 (mmmt) cc_final: 0.8436 (mmtm) REVERT: J 39 ASP cc_start: 0.9022 (t0) cc_final: 0.8754 (t0) REVERT: J 117 ASP cc_start: 0.8992 (t70) cc_final: 0.8575 (t70) REVERT: F 94 ASP cc_start: 0.7928 (t0) cc_final: 0.7579 (t0) REVERT: F 98 SER cc_start: 0.8171 (m) cc_final: 0.7936 (m) REVERT: K 14 SER cc_start: 0.9266 (p) cc_final: 0.8987 (p) REVERT: K 39 ASP cc_start: 0.9133 (t0) cc_final: 0.8775 (t0) REVERT: P 114 PHE cc_start: 0.8440 (t80) cc_final: 0.8189 (t80) REVERT: G 94 ASP cc_start: 0.8076 (t0) cc_final: 0.7798 (t0) REVERT: L 39 ASP cc_start: 0.9072 (t0) cc_final: 0.8793 (t0) REVERT: L 112 ASP cc_start: 0.9072 (t70) cc_final: 0.8844 (t70) REVERT: L 117 ASP cc_start: 0.8899 (t0) cc_final: 0.8651 (t0) REVERT: M 44 GLU cc_start: 0.9089 (pm20) cc_final: 0.8861 (pm20) REVERT: M 94 ASP cc_start: 0.8403 (t0) cc_final: 0.8125 (t0) REVERT: M 117 ASP cc_start: 0.9041 (t70) cc_final: 0.8794 (t0) REVERT: R 114 PHE cc_start: 0.8263 (t80) cc_final: 0.8046 (t80) REVERT: X 18 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.8251 (p0) outliers start: 29 outliers final: 5 residues processed: 613 average time/residue: 0.6583 time to fit residues: 493.9634 Evaluate side-chains 522 residues out of total 4176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 513 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 153 TRP Chi-restraints excluded: chain T residue 154 SER Chi-restraints excluded: chain S residue 430 GLU Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain V residue 381 THR Chi-restraints excluded: chain X residue 18 ASN Chi-restraints excluded: chain X residue 129 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 chunk 470 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS B 45 ASN C 7 ASN C 28 ASN C 76 ASN D 58 HIS D 68 ASN I 45 ASN ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 GLN N 7 ASN N 76 ASN E 58 HIS E 68 ASN J 45 ASN O 28 ASN O 53 ASN O 76 ASN F 58 HIS F 68 ASN K 45 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 ASN P 28 ASN P 76 ASN V 225 GLN G 58 HIS G 68 ASN G 100 GLN L 45 ASN Q 28 ASN Q 53 ASN Q 58 HIS Q 76 ASN H 58 HIS M 45 ASN ** M 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.063860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.049636 restraints weight = 93748.574| |-----------------------------------------------------------------------------| r_work (start): 0.2633 rms_B_bonded: 2.90 r_work: 0.2519 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2398 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 39690 Z= 0.253 Angle : 0.679 9.025 53922 Z= 0.365 Chirality : 0.052 0.211 5868 Planarity : 0.004 0.056 7104 Dihedral : 5.349 50.013 5452 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 1.92 % Allowed : 9.17 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.11), residues: 4926 helix: -0.41 (0.33), residues: 252 sheet: -1.14 (0.14), residues: 1380 loop : -1.66 (0.10), residues: 3294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG W 146 TYR 0.015 0.001 TYR V 338 PHE 0.023 0.001 PHE C 114 TRP 0.019 0.002 TRP X 153 HIS 0.006 0.001 HIS V 377 Details of bonding type rmsd covalent geometry : bond 0.00620 (39690) covalent geometry : angle 0.67882 (53922) hydrogen bonds : bond 0.04203 ( 894) hydrogen bonds : angle 6.19855 ( 2163) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 4176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 541 time to evaluate : 1.725 Fit side-chains REVERT: B 14 SER cc_start: 0.9496 (p) cc_final: 0.9243 (p) REVERT: B 39 ASP cc_start: 0.8933 (t70) cc_final: 0.8532 (t0) REVERT: B 47 ILE cc_start: 0.8833 (mm) cc_final: 0.8586 (mp) REVERT: B 85 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8411 (tm-30) REVERT: C 6 THR cc_start: 0.8866 (m) cc_final: 0.8634 (m) REVERT: T 137 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7535 (tm-30) REVERT: I 39 ASP cc_start: 0.9041 (t0) cc_final: 0.8637 (t0) REVERT: I 45 ASN cc_start: 0.8461 (m-40) cc_final: 0.8257 (m110) REVERT: I 94 ASP cc_start: 0.8701 (t0) cc_final: 0.8489 (t0) REVERT: E 94 ASP cc_start: 0.8656 (t0) cc_final: 0.8230 (t0) REVERT: J 24 LYS cc_start: 0.8787 (mmmt) cc_final: 0.8556 (mmtm) REVERT: J 39 ASP cc_start: 0.9076 (t0) cc_final: 0.8619 (t0) REVERT: J 44 GLU cc_start: 0.9297 (pm20) cc_final: 0.9061 (pm20) REVERT: J 117 ASP cc_start: 0.8681 (t70) cc_final: 0.8463 (t0) REVERT: O 28 ASN cc_start: 0.8468 (m-40) cc_final: 0.8140 (m-40) REVERT: K 14 SER cc_start: 0.9440 (p) cc_final: 0.9192 (p) REVERT: K 39 ASP cc_start: 0.9092 (t0) cc_final: 0.8639 (t0) REVERT: P 114 PHE cc_start: 0.8342 (t80) cc_final: 0.8004 (t80) REVERT: V 294 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8197 (pt0) REVERT: G 94 ASP cc_start: 0.8679 (t0) cc_final: 0.8263 (t0) REVERT: L 39 ASP cc_start: 0.9112 (t0) cc_final: 0.8648 (t0) REVERT: L 44 GLU cc_start: 0.9348 (pm20) cc_final: 0.8936 (pm20) REVERT: L 85 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8181 (tm-30) REVERT: Q 28 ASN cc_start: 0.8534 (m-40) cc_final: 0.8085 (m-40) REVERT: H 94 ASP cc_start: 0.8529 (t0) cc_final: 0.8288 (t0) REVERT: M 44 GLU cc_start: 0.9223 (pm20) cc_final: 0.8869 (pm20) REVERT: M 94 ASP cc_start: 0.8714 (t0) cc_final: 0.8501 (t0) REVERT: R 28 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.8245 (m-40) outliers start: 80 outliers final: 39 residues processed: 569 average time/residue: 0.6774 time to fit residues: 474.0145 Evaluate side-chains 554 residues out of total 4176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 513 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 170 SER Chi-restraints excluded: chain T residue 229 MET Chi-restraints excluded: chain T residue 454 LEU Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain N residue 5 ILE Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 454 LEU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain V residue 36 ILE Chi-restraints excluded: chain V residue 129 THR Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain V residue 131 SER Chi-restraints excluded: chain V residue 229 MET Chi-restraints excluded: chain V residue 294 GLU Chi-restraints excluded: chain V residue 381 THR Chi-restraints excluded: chain V residue 454 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain R residue 28 ASN Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 119 ILE Chi-restraints excluded: chain X residue 66 MET Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain X residue 454 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 329 optimal weight: 8.9990 chunk 242 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 225 optimal weight: 1.9990 chunk 369 optimal weight: 1.9990 chunk 426 optimal weight: 9.9990 chunk 406 optimal weight: 4.9990 chunk 306 optimal weight: 5.9990 chunk 385 optimal weight: 10.0000 chunk 481 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 ASN C 76 ASN D 68 ASN ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 ASN N 76 ASN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 ASN O 76 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 ASN P 76 ASN Q 76 ASN H 68 ASN M 45 ASN ** M 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.064962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.050739 restraints weight = 93297.445| |-----------------------------------------------------------------------------| r_work (start): 0.2659 rms_B_bonded: 2.91 r_work: 0.2546 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2425 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 39690 Z= 0.172 Angle : 0.616 7.374 53922 Z= 0.328 Chirality : 0.050 0.213 5868 Planarity : 0.004 0.057 7104 Dihedral : 5.022 48.068 5442 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 2.23 % Allowed : 10.75 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.11), residues: 4926 helix: -0.34 (0.33), residues: 252 sheet: -1.01 (0.14), residues: 1392 loop : -1.68 (0.10), residues: 3282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 297 TYR 0.011 0.001 TYR R 93 PHE 0.024 0.001 PHE C 114 TRP 0.018 0.001 TRP W 153 HIS 0.007 0.001 HIS J 88 Details of bonding type rmsd covalent geometry : bond 0.00411 (39690) covalent geometry : angle 0.61572 (53922) hydrogen bonds : bond 0.03490 ( 894) hydrogen bonds : angle 5.78249 ( 2163) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 4176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 549 time to evaluate : 1.528 Fit side-chains REVERT: A 94 ASP cc_start: 0.8475 (t0) cc_final: 0.8070 (t0) REVERT: B 14 SER cc_start: 0.9497 (p) cc_final: 0.9224 (p) REVERT: B 39 ASP cc_start: 0.8909 (t70) cc_final: 0.8526 (t0) REVERT: B 85 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8297 (tm-30) REVERT: B 117 ASP cc_start: 0.8558 (t0) cc_final: 0.8299 (t0) REVERT: C 5 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8452 (pt) REVERT: C 6 THR cc_start: 0.8813 (m) cc_final: 0.8571 (m) REVERT: C 7 ASN cc_start: 0.8834 (m-40) cc_final: 0.8193 (m-40) REVERT: T 137 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7517 (tm-30) REVERT: I 14 SER cc_start: 0.9436 (p) cc_final: 0.9167 (p) REVERT: I 39 ASP cc_start: 0.9038 (t0) cc_final: 0.8580 (t0) REVERT: I 45 ASN cc_start: 0.8383 (m-40) cc_final: 0.8139 (m110) REVERT: N 28 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.8236 (m-40) REVERT: S 137 GLU cc_start: 0.9224 (tp30) cc_final: 0.8754 (tp30) REVERT: E 39 ASP cc_start: 0.9303 (t0) cc_final: 0.9075 (t0) REVERT: E 74 VAL cc_start: 0.9379 (OUTLIER) cc_final: 0.9174 (p) REVERT: E 94 ASP cc_start: 0.8648 (t0) cc_final: 0.8197 (t0) REVERT: J 24 LYS cc_start: 0.8782 (mmmt) cc_final: 0.8553 (mmtm) REVERT: J 39 ASP cc_start: 0.9107 (t0) cc_final: 0.8601 (t0) REVERT: J 44 GLU cc_start: 0.9255 (pm20) cc_final: 0.9000 (pm20) REVERT: J 47 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8673 (pt) REVERT: O 28 ASN cc_start: 0.8457 (m-40) cc_final: 0.8000 (m-40) REVERT: F 94 ASP cc_start: 0.8492 (t0) cc_final: 0.8064 (t0) REVERT: K 14 SER cc_start: 0.9439 (p) cc_final: 0.9170 (p) REVERT: K 39 ASP cc_start: 0.9076 (t0) cc_final: 0.8598 (t0) REVERT: P 114 PHE cc_start: 0.8331 (t80) cc_final: 0.7995 (t80) REVERT: V 294 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8104 (pt0) REVERT: G 74 VAL cc_start: 0.9398 (OUTLIER) cc_final: 0.9194 (p) REVERT: G 94 ASP cc_start: 0.8659 (t0) cc_final: 0.8213 (t0) REVERT: L 24 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8452 (mtpp) REVERT: L 39 ASP cc_start: 0.9113 (t0) cc_final: 0.8584 (t0) REVERT: L 44 GLU cc_start: 0.9347 (pm20) cc_final: 0.8923 (pm20) REVERT: L 47 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8790 (pt) REVERT: L 85 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8087 (tm-30) REVERT: L 94 ASP cc_start: 0.8325 (t0) cc_final: 0.8125 (t0) REVERT: L 96 TYR cc_start: 0.9016 (m-80) cc_final: 0.8787 (m-80) REVERT: Q 28 ASN cc_start: 0.8579 (m-40) cc_final: 0.8114 (m-40) REVERT: W 101 ARG cc_start: 0.8885 (mmm160) cc_final: 0.8646 (mmt180) REVERT: W 137 GLU cc_start: 0.9178 (OUTLIER) cc_final: 0.8484 (tm-30) REVERT: H 94 ASP cc_start: 0.8525 (t0) cc_final: 0.8317 (t0) REVERT: M 14 SER cc_start: 0.9400 (p) cc_final: 0.9141 (p) REVERT: M 39 ASP cc_start: 0.8962 (t0) cc_final: 0.8756 (t0) REVERT: M 44 GLU cc_start: 0.9216 (pm20) cc_final: 0.8954 (pm20) REVERT: M 94 ASP cc_start: 0.8731 (t0) cc_final: 0.8529 (t0) REVERT: M 96 TYR cc_start: 0.9119 (m-80) cc_final: 0.8843 (m-80) REVERT: R 28 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8242 (m-40) outliers start: 93 outliers final: 48 residues processed: 592 average time/residue: 0.6413 time to fit residues: 466.9207 Evaluate side-chains 578 residues out of total 4176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 520 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 454 LEU Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain N residue 28 ASN Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 454 LEU Chi-restraints excluded: chain S residue 456 VAL Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain U residue 298 PHE Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain V residue 36 ILE Chi-restraints excluded: chain V residue 129 THR Chi-restraints excluded: chain V residue 294 GLU Chi-restraints excluded: chain V residue 381 THR Chi-restraints excluded: chain V residue 409 LEU Chi-restraints excluded: chain V residue 454 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain W residue 137 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain M residue 24 LYS Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain R residue 28 ASN Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain X residue 66 MET Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain X residue 379 LEU Chi-restraints excluded: chain X residue 454 LEU Chi-restraints excluded: chain X residue 456 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 434 optimal weight: 8.9990 chunk 428 optimal weight: 0.2980 chunk 389 optimal weight: 10.0000 chunk 433 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 463 optimal weight: 5.9990 chunk 271 optimal weight: 10.0000 chunk 406 optimal weight: 9.9990 chunk 171 optimal weight: 7.9990 chunk 486 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN C 28 ASN C 76 ASN D 68 ASN ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN E 68 ASN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN F 68 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 ASN P 76 ASN P 121 GLN G 68 ASN Q 76 ASN W 225 GLN H 68 ASN R 76 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.063807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.049546 restraints weight = 93177.668| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 2.89 r_work: 0.2518 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2398 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 39690 Z= 0.213 Angle : 0.644 9.626 53922 Z= 0.343 Chirality : 0.051 0.221 5868 Planarity : 0.004 0.062 7104 Dihedral : 5.075 49.306 5438 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 2.97 % Allowed : 11.78 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.11), residues: 4926 helix: -0.34 (0.32), residues: 252 sheet: -1.09 (0.13), residues: 1464 loop : -1.71 (0.10), residues: 3210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 21 TYR 0.012 0.001 TYR R 93 PHE 0.028 0.001 PHE R 114 TRP 0.019 0.002 TRP X 153 HIS 0.006 0.001 HIS J 88 Details of bonding type rmsd covalent geometry : bond 0.00516 (39690) covalent geometry : angle 0.64371 (53922) hydrogen bonds : bond 0.03544 ( 894) hydrogen bonds : angle 5.64801 ( 2163) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 4176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 531 time to evaluate : 1.449 Fit side-chains REVERT: A 94 ASP cc_start: 0.8554 (t0) cc_final: 0.8232 (t0) REVERT: B 14 SER cc_start: 0.9523 (p) cc_final: 0.9241 (p) REVERT: B 39 ASP cc_start: 0.8925 (t70) cc_final: 0.8538 (t0) REVERT: B 44 GLU cc_start: 0.9362 (pm20) cc_final: 0.9037 (pm20) REVERT: B 85 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8335 (tm-30) REVERT: C 6 THR cc_start: 0.8814 (m) cc_final: 0.8561 (m) REVERT: C 28 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8297 (m-40) REVERT: T 137 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7447 (tm-30) REVERT: I 14 SER cc_start: 0.9469 (p) cc_final: 0.9206 (p) REVERT: I 39 ASP cc_start: 0.9098 (t0) cc_final: 0.8714 (t0) REVERT: I 94 ASP cc_start: 0.8496 (t0) cc_final: 0.8279 (t0) REVERT: N 5 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8700 (pt) REVERT: N 24 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8811 (ptmm) REVERT: N 50 TYR cc_start: 0.9395 (m-80) cc_final: 0.9013 (m-80) REVERT: S 137 GLU cc_start: 0.9221 (tp30) cc_final: 0.8741 (tp30) REVERT: S 298 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7874 (m-10) REVERT: E 52 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.8941 (mm-30) REVERT: E 74 VAL cc_start: 0.9396 (OUTLIER) cc_final: 0.9194 (p) REVERT: E 94 ASP cc_start: 0.8680 (t0) cc_final: 0.8226 (t0) REVERT: J 24 LYS cc_start: 0.8814 (mmmt) cc_final: 0.8582 (mmtm) REVERT: J 39 ASP cc_start: 0.9131 (t0) cc_final: 0.8678 (t0) REVERT: J 44 GLU cc_start: 0.9238 (pm20) cc_final: 0.8954 (pm20) REVERT: O 6 THR cc_start: 0.8949 (m) cc_final: 0.8722 (m) REVERT: O 24 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8323 (ptmm) REVERT: O 28 ASN cc_start: 0.8713 (m-40) cc_final: 0.8208 (m-40) REVERT: F 94 ASP cc_start: 0.8573 (t0) cc_final: 0.8220 (t0) REVERT: K 14 SER cc_start: 0.9480 (p) cc_final: 0.9206 (p) REVERT: K 39 ASP cc_start: 0.9130 (t0) cc_final: 0.8650 (t0) REVERT: K 85 GLU cc_start: 0.8869 (tt0) cc_final: 0.8668 (tt0) REVERT: P 28 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8218 (m-40) REVERT: P 114 PHE cc_start: 0.8348 (t80) cc_final: 0.8014 (t80) REVERT: V 137 GLU cc_start: 0.9176 (tp30) cc_final: 0.8721 (tp30) REVERT: V 294 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8219 (pt0) REVERT: G 52 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8921 (mm-30) REVERT: G 94 ASP cc_start: 0.8672 (t0) cc_final: 0.8243 (t0) REVERT: L 24 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8486 (mtpp) REVERT: L 39 ASP cc_start: 0.9171 (t0) cc_final: 0.8645 (t0) REVERT: L 44 GLU cc_start: 0.9357 (pm20) cc_final: 0.9028 (pm20) REVERT: L 47 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8817 (pt) REVERT: L 85 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8222 (tm-30) REVERT: Q 24 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8317 (ptmm) REVERT: Q 28 ASN cc_start: 0.8674 (m-40) cc_final: 0.8224 (m-40) REVERT: W 35 GLU cc_start: 0.9101 (tt0) cc_final: 0.8535 (tp30) REVERT: W 101 ARG cc_start: 0.8909 (mmm160) cc_final: 0.8698 (mmm160) REVERT: W 137 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8647 (tp30) REVERT: H 94 ASP cc_start: 0.8599 (t0) cc_final: 0.8348 (t0) REVERT: M 14 SER cc_start: 0.9445 (p) cc_final: 0.9183 (p) REVERT: M 39 ASP cc_start: 0.9005 (t0) cc_final: 0.8655 (t0) REVERT: M 44 GLU cc_start: 0.9206 (pm20) cc_final: 0.8945 (pm20) REVERT: M 96 TYR cc_start: 0.9151 (m-80) cc_final: 0.8893 (m-80) REVERT: R 28 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8341 (m-40) REVERT: X 137 GLU cc_start: 0.9257 (tp30) cc_final: 0.8855 (tp30) REVERT: X 298 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.7922 (m-10) outliers start: 124 outliers final: 62 residues processed: 596 average time/residue: 0.6209 time to fit residues: 456.8623 Evaluate side-chains 598 residues out of total 4176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 520 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 229 MET Chi-restraints excluded: chain T residue 379 LEU Chi-restraints excluded: chain T residue 409 LEU Chi-restraints excluded: chain T residue 454 LEU Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain N residue 5 ILE Chi-restraints excluded: chain N residue 24 LYS Chi-restraints excluded: chain N residue 30 LYS Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 298 PHE Chi-restraints excluded: chain S residue 379 LEU Chi-restraints excluded: chain S residue 454 LEU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain O residue 24 LYS Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain U residue 205 THR Chi-restraints excluded: chain U residue 269 SER Chi-restraints excluded: chain U residue 298 PHE Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain P residue 28 ASN Chi-restraints excluded: chain P residue 122 LEU Chi-restraints excluded: chain V residue 36 ILE Chi-restraints excluded: chain V residue 129 THR Chi-restraints excluded: chain V residue 131 SER Chi-restraints excluded: chain V residue 229 MET Chi-restraints excluded: chain V residue 294 GLU Chi-restraints excluded: chain V residue 381 THR Chi-restraints excluded: chain V residue 409 LEU Chi-restraints excluded: chain V residue 454 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain Q residue 24 LYS Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 137 GLU Chi-restraints excluded: chain W residue 269 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain M residue 24 LYS Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 28 ASN Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain X residue 66 MET Chi-restraints excluded: chain X residue 298 PHE Chi-restraints excluded: chain X residue 379 LEU Chi-restraints excluded: chain X residue 454 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 208 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 364 optimal weight: 9.9990 chunk 488 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 395 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 chunk 126 optimal weight: 0.0050 chunk 315 optimal weight: 6.9990 overall best weight: 5.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN C 100 GLN D 68 ASN ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 ASN N 76 ASN N 100 GLN E 68 ASN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 ASN G 68 ASN Q 76 ASN H 68 ASN ** M 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.063817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.049584 restraints weight = 93405.323| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 2.89 r_work: 0.2518 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2398 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 39690 Z= 0.211 Angle : 0.650 8.685 53922 Z= 0.346 Chirality : 0.051 0.228 5868 Planarity : 0.004 0.065 7104 Dihedral : 5.085 49.643 5437 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer: Outliers : 2.75 % Allowed : 12.91 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.11), residues: 4926 helix: -0.31 (0.32), residues: 252 sheet: -1.02 (0.13), residues: 1440 loop : -1.78 (0.10), residues: 3234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 146 TYR 0.012 0.001 TYR N 93 PHE 0.031 0.001 PHE R 114 TRP 0.019 0.001 TRP V 153 HIS 0.006 0.001 HIS J 88 Details of bonding type rmsd covalent geometry : bond 0.00510 (39690) covalent geometry : angle 0.65036 (53922) hydrogen bonds : bond 0.03448 ( 894) hydrogen bonds : angle 5.59904 ( 2163) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 4176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 534 time to evaluate : 1.503 Fit side-chains REVERT: A 94 ASP cc_start: 0.8593 (t0) cc_final: 0.8283 (t0) REVERT: B 39 ASP cc_start: 0.8944 (t70) cc_final: 0.8514 (t0) REVERT: B 44 GLU cc_start: 0.9396 (pm20) cc_final: 0.9044 (pm20) REVERT: B 85 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8328 (tm-30) REVERT: T 137 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7464 (tm-30) REVERT: I 14 SER cc_start: 0.9482 (p) cc_final: 0.9207 (p) REVERT: I 39 ASP cc_start: 0.9098 (t0) cc_final: 0.8727 (t0) REVERT: I 94 ASP cc_start: 0.8603 (t0) cc_final: 0.8380 (t0) REVERT: N 5 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8656 (pt) REVERT: N 24 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8839 (ptmm) REVERT: N 50 TYR cc_start: 0.9417 (m-80) cc_final: 0.9021 (m-80) REVERT: S 137 GLU cc_start: 0.9223 (tp30) cc_final: 0.8749 (tp30) REVERT: S 298 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7924 (m-10) REVERT: E 52 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8904 (mm-30) REVERT: E 74 VAL cc_start: 0.9395 (OUTLIER) cc_final: 0.9193 (p) REVERT: E 94 ASP cc_start: 0.8671 (t0) cc_final: 0.8242 (t0) REVERT: J 24 LYS cc_start: 0.8814 (mmmt) cc_final: 0.8581 (mmtm) REVERT: J 39 ASP cc_start: 0.9204 (t0) cc_final: 0.8726 (t0) REVERT: J 44 GLU cc_start: 0.9249 (pm20) cc_final: 0.8952 (pm20) REVERT: J 47 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8789 (pt) REVERT: O 6 THR cc_start: 0.8889 (m) cc_final: 0.8684 (m) REVERT: O 24 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8339 (ptmm) REVERT: F 94 ASP cc_start: 0.8608 (t0) cc_final: 0.8281 (t0) REVERT: K 39 ASP cc_start: 0.9155 (t0) cc_final: 0.8718 (t0) REVERT: P 114 PHE cc_start: 0.8332 (t80) cc_final: 0.7988 (t80) REVERT: V 137 GLU cc_start: 0.9174 (tp30) cc_final: 0.8722 (tp30) REVERT: V 294 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8123 (pt0) REVERT: L 24 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8481 (mtpp) REVERT: L 39 ASP cc_start: 0.9189 (t0) cc_final: 0.8673 (t0) REVERT: L 44 GLU cc_start: 0.9401 (pm20) cc_final: 0.9062 (pm20) REVERT: L 47 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8839 (pt) REVERT: L 85 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8188 (tm-30) REVERT: Q 24 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8402 (ptmm) REVERT: Q 28 ASN cc_start: 0.8725 (m-40) cc_final: 0.8258 (m-40) REVERT: W 35 GLU cc_start: 0.9103 (tt0) cc_final: 0.8504 (tp30) REVERT: W 101 ARG cc_start: 0.8923 (mmm160) cc_final: 0.8702 (mmm160) REVERT: W 137 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.8687 (tp30) REVERT: H 94 ASP cc_start: 0.8643 (t70) cc_final: 0.8351 (t0) REVERT: M 14 SER cc_start: 0.9472 (p) cc_final: 0.9192 (p) REVERT: M 39 ASP cc_start: 0.9027 (t0) cc_final: 0.8618 (t0) REVERT: M 44 GLU cc_start: 0.9229 (pm20) cc_final: 0.8919 (pm20) REVERT: R 28 ASN cc_start: 0.8553 (OUTLIER) cc_final: 0.8325 (m-40) REVERT: R 50 TYR cc_start: 0.9400 (m-80) cc_final: 0.8962 (m-80) REVERT: X 137 GLU cc_start: 0.9257 (tp30) cc_final: 0.8839 (tp30) REVERT: X 298 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.7968 (m-10) outliers start: 115 outliers final: 70 residues processed: 598 average time/residue: 0.6327 time to fit residues: 465.4534 Evaluate side-chains 605 residues out of total 4176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 521 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 229 MET Chi-restraints excluded: chain T residue 409 LEU Chi-restraints excluded: chain T residue 454 LEU Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain N residue 5 ILE Chi-restraints excluded: chain N residue 24 LYS Chi-restraints excluded: chain N residue 30 LYS Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 298 PHE Chi-restraints excluded: chain S residue 379 LEU Chi-restraints excluded: chain S residue 454 LEU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain O residue 24 LYS Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain U residue 205 THR Chi-restraints excluded: chain U residue 298 PHE Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain P residue 122 LEU Chi-restraints excluded: chain V residue 36 ILE Chi-restraints excluded: chain V residue 129 THR Chi-restraints excluded: chain V residue 131 SER Chi-restraints excluded: chain V residue 229 MET Chi-restraints excluded: chain V residue 294 GLU Chi-restraints excluded: chain V residue 381 THR Chi-restraints excluded: chain V residue 409 LEU Chi-restraints excluded: chain V residue 454 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain Q residue 24 LYS Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 137 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain M residue 24 LYS Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 28 ASN Chi-restraints excluded: chain R residue 30 LYS Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 66 MET Chi-restraints excluded: chain X residue 298 PHE Chi-restraints excluded: chain X residue 379 LEU Chi-restraints excluded: chain X residue 409 LEU Chi-restraints excluded: chain X residue 454 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 215 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 307 optimal weight: 0.2980 chunk 173 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 chunk 198 optimal weight: 3.9990 chunk 377 optimal weight: 10.0000 chunk 486 optimal weight: 7.9990 chunk 470 optimal weight: 10.0000 chunk 332 optimal weight: 7.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN C 76 ASN D 68 ASN ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 ASN N 76 ASN E 68 ASN E 100 GLN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 ASN P 76 ASN P 100 GLN G 68 ASN Q 76 ASN H 68 ASN ** M 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.063749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.049490 restraints weight = 93482.814| |-----------------------------------------------------------------------------| r_work (start): 0.2629 rms_B_bonded: 2.90 r_work: 0.2515 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2395 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 39690 Z= 0.207 Angle : 0.650 8.641 53922 Z= 0.345 Chirality : 0.051 0.229 5868 Planarity : 0.004 0.065 7104 Dihedral : 5.076 49.777 5437 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.80 % Favored : 89.20 % Rotamer: Outliers : 2.92 % Allowed : 13.75 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.11), residues: 4926 helix: -0.32 (0.33), residues: 252 sheet: -1.01 (0.13), residues: 1440 loop : -1.79 (0.10), residues: 3234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 21 TYR 0.014 0.001 TYR J 75 PHE 0.033 0.001 PHE R 114 TRP 0.019 0.001 TRP W 153 HIS 0.006 0.001 HIS J 88 Details of bonding type rmsd covalent geometry : bond 0.00500 (39690) covalent geometry : angle 0.65006 (53922) hydrogen bonds : bond 0.03376 ( 894) hydrogen bonds : angle 5.56200 ( 2163) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 4176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 535 time to evaluate : 1.455 Fit side-chains REVERT: A 94 ASP cc_start: 0.8610 (t0) cc_final: 0.8326 (t0) REVERT: B 39 ASP cc_start: 0.8956 (t70) cc_final: 0.8527 (t0) REVERT: B 44 GLU cc_start: 0.9369 (pm20) cc_final: 0.9066 (pm20) REVERT: B 85 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8335 (tm-30) REVERT: T 137 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7577 (tm-30) REVERT: D 68 ASN cc_start: 0.8715 (t0) cc_final: 0.8454 (t0) REVERT: I 14 SER cc_start: 0.9508 (p) cc_final: 0.9224 (p) REVERT: I 39 ASP cc_start: 0.9108 (t0) cc_final: 0.8752 (t0) REVERT: I 52 GLU cc_start: 0.9318 (tt0) cc_final: 0.9115 (tt0) REVERT: I 94 ASP cc_start: 0.8674 (t0) cc_final: 0.8467 (t0) REVERT: N 24 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8841 (ptmm) REVERT: N 28 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.8299 (m-40) REVERT: N 50 TYR cc_start: 0.9429 (m-80) cc_final: 0.8897 (m-80) REVERT: S 137 GLU cc_start: 0.9195 (tp30) cc_final: 0.8741 (tp30) REVERT: S 298 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.7949 (m-10) REVERT: E 52 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8844 (mm-30) REVERT: J 24 LYS cc_start: 0.8815 (mmmt) cc_final: 0.8581 (mmtm) REVERT: J 39 ASP cc_start: 0.9225 (t0) cc_final: 0.8756 (t0) REVERT: J 44 GLU cc_start: 0.9238 (pm20) cc_final: 0.8939 (pm20) REVERT: J 47 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8804 (pt) REVERT: O 6 THR cc_start: 0.8867 (m) cc_final: 0.8661 (m) REVERT: O 24 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8330 (ptmm) REVERT: O 28 ASN cc_start: 0.8570 (m-40) cc_final: 0.8131 (m-40) REVERT: F 94 ASP cc_start: 0.8616 (t0) cc_final: 0.8369 (t0) REVERT: K 39 ASP cc_start: 0.9158 (t0) cc_final: 0.8754 (t0) REVERT: P 114 PHE cc_start: 0.8334 (t80) cc_final: 0.7980 (t80) REVERT: V 137 GLU cc_start: 0.9183 (tp30) cc_final: 0.8707 (tp30) REVERT: V 294 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8195 (pt0) REVERT: G 94 ASP cc_start: 0.8609 (t0) cc_final: 0.8223 (t0) REVERT: L 24 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8478 (mtpp) REVERT: L 39 ASP cc_start: 0.9211 (t0) cc_final: 0.8689 (t0) REVERT: L 44 GLU cc_start: 0.9393 (pm20) cc_final: 0.9047 (pm20) REVERT: L 47 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8888 (pt) REVERT: L 85 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8089 (tm-30) REVERT: Q 24 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8305 (ptmm) REVERT: W 35 GLU cc_start: 0.9062 (tt0) cc_final: 0.8503 (tp30) REVERT: W 101 ARG cc_start: 0.8960 (mmm160) cc_final: 0.8737 (mmm160) REVERT: W 137 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8674 (tp30) REVERT: H 68 ASN cc_start: 0.8727 (t0) cc_final: 0.8460 (t0) REVERT: H 94 ASP cc_start: 0.8701 (t70) cc_final: 0.8465 (t0) REVERT: M 14 SER cc_start: 0.9483 (p) cc_final: 0.9195 (p) REVERT: M 39 ASP cc_start: 0.9125 (t0) cc_final: 0.8679 (t0) REVERT: M 44 GLU cc_start: 0.9226 (pm20) cc_final: 0.8905 (pm20) REVERT: R 28 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8356 (m-40) REVERT: R 50 TYR cc_start: 0.9437 (m-80) cc_final: 0.9018 (m-80) REVERT: X 137 GLU cc_start: 0.9262 (tp30) cc_final: 0.8826 (tp30) REVERT: X 298 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.7968 (m-10) outliers start: 122 outliers final: 76 residues processed: 604 average time/residue: 0.6321 time to fit residues: 470.8046 Evaluate side-chains 610 residues out of total 4176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 521 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 229 MET Chi-restraints excluded: chain T residue 409 LEU Chi-restraints excluded: chain T residue 454 LEU Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain N residue 5 ILE Chi-restraints excluded: chain N residue 24 LYS Chi-restraints excluded: chain N residue 28 ASN Chi-restraints excluded: chain N residue 30 LYS Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 298 PHE Chi-restraints excluded: chain S residue 379 LEU Chi-restraints excluded: chain S residue 454 LEU Chi-restraints excluded: chain S residue 456 VAL Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain O residue 24 LYS Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain U residue 32 THR Chi-restraints excluded: chain U residue 205 THR Chi-restraints excluded: chain U residue 298 PHE Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain P residue 122 LEU Chi-restraints excluded: chain V residue 36 ILE Chi-restraints excluded: chain V residue 129 THR Chi-restraints excluded: chain V residue 131 SER Chi-restraints excluded: chain V residue 229 MET Chi-restraints excluded: chain V residue 294 GLU Chi-restraints excluded: chain V residue 381 THR Chi-restraints excluded: chain V residue 409 LEU Chi-restraints excluded: chain V residue 454 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain Q residue 24 LYS Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 137 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain M residue 24 LYS Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 28 ASN Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 66 MET Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain X residue 298 PHE Chi-restraints excluded: chain X residue 379 LEU Chi-restraints excluded: chain X residue 409 LEU Chi-restraints excluded: chain X residue 454 LEU Chi-restraints excluded: chain X residue 456 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 391 optimal weight: 6.9990 chunk 265 optimal weight: 3.9990 chunk 386 optimal weight: 2.9990 chunk 412 optimal weight: 9.9990 chunk 162 optimal weight: 7.9990 chunk 223 optimal weight: 3.9990 chunk 450 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 125 optimal weight: 0.1980 chunk 144 optimal weight: 9.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 ASN N 76 ASN S 225 GLN E 68 ASN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN F 68 ASN K 88 HIS P 76 ASN G 68 ASN Q 76 ASN H 100 GLN ** M 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN X 267 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.064697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.050494 restraints weight = 93093.725| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 2.90 r_work: 0.2539 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2420 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 39690 Z= 0.164 Angle : 0.627 8.951 53922 Z= 0.331 Chirality : 0.050 0.230 5868 Planarity : 0.004 0.065 7104 Dihedral : 4.946 50.053 5437 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 2.80 % Allowed : 14.27 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.11), residues: 4926 helix: -0.30 (0.33), residues: 252 sheet: -0.97 (0.14), residues: 1446 loop : -1.73 (0.10), residues: 3228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 21 TYR 0.017 0.001 TYR L 75 PHE 0.030 0.001 PHE R 114 TRP 0.018 0.001 TRP W 153 HIS 0.006 0.001 HIS J 88 Details of bonding type rmsd covalent geometry : bond 0.00389 (39690) covalent geometry : angle 0.62654 (53922) hydrogen bonds : bond 0.03075 ( 894) hydrogen bonds : angle 5.47893 ( 2163) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 4176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 538 time to evaluate : 1.473 Fit side-chains REVERT: A 120 GLU cc_start: 0.5957 (tm-30) cc_final: 0.5507 (pp20) REVERT: B 39 ASP cc_start: 0.8957 (t70) cc_final: 0.8524 (t0) REVERT: B 44 GLU cc_start: 0.9372 (pm20) cc_final: 0.9036 (pm20) REVERT: B 85 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8295 (tm-30) REVERT: C 6 THR cc_start: 0.8950 (m) cc_final: 0.8723 (m) REVERT: C 28 ASN cc_start: 0.8226 (OUTLIER) cc_final: 0.7972 (m-40) REVERT: T 245 ASP cc_start: 0.8067 (t0) cc_final: 0.7863 (m-30) REVERT: D 68 ASN cc_start: 0.8660 (t0) cc_final: 0.8360 (t0) REVERT: I 14 SER cc_start: 0.9503 (p) cc_final: 0.9210 (p) REVERT: I 39 ASP cc_start: 0.9097 (t0) cc_final: 0.8735 (t0) REVERT: N 28 ASN cc_start: 0.8575 (m110) cc_final: 0.8345 (m-40) REVERT: N 37 ASP cc_start: 0.8957 (t0) cc_final: 0.8730 (t0) REVERT: N 50 TYR cc_start: 0.9425 (m-80) cc_final: 0.8935 (m-80) REVERT: S 137 GLU cc_start: 0.9200 (tp30) cc_final: 0.8753 (tp30) REVERT: S 298 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7860 (m-10) REVERT: E 94 ASP cc_start: 0.8540 (t0) cc_final: 0.8200 (t0) REVERT: J 24 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8570 (mmtm) REVERT: J 39 ASP cc_start: 0.9228 (t0) cc_final: 0.8755 (t0) REVERT: J 44 GLU cc_start: 0.9267 (pm20) cc_final: 0.8931 (pm20) REVERT: J 47 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8774 (pt) REVERT: O 24 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8331 (ptmm) REVERT: O 28 ASN cc_start: 0.8586 (m-40) cc_final: 0.8123 (m-40) REVERT: K 14 SER cc_start: 0.9498 (p) cc_final: 0.9211 (p) REVERT: K 39 ASP cc_start: 0.9153 (t0) cc_final: 0.8747 (t0) REVERT: P 28 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7941 (m-40) REVERT: P 114 PHE cc_start: 0.8316 (t80) cc_final: 0.7984 (t80) REVERT: V 137 GLU cc_start: 0.9173 (tp30) cc_final: 0.8697 (tp30) REVERT: V 294 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8102 (pt0) REVERT: G 94 ASP cc_start: 0.8581 (t0) cc_final: 0.8199 (t0) REVERT: L 24 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8461 (mtpp) REVERT: L 39 ASP cc_start: 0.9216 (t0) cc_final: 0.8731 (t0) REVERT: L 44 GLU cc_start: 0.9401 (pm20) cc_final: 0.9051 (pm20) REVERT: L 47 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8883 (pt) REVERT: L 85 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8058 (tm-30) REVERT: Q 24 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8307 (ptmm) REVERT: Q 28 ASN cc_start: 0.8428 (m-40) cc_final: 0.8062 (m-40) REVERT: W 35 GLU cc_start: 0.9027 (tt0) cc_final: 0.8407 (tp30) REVERT: W 101 ARG cc_start: 0.8984 (mmm160) cc_final: 0.8762 (mmm160) REVERT: W 137 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.8678 (tp30) REVERT: H 68 ASN cc_start: 0.8675 (t0) cc_final: 0.8378 (t0) REVERT: H 94 ASP cc_start: 0.8683 (t70) cc_final: 0.8454 (t0) REVERT: M 14 SER cc_start: 0.9480 (p) cc_final: 0.9187 (p) REVERT: M 39 ASP cc_start: 0.9121 (t0) cc_final: 0.8664 (t0) REVERT: M 44 GLU cc_start: 0.9230 (pm20) cc_final: 0.8900 (pm20) REVERT: R 28 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8208 (m-40) REVERT: R 50 TYR cc_start: 0.9429 (m-80) cc_final: 0.8924 (m-80) REVERT: R 94 ASP cc_start: 0.8747 (t0) cc_final: 0.8545 (t0) REVERT: X 137 GLU cc_start: 0.9266 (tp30) cc_final: 0.8837 (tp30) REVERT: X 298 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.7894 (m-10) outliers start: 117 outliers final: 79 residues processed: 599 average time/residue: 0.6411 time to fit residues: 472.0430 Evaluate side-chains 616 residues out of total 4176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 525 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 205 THR Chi-restraints excluded: chain T residue 229 MET Chi-restraints excluded: chain T residue 409 LEU Chi-restraints excluded: chain T residue 454 LEU Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain N residue 30 LYS Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 205 THR Chi-restraints excluded: chain S residue 298 PHE Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 379 LEU Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 454 LEU Chi-restraints excluded: chain S residue 456 VAL Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain O residue 24 LYS Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain U residue 32 THR Chi-restraints excluded: chain U residue 298 PHE Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain P residue 28 ASN Chi-restraints excluded: chain P residue 90 MET Chi-restraints excluded: chain P residue 122 LEU Chi-restraints excluded: chain V residue 36 ILE Chi-restraints excluded: chain V residue 129 THR Chi-restraints excluded: chain V residue 131 SER Chi-restraints excluded: chain V residue 229 MET Chi-restraints excluded: chain V residue 294 GLU Chi-restraints excluded: chain V residue 381 THR Chi-restraints excluded: chain V residue 409 LEU Chi-restraints excluded: chain V residue 454 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain Q residue 24 LYS Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 137 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain M residue 24 LYS Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 28 ASN Chi-restraints excluded: chain R residue 30 LYS Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 66 MET Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain X residue 298 PHE Chi-restraints excluded: chain X residue 363 LEU Chi-restraints excluded: chain X residue 379 LEU Chi-restraints excluded: chain X residue 381 THR Chi-restraints excluded: chain X residue 409 LEU Chi-restraints excluded: chain X residue 426 ILE Chi-restraints excluded: chain X residue 454 LEU Chi-restraints excluded: chain X residue 456 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 411 optimal weight: 10.0000 chunk 381 optimal weight: 6.9990 chunk 431 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 311 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 428 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 372 optimal weight: 6.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN E 68 ASN O 76 ASN F 68 ASN P 76 ASN G 68 ASN Q 76 ASN ** M 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN X 267 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.064554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.050365 restraints weight = 93011.659| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 2.90 r_work: 0.2536 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2416 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 39690 Z= 0.173 Angle : 0.639 9.155 53922 Z= 0.337 Chirality : 0.050 0.230 5868 Planarity : 0.004 0.065 7104 Dihedral : 4.919 49.640 5437 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 2.68 % Allowed : 14.77 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.11), residues: 4926 helix: -0.28 (0.33), residues: 252 sheet: -0.94 (0.14), residues: 1428 loop : -1.76 (0.10), residues: 3246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 21 TYR 0.019 0.001 TYR K 75 PHE 0.031 0.001 PHE R 114 TRP 0.018 0.001 TRP V 153 HIS 0.006 0.001 HIS J 88 Details of bonding type rmsd covalent geometry : bond 0.00415 (39690) covalent geometry : angle 0.63895 (53922) hydrogen bonds : bond 0.03102 ( 894) hydrogen bonds : angle 5.43750 ( 2163) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 4176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 535 time to evaluate : 1.749 Fit side-chains REVERT: A 94 ASP cc_start: 0.8549 (t0) cc_final: 0.8229 (t0) REVERT: B 39 ASP cc_start: 0.8970 (t70) cc_final: 0.8539 (t0) REVERT: B 44 GLU cc_start: 0.9356 (pm20) cc_final: 0.9023 (pm20) REVERT: B 85 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8370 (tm-30) REVERT: C 6 THR cc_start: 0.8870 (m) cc_final: 0.8635 (m) REVERT: C 28 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7948 (m-40) REVERT: T 245 ASP cc_start: 0.8144 (t0) cc_final: 0.7942 (m-30) REVERT: D 68 ASN cc_start: 0.8673 (t0) cc_final: 0.8361 (t0) REVERT: I 14 SER cc_start: 0.9507 (p) cc_final: 0.9218 (p) REVERT: I 39 ASP cc_start: 0.9092 (t0) cc_final: 0.8745 (t0) REVERT: N 28 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8226 (m-40) REVERT: N 37 ASP cc_start: 0.8963 (t0) cc_final: 0.8726 (t0) REVERT: N 50 TYR cc_start: 0.9422 (m-80) cc_final: 0.8941 (m-80) REVERT: S 137 GLU cc_start: 0.9205 (tp30) cc_final: 0.8753 (tp30) REVERT: S 298 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.7904 (m-10) REVERT: E 52 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8729 (mm-30) REVERT: E 94 ASP cc_start: 0.8580 (t0) cc_final: 0.8244 (t0) REVERT: J 24 LYS cc_start: 0.8818 (mmmt) cc_final: 0.8588 (mmtm) REVERT: J 39 ASP cc_start: 0.9232 (t0) cc_final: 0.8756 (t0) REVERT: J 44 GLU cc_start: 0.9260 (pm20) cc_final: 0.8922 (pm20) REVERT: J 47 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8771 (pt) REVERT: O 24 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8329 (ptmm) REVERT: O 28 ASN cc_start: 0.8621 (m-40) cc_final: 0.8143 (m-40) REVERT: K 14 SER cc_start: 0.9501 (p) cc_final: 0.9213 (p) REVERT: K 39 ASP cc_start: 0.9158 (t0) cc_final: 0.8754 (t0) REVERT: P 28 ASN cc_start: 0.8226 (OUTLIER) cc_final: 0.7970 (m-40) REVERT: P 114 PHE cc_start: 0.8220 (t80) cc_final: 0.7851 (t80) REVERT: V 137 GLU cc_start: 0.9176 (tp30) cc_final: 0.8694 (tp30) REVERT: V 294 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8157 (pt0) REVERT: G 94 ASP cc_start: 0.8604 (t0) cc_final: 0.8227 (t0) REVERT: L 24 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8480 (mtpp) REVERT: L 39 ASP cc_start: 0.9224 (t0) cc_final: 0.8739 (t0) REVERT: L 44 GLU cc_start: 0.9387 (pm20) cc_final: 0.9059 (pm20) REVERT: L 47 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8875 (pt) REVERT: L 85 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8237 (tm-30) REVERT: Q 28 ASN cc_start: 0.8569 (m-40) cc_final: 0.8152 (m-40) REVERT: W 35 GLU cc_start: 0.9045 (tt0) cc_final: 0.8431 (tp30) REVERT: W 101 ARG cc_start: 0.8993 (mmm160) cc_final: 0.8767 (mmm160) REVERT: W 137 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.8681 (tp30) REVERT: H 52 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8775 (mm-30) REVERT: H 68 ASN cc_start: 0.8687 (t0) cc_final: 0.8376 (t0) REVERT: M 14 SER cc_start: 0.9486 (p) cc_final: 0.9191 (p) REVERT: M 39 ASP cc_start: 0.9133 (t0) cc_final: 0.8644 (t0) REVERT: M 44 GLU cc_start: 0.9227 (pm20) cc_final: 0.8938 (pm20) REVERT: M 94 ASP cc_start: 0.8053 (t0) cc_final: 0.7790 (t0) REVERT: M 122 LEU cc_start: 0.8293 (tm) cc_final: 0.8078 (mt) REVERT: R 28 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8258 (m-40) REVERT: R 50 TYR cc_start: 0.9434 (m-80) cc_final: 0.8977 (m-80) REVERT: R 94 ASP cc_start: 0.8754 (t0) cc_final: 0.8543 (t0) REVERT: X 137 GLU cc_start: 0.9268 (tp30) cc_final: 0.8837 (tp30) REVERT: X 298 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7965 (m-10) outliers start: 112 outliers final: 83 residues processed: 597 average time/residue: 0.6329 time to fit residues: 465.1383 Evaluate side-chains 619 residues out of total 4176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 524 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 205 THR Chi-restraints excluded: chain T residue 229 MET Chi-restraints excluded: chain T residue 409 LEU Chi-restraints excluded: chain T residue 454 LEU Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain N residue 28 ASN Chi-restraints excluded: chain N residue 30 LYS Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 205 THR Chi-restraints excluded: chain S residue 298 PHE Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 379 LEU Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 454 LEU Chi-restraints excluded: chain S residue 456 VAL Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain O residue 24 LYS Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain U residue 32 THR Chi-restraints excluded: chain U residue 298 PHE Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain P residue 28 ASN Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain P residue 122 LEU Chi-restraints excluded: chain V residue 36 ILE Chi-restraints excluded: chain V residue 129 THR Chi-restraints excluded: chain V residue 131 SER Chi-restraints excluded: chain V residue 229 MET Chi-restraints excluded: chain V residue 294 GLU Chi-restraints excluded: chain V residue 381 THR Chi-restraints excluded: chain V residue 409 LEU Chi-restraints excluded: chain V residue 454 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 137 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain R residue 28 ASN Chi-restraints excluded: chain R residue 30 LYS Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 66 MET Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain X residue 205 THR Chi-restraints excluded: chain X residue 298 PHE Chi-restraints excluded: chain X residue 363 LEU Chi-restraints excluded: chain X residue 379 LEU Chi-restraints excluded: chain X residue 381 THR Chi-restraints excluded: chain X residue 409 LEU Chi-restraints excluded: chain X residue 426 ILE Chi-restraints excluded: chain X residue 454 LEU Chi-restraints excluded: chain X residue 456 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 136 optimal weight: 2.9990 chunk 434 optimal weight: 10.0000 chunk 396 optimal weight: 5.9990 chunk 480 optimal weight: 9.9990 chunk 431 optimal weight: 10.0000 chunk 361 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 286 optimal weight: 8.9990 chunk 241 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN T 225 GLN ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN E 68 ASN O 76 ASN P 76 ASN G 68 ASN Q 53 ASN Q 76 ASN ** M 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 ASN R 76 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.062755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.048490 restraints weight = 94034.384| |-----------------------------------------------------------------------------| r_work (start): 0.2606 rms_B_bonded: 2.90 r_work: 0.2491 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2371 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 39690 Z= 0.266 Angle : 0.710 9.308 53922 Z= 0.378 Chirality : 0.053 0.258 5868 Planarity : 0.004 0.067 7104 Dihedral : 5.242 49.870 5437 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.23 % Favored : 88.77 % Rotamer: Outliers : 2.83 % Allowed : 14.92 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.11), residues: 4926 helix: -0.33 (0.33), residues: 252 sheet: -1.03 (0.14), residues: 1380 loop : -1.83 (0.10), residues: 3294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 21 TYR 0.020 0.001 TYR L 75 PHE 0.031 0.001 PHE C 114 TRP 0.022 0.002 TRP W 153 HIS 0.007 0.001 HIS V 377 Details of bonding type rmsd covalent geometry : bond 0.00651 (39690) covalent geometry : angle 0.71002 (53922) hydrogen bonds : bond 0.03696 ( 894) hydrogen bonds : angle 5.61935 ( 2163) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 4176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 518 time to evaluate : 1.529 Fit side-chains REVERT: A 94 ASP cc_start: 0.8617 (t0) cc_final: 0.8282 (t0) REVERT: A 120 GLU cc_start: 0.5499 (tm-30) cc_final: 0.5037 (pp20) REVERT: B 39 ASP cc_start: 0.8983 (t70) cc_final: 0.8581 (t0) REVERT: B 44 GLU cc_start: 0.9373 (pm20) cc_final: 0.9052 (pm20) REVERT: B 85 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8407 (tm-30) REVERT: C 6 THR cc_start: 0.8867 (m) cc_final: 0.8655 (m) REVERT: C 28 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.8111 (m-40) REVERT: T 137 GLU cc_start: 0.9139 (tp30) cc_final: 0.8741 (tp30) REVERT: T 294 GLU cc_start: 0.8711 (pt0) cc_final: 0.8458 (pt0) REVERT: D 68 ASN cc_start: 0.8850 (t0) cc_final: 0.8510 (t0) REVERT: I 14 SER cc_start: 0.9530 (p) cc_final: 0.9242 (p) REVERT: I 39 ASP cc_start: 0.9141 (t0) cc_final: 0.8782 (t0) REVERT: N 28 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8455 (m-40) REVERT: S 137 GLU cc_start: 0.9211 (tp30) cc_final: 0.8754 (tp30) REVERT: S 298 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.7974 (m-10) REVERT: E 52 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8716 (mm-30) REVERT: E 94 ASP cc_start: 0.8653 (t0) cc_final: 0.8290 (t0) REVERT: J 24 LYS cc_start: 0.8841 (mmmt) cc_final: 0.8603 (mmtm) REVERT: J 39 ASP cc_start: 0.9257 (t0) cc_final: 0.8767 (t0) REVERT: J 44 GLU cc_start: 0.9225 (pm20) cc_final: 0.9008 (pm20) REVERT: J 47 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8774 (pt) REVERT: O 6 THR cc_start: 0.9004 (m) cc_final: 0.8772 (m) REVERT: O 24 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8342 (ptmm) REVERT: K 39 ASP cc_start: 0.9185 (t0) cc_final: 0.8786 (t0) REVERT: P 28 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.8113 (m-40) REVERT: P 114 PHE cc_start: 0.8283 (t80) cc_final: 0.7946 (t80) REVERT: V 137 GLU cc_start: 0.9224 (tp30) cc_final: 0.8766 (tp30) REVERT: V 294 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8272 (pt0) REVERT: G 94 ASP cc_start: 0.8643 (t0) cc_final: 0.8244 (t0) REVERT: L 24 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8510 (mtpp) REVERT: L 39 ASP cc_start: 0.9233 (t0) cc_final: 0.8724 (t0) REVERT: L 44 GLU cc_start: 0.9380 (pm20) cc_final: 0.9072 (pm20) REVERT: L 47 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8858 (pt) REVERT: L 85 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8297 (tm-30) REVERT: W 35 GLU cc_start: 0.9056 (tt0) cc_final: 0.8433 (tp30) REVERT: W 101 ARG cc_start: 0.9003 (mmm160) cc_final: 0.8753 (mmm160) REVERT: W 137 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8680 (tp30) REVERT: H 68 ASN cc_start: 0.8863 (t0) cc_final: 0.8521 (t0) REVERT: M 14 SER cc_start: 0.9502 (p) cc_final: 0.9217 (p) REVERT: M 39 ASP cc_start: 0.9179 (t0) cc_final: 0.8673 (t0) REVERT: M 44 GLU cc_start: 0.9230 (pm20) cc_final: 0.8930 (pm20) REVERT: M 94 ASP cc_start: 0.8345 (t0) cc_final: 0.8143 (t0) REVERT: R 28 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8410 (m-40) REVERT: X 137 GLU cc_start: 0.9271 (tp30) cc_final: 0.8823 (tp30) REVERT: X 298 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.8004 (m-10) outliers start: 118 outliers final: 82 residues processed: 585 average time/residue: 0.6388 time to fit residues: 459.7584 Evaluate side-chains 604 residues out of total 4176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 510 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 229 MET Chi-restraints excluded: chain T residue 409 LEU Chi-restraints excluded: chain T residue 454 LEU Chi-restraints excluded: chain T residue 456 VAL Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain N residue 5 ILE Chi-restraints excluded: chain N residue 28 ASN Chi-restraints excluded: chain N residue 30 LYS Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 237 THR Chi-restraints excluded: chain S residue 298 PHE Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 379 LEU Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 409 LEU Chi-restraints excluded: chain S residue 454 LEU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain O residue 5 ILE Chi-restraints excluded: chain O residue 24 LYS Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain U residue 32 THR Chi-restraints excluded: chain U residue 298 PHE Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain P residue 28 ASN Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 122 LEU Chi-restraints excluded: chain V residue 36 ILE Chi-restraints excluded: chain V residue 129 THR Chi-restraints excluded: chain V residue 131 SER Chi-restraints excluded: chain V residue 229 MET Chi-restraints excluded: chain V residue 294 GLU Chi-restraints excluded: chain V residue 381 THR Chi-restraints excluded: chain V residue 409 LEU Chi-restraints excluded: chain V residue 454 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 137 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain M residue 24 LYS Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain R residue 28 ASN Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 66 MET Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain X residue 298 PHE Chi-restraints excluded: chain X residue 363 LEU Chi-restraints excluded: chain X residue 379 LEU Chi-restraints excluded: chain X residue 381 THR Chi-restraints excluded: chain X residue 409 LEU Chi-restraints excluded: chain X residue 426 ILE Chi-restraints excluded: chain X residue 454 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 100 optimal weight: 0.5980 chunk 264 optimal weight: 8.9990 chunk 309 optimal weight: 0.0870 chunk 224 optimal weight: 0.0570 chunk 183 optimal weight: 9.9990 chunk 243 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 312 optimal weight: 8.9990 overall best weight: 1.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN I 76 ASN ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN S 267 GLN E 68 ASN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN P 76 ASN G 68 ASN Q 76 ASN ** M 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.066628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.052481 restraints weight = 92457.726| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 2.90 r_work: 0.2587 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39690 Z= 0.122 Angle : 0.613 9.503 53922 Z= 0.320 Chirality : 0.049 0.219 5868 Planarity : 0.004 0.063 7104 Dihedral : 4.698 52.524 5437 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 1.94 % Allowed : 16.02 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.11), residues: 4926 helix: -0.17 (0.33), residues: 252 sheet: -1.00 (0.13), residues: 1482 loop : -1.68 (0.10), residues: 3192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 297 TYR 0.010 0.001 TYR K 93 PHE 0.029 0.001 PHE C 114 TRP 0.018 0.001 TRP V 153 HIS 0.005 0.001 HIS J 88 Details of bonding type rmsd covalent geometry : bond 0.00280 (39690) covalent geometry : angle 0.61255 (53922) hydrogen bonds : bond 0.02605 ( 894) hydrogen bonds : angle 5.33571 ( 2163) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9852 Ramachandran restraints generated. 4926 Oldfield, 0 Emsley, 4926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 4176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 556 time to evaluate : 1.233 Fit side-chains REVERT: A 94 ASP cc_start: 0.8525 (t0) cc_final: 0.8226 (t0) REVERT: A 120 GLU cc_start: 0.5707 (tm-30) cc_final: 0.5297 (pp20) REVERT: B 14 SER cc_start: 0.9530 (p) cc_final: 0.9231 (p) REVERT: B 39 ASP cc_start: 0.8972 (t70) cc_final: 0.8551 (t0) REVERT: B 44 GLU cc_start: 0.9357 (pm20) cc_final: 0.9018 (pm20) REVERT: B 85 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8284 (tm-30) REVERT: C 6 THR cc_start: 0.8917 (m) cc_final: 0.8677 (m) REVERT: T 29 MET cc_start: 0.9373 (mmt) cc_final: 0.8491 (mmt) REVERT: T 137 GLU cc_start: 0.9102 (tp30) cc_final: 0.8686 (tp30) REVERT: T 294 GLU cc_start: 0.8623 (pt0) cc_final: 0.8318 (pt0) REVERT: D 68 ASN cc_start: 0.8602 (t0) cc_final: 0.8327 (t0) REVERT: I 14 SER cc_start: 0.9491 (p) cc_final: 0.9182 (p) REVERT: I 39 ASP cc_start: 0.9069 (t0) cc_final: 0.8724 (t0) REVERT: N 28 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.8019 (m-40) REVERT: N 50 TYR cc_start: 0.9405 (m-80) cc_final: 0.8946 (m-80) REVERT: S 137 GLU cc_start: 0.9220 (tp30) cc_final: 0.8760 (tp30) REVERT: S 381 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8873 (t) REVERT: E 52 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8721 (mm-30) REVERT: E 94 ASP cc_start: 0.8460 (t0) cc_final: 0.8152 (t0) REVERT: E 120 GLU cc_start: 0.6809 (tm-30) cc_final: 0.6334 (pp20) REVERT: J 24 LYS cc_start: 0.8793 (mmmt) cc_final: 0.8567 (mmtm) REVERT: J 39 ASP cc_start: 0.9221 (t0) cc_final: 0.8744 (t0) REVERT: J 44 GLU cc_start: 0.9244 (pm20) cc_final: 0.8920 (pm20) REVERT: J 47 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8787 (pt) REVERT: J 85 GLU cc_start: 0.8679 (tt0) cc_final: 0.8145 (tm-30) REVERT: J 112 ASP cc_start: 0.9135 (t0) cc_final: 0.8787 (t0) REVERT: O 6 THR cc_start: 0.8894 (m) cc_final: 0.8654 (m) REVERT: K 14 SER cc_start: 0.9483 (p) cc_final: 0.9194 (p) REVERT: K 39 ASP cc_start: 0.9141 (t0) cc_final: 0.8736 (t0) REVERT: P 28 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7883 (m-40) REVERT: P 112 ASP cc_start: 0.8803 (OUTLIER) cc_final: 0.8603 (m-30) REVERT: P 114 PHE cc_start: 0.8213 (t80) cc_final: 0.7784 (t80) REVERT: V 137 GLU cc_start: 0.9171 (tp30) cc_final: 0.8705 (tp30) REVERT: V 294 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7959 (pt0) REVERT: V 454 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9248 (tp) REVERT: G 94 ASP cc_start: 0.8554 (t0) cc_final: 0.8212 (t0) REVERT: L 24 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8419 (mtpp) REVERT: L 39 ASP cc_start: 0.9225 (t0) cc_final: 0.8742 (t0) REVERT: L 44 GLU cc_start: 0.9399 (pm20) cc_final: 0.9069 (pm20) REVERT: L 47 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8864 (pt) REVERT: L 85 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8197 (tm-30) REVERT: H 68 ASN cc_start: 0.8626 (t0) cc_final: 0.8338 (t0) REVERT: M 14 SER cc_start: 0.9470 (p) cc_final: 0.9165 (p) REVERT: M 21 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8744 (mtm-85) REVERT: M 39 ASP cc_start: 0.9063 (t0) cc_final: 0.8577 (t0) REVERT: M 44 GLU cc_start: 0.9236 (pm20) cc_final: 0.8950 (pm20) REVERT: R 28 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.8168 (m-40) REVERT: X 137 GLU cc_start: 0.9276 (tp30) cc_final: 0.8832 (tp30) REVERT: X 381 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8873 (t) outliers start: 81 outliers final: 52 residues processed: 600 average time/residue: 0.6428 time to fit residues: 474.4207 Evaluate side-chains 600 residues out of total 4176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 536 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 409 LEU Chi-restraints excluded: chain T residue 454 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain N residue 28 ASN Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 237 THR Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 409 LEU Chi-restraints excluded: chain S residue 454 LEU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain U residue 32 THR Chi-restraints excluded: chain U residue 298 PHE Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain P residue 28 ASN Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 112 ASP Chi-restraints excluded: chain V residue 36 ILE Chi-restraints excluded: chain V residue 129 THR Chi-restraints excluded: chain V residue 131 SER Chi-restraints excluded: chain V residue 294 GLU Chi-restraints excluded: chain V residue 381 THR Chi-restraints excluded: chain V residue 454 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain M residue 21 ARG Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 28 ASN Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain X residue 363 LEU Chi-restraints excluded: chain X residue 381 THR Chi-restraints excluded: chain X residue 409 LEU Chi-restraints excluded: chain X residue 426 ILE Chi-restraints excluded: chain X residue 454 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 171 optimal weight: 7.9990 chunk 479 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 chunk 384 optimal weight: 30.0000 chunk 141 optimal weight: 8.9990 chunk 292 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 300 optimal weight: 6.9990 chunk 436 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN C 76 ASN T 38 ASN I 45 ASN ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN E 68 ASN O 28 ASN O 76 ASN F 68 ASN P 76 ASN V 38 ASN G 68 ASN Q 28 ASN Q 76 ASN R 76 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.063984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.049787 restraints weight = 93531.801| |-----------------------------------------------------------------------------| r_work (start): 0.2635 rms_B_bonded: 2.90 r_work: 0.2521 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2401 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 39690 Z= 0.209 Angle : 0.680 9.548 53922 Z= 0.359 Chirality : 0.051 0.249 5868 Planarity : 0.004 0.065 7104 Dihedral : 4.973 49.715 5437 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 1.77 % Allowed : 16.64 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.11), residues: 4926 helix: -0.16 (0.33), residues: 252 sheet: -1.00 (0.14), residues: 1458 loop : -1.70 (0.10), residues: 3216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG W 297 TYR 0.026 0.001 TYR B 75 PHE 0.031 0.001 PHE C 114 TRP 0.019 0.001 TRP W 153 HIS 0.006 0.001 HIS V 377 Details of bonding type rmsd covalent geometry : bond 0.00507 (39690) covalent geometry : angle 0.68042 (53922) hydrogen bonds : bond 0.03304 ( 894) hydrogen bonds : angle 5.41551 ( 2163) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12936.14 seconds wall clock time: 220 minutes 39.20 seconds (13239.20 seconds total)