Starting phenix.real_space_refine on Thu Jan 15 03:45:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dwo_27757/01_2026/8dwo_27757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dwo_27757/01_2026/8dwo_27757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dwo_27757/01_2026/8dwo_27757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dwo_27757/01_2026/8dwo_27757.map" model { file = "/net/cci-nas-00/data/ceres_data/8dwo_27757/01_2026/8dwo_27757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dwo_27757/01_2026/8dwo_27757.cif" } resolution = 3.5 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= 0.061 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 129 5.16 5 C 14262 2.51 5 N 3912 2.21 5 O 4269 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22572 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3000 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 363} Chain breaks: 1 Chain: "B" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2720 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 26, 'TRANS': 319} Chain: "F" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3000 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 363} Chain breaks: 1 Chain: "G" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2720 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 26, 'TRANS': 319} Chain: "H" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "J" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3000 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 363} Chain breaks: 1 Chain: "K" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2720 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 26, 'TRANS': 319} Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 832 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "S" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "T" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 832 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "U" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "V" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 832 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Time building chain proxies: 5.69, per 1000 atoms: 0.25 Number of scatterers: 22572 At special positions: 0 Unit cell: (161.02, 177.62, 164.34, 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 129 16.00 O 4269 8.00 N 3912 7.00 C 14262 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.04 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 272 " distance=2.05 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 377 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 371 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 27 " distance=2.03 Simple disulfide: pdb=" SG CYS B 89 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 263 " distance=2.03 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 223 " distance=2.04 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 114 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 94 " distance=2.03 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 68 " - pdb=" SG CYS F 78 " distance=2.03 Simple disulfide: pdb=" SG CYS F 260 " - pdb=" SG CYS F 272 " distance=2.04 Simple disulfide: pdb=" SG CYS F 302 " - pdb=" SG CYS F 377 " distance=2.04 Simple disulfide: pdb=" SG CYS F 329 " - pdb=" SG CYS F 371 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 122 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 27 " distance=2.03 Simple disulfide: pdb=" SG CYS G 89 " - pdb=" SG CYS G 103 " distance=2.03 Simple disulfide: pdb=" SG CYS G 150 " - pdb=" SG CYS G 263 " distance=2.03 Simple disulfide: pdb=" SG CYS G 199 " - pdb=" SG CYS G 223 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 68 " - pdb=" SG CYS J 78 " distance=2.03 Simple disulfide: pdb=" SG CYS J 260 " - pdb=" SG CYS J 272 " distance=2.03 Simple disulfide: pdb=" SG CYS J 302 " - pdb=" SG CYS J 377 " distance=2.03 Simple disulfide: pdb=" SG CYS J 329 " - pdb=" SG CYS J 371 " distance=2.04 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 122 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 27 " distance=2.03 Simple disulfide: pdb=" SG CYS K 89 " - pdb=" SG CYS K 103 " distance=2.03 Simple disulfide: pdb=" SG CYS K 150 " - pdb=" SG CYS K 263 " distance=2.03 Simple disulfide: pdb=" SG CYS K 199 " - pdb=" SG CYS K 223 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 92 " distance=2.03 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.04 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: 2.04 Conformation dependent library (CDL) restraints added in 1.2 seconds 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5364 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 66 sheets defined 4.9% alpha, 39.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.744A pdb=" N SER A 115 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 248 Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'F' and resid 112 through 116 removed outlier: 4.097A pdb=" N SER F 115 " --> pdb=" O GLU F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 248 removed outlier: 3.586A pdb=" N ARG F 243 " --> pdb=" O SER F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 260 removed outlier: 3.982A pdb=" N GLY F 259 " --> pdb=" O ALA F 256 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N CYS F 260 " --> pdb=" O PRO F 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 256 through 260' Processing helix chain 'F' and resid 284 through 288 Processing helix chain 'F' and resid 290 through 294 removed outlier: 3.524A pdb=" N GLU F 293 " --> pdb=" O ARG F 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 10 removed outlier: 3.804A pdb=" N PHE G 6 " --> pdb=" O LEU G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 223 removed outlier: 3.607A pdb=" N GLN G 222 " --> pdb=" O ASP G 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.775A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 116 removed outlier: 3.594A pdb=" N SER J 115 " --> pdb=" O GLU J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 248 Processing helix chain 'J' and resid 284 through 288 removed outlier: 3.665A pdb=" N ALA J 287 " --> pdb=" O PRO J 284 " (cutoff:3.500A) Processing helix chain 'J' and resid 290 through 294 Processing helix chain 'K' and resid 2 through 9 Processing helix chain 'K' and resid 219 through 223 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.630A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 64 Processing helix chain 'S' and resid 83 through 87 removed outlier: 4.044A pdb=" N THR S 87 " --> pdb=" O ALA S 84 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 83 removed outlier: 3.658A pdb=" N VAL T 83 " --> pdb=" O ALA T 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 79 through 83 removed outlier: 3.544A pdb=" N VAL V 83 " --> pdb=" O ALA V 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 19 removed outlier: 7.281A pdb=" N GLN A 30 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N TYR A 137 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLN A 32 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE A 135 " --> pdb=" O GLN A 32 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL A 34 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL A 133 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR A 36 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA A 131 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 38 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL A 129 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N GLY A 127 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N THR A 42 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N HIS A 125 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU A 44 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS A 123 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR A 46 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 148 removed outlier: 5.918A pdb=" N SER A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N TYR A 137 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR A 46 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS A 123 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU A 44 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N HIS A 125 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N THR A 42 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N GLY A 127 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL A 129 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 38 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA A 131 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR A 36 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL A 133 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL A 34 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE A 135 " --> pdb=" O GLN A 32 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLN A 32 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N TYR A 137 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLN A 30 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 206 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 222 Processing sheet with id=AA6, first strand: chain 'A' and resid 298 through 307 removed outlier: 5.284A pdb=" N ASP A 299 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE A 316 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 344 through 347 removed outlier: 3.606A pdb=" N SER A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AA9, first strand: chain 'B' and resid 33 through 37 removed outlier: 7.736A pdb=" N ILE B 33 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N SER B 50 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLU B 35 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN B 48 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 10.145A pdb=" N SER B 50 " --> pdb=" O MET B 68 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N MET B 68 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR B 72 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 33 through 37 removed outlier: 7.736A pdb=" N ILE B 33 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N SER B 50 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLU B 35 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN B 48 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TYR B 97 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ALA B 51 " --> pdb=" O HIS B 95 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N HIS B 95 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N PHE B 53 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 10.805A pdb=" N SER B 93 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 81 through 84 Processing sheet with id=AB3, first strand: chain 'B' and resid 146 through 153 Processing sheet with id=AB4, first strand: chain 'B' and resid 163 through 166 Processing sheet with id=AB5, first strand: chain 'B' and resid 172 through 174 Processing sheet with id=AB6, first strand: chain 'B' and resid 178 through 180 Processing sheet with id=AB7, first strand: chain 'B' and resid 272 through 274 Processing sheet with id=AB8, first strand: chain 'B' and resid 304 through 308 Processing sheet with id=AB9, first strand: chain 'F' and resid 2 through 8 removed outlier: 4.882A pdb=" N ILE F 164 " --> pdb=" O THR F 153 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N THR F 153 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 14 through 19 removed outlier: 6.158A pdb=" N MET F 132 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR F 36 " --> pdb=" O GLN F 130 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN F 130 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ILE F 38 " --> pdb=" O THR F 128 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR F 128 " --> pdb=" O ILE F 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 14 through 19 removed outlier: 3.936A pdb=" N ILE F 38 " --> pdb=" O ALA F 269 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 44 through 48 removed outlier: 6.041A pdb=" N LEU F 44 " --> pdb=" O LYS F 123 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS F 123 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR F 46 " --> pdb=" O ALA F 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 51 through 54 Processing sheet with id=AC5, first strand: chain 'F' and resid 221 through 222 Processing sheet with id=AC6, first strand: chain 'F' and resid 297 through 307 removed outlier: 4.962A pdb=" N ASP F 299 " --> pdb=" O LYS F 322 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR F 305 " --> pdb=" O ILE F 316 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE F 316 " --> pdb=" O THR F 305 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL F 339 " --> pdb=" O SER F 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 344 through 347 removed outlier: 4.212A pdb=" N PHE F 366 " --> pdb=" O CYS F 377 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 19 through 22 removed outlier: 3.954A pdb=" N ASN G 21 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N SER G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 73 through 77 removed outlier: 5.984A pdb=" N MET G 68 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 9.787A pdb=" N SER G 50 " --> pdb=" O MET G 68 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N TYR G 97 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N ALA G 51 " --> pdb=" O HIS G 95 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N HIS G 95 " --> pdb=" O ALA G 51 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N PHE G 53 " --> pdb=" O SER G 93 " (cutoff:3.500A) removed outlier: 10.802A pdb=" N SER G 93 " --> pdb=" O PHE G 53 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 81 through 84 Processing sheet with id=AD2, first strand: chain 'G' and resid 146 through 153 Processing sheet with id=AD3, first strand: chain 'G' and resid 234 through 235 Processing sheet with id=AD4, first strand: chain 'G' and resid 172 through 174 Processing sheet with id=AD5, first strand: chain 'G' and resid 178 through 180 removed outlier: 4.091A pdb=" N VAL G 185 " --> pdb=" O THR G 214 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR G 214 " --> pdb=" O VAL G 185 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 272 through 274 Processing sheet with id=AD7, first strand: chain 'G' and resid 304 through 308 Processing sheet with id=AD8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.406A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.748A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 2 through 8 removed outlier: 5.571A pdb=" N ILE J 164 " --> pdb=" O THR J 153 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR J 153 " --> pdb=" O ILE J 164 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 14 through 21 removed outlier: 5.194A pdb=" N ARG J 21 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ALA J 25 " --> pdb=" O ARG J 21 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N MET J 132 " --> pdb=" O VAL J 34 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N THR J 36 " --> pdb=" O GLN J 130 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLN J 130 " --> pdb=" O THR J 36 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ILE J 38 " --> pdb=" O THR J 128 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N THR J 128 " --> pdb=" O ILE J 38 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR J 126 " --> pdb=" O PRO J 40 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N THR J 42 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL J 124 " --> pdb=" O THR J 42 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU J 44 " --> pdb=" O TYR J 122 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR J 122 " --> pdb=" O LEU J 44 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR J 46 " --> pdb=" O LYS J 120 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS J 120 " --> pdb=" O TYR J 46 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 143 through 148 removed outlier: 4.585A pdb=" N LYS J 120 " --> pdb=" O TYR J 46 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR J 46 " --> pdb=" O LYS J 120 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR J 122 " --> pdb=" O LEU J 44 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU J 44 " --> pdb=" O TYR J 122 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL J 124 " --> pdb=" O THR J 42 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N THR J 42 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR J 126 " --> pdb=" O PRO J 40 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N THR J 128 " --> pdb=" O ILE J 38 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ILE J 38 " --> pdb=" O THR J 128 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLN J 130 " --> pdb=" O THR J 36 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N THR J 36 " --> pdb=" O GLN J 130 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N MET J 132 " --> pdb=" O VAL J 34 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 51 through 54 removed outlier: 3.753A pdb=" N GLN J 77 " --> pdb=" O ALA J 106 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 221 through 222 removed outlier: 3.658A pdb=" N THR J 235 " --> pdb=" O LYS J 221 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 297 through 307 removed outlier: 5.948A pdb=" N LEU J 300 " --> pdb=" O LYS J 322 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LYS J 322 " --> pdb=" O LEU J 300 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N CYS J 302 " --> pdb=" O ALA J 320 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ALA J 320 " --> pdb=" O CYS J 302 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ILE J 304 " --> pdb=" O THR J 318 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR J 318 " --> pdb=" O ILE J 304 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 344 through 347 Processing sheet with id=AE9, first strand: chain 'K' and resid 17 through 22 removed outlier: 5.335A pdb=" N ASP K 18 " --> pdb=" O SER K 29 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N SER K 29 " --> pdb=" O ASP K 18 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N CYS K 27 " --> pdb=" O PRO K 20 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 34 through 37 removed outlier: 4.773A pdb=" N GLU K 35 " --> pdb=" O GLN K 48 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN K 48 " --> pdb=" O GLU K 35 " (cutoff:3.500A) removed outlier: 10.529A pdb=" N SER K 50 " --> pdb=" O MET K 68 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N MET K 68 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR K 64 " --> pdb=" O GLY K 54 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 34 through 37 removed outlier: 4.773A pdb=" N GLU K 35 " --> pdb=" O GLN K 48 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN K 48 " --> pdb=" O GLU K 35 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N TYR K 97 " --> pdb=" O THR K 49 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ALA K 51 " --> pdb=" O HIS K 95 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N HIS K 95 " --> pdb=" O ALA K 51 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N PHE K 53 " --> pdb=" O SER K 93 " (cutoff:3.500A) removed outlier: 11.296A pdb=" N SER K 93 " --> pdb=" O PHE K 53 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VAL K 83 " --> pdb=" O CYS K 89 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 146 through 153 Processing sheet with id=AF4, first strand: chain 'K' and resid 163 through 164 Processing sheet with id=AF5, first strand: chain 'K' and resid 166 through 167 Processing sheet with id=AF6, first strand: chain 'K' and resid 172 through 174 removed outlier: 3.798A pdb=" N ALA K 225 " --> pdb=" O ASP K 174 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 178 through 180 removed outlier: 4.058A pdb=" N VAL K 185 " --> pdb=" O THR K 214 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP K 212 " --> pdb=" O ILE K 187 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 272 through 274 Processing sheet with id=AF9, first strand: chain 'K' and resid 304 through 308 Processing sheet with id=AG1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.903A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AG4, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.841A pdb=" N GLY S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.928A pdb=" N VAL S 102 " --> pdb=" O ARG S 94 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'T' and resid 4 through 7 Processing sheet with id=AG7, first strand: chain 'T' and resid 10 through 12 removed outlier: 3.939A pdb=" N ASP T 105 " --> pdb=" O LEU T 11 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU T 33 " --> pdb=" O TYR T 49 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N TYR T 49 " --> pdb=" O LEU T 33 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'U' and resid 3 through 6 Processing sheet with id=AG9, first strand: chain 'U' and resid 10 through 12 removed outlier: 6.404A pdb=" N ARG U 38 " --> pdb=" O TRP U 47 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N TRP U 47 " --> pdb=" O ARG U 38 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'U' and resid 10 through 12 removed outlier: 3.933A pdb=" N VAL U 102 " --> pdb=" O ARG U 94 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'V' and resid 4 through 7 Processing sheet with id=AH3, first strand: chain 'V' and resid 10 through 13 removed outlier: 3.511A pdb=" N ASP V 105 " --> pdb=" O LEU V 11 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU V 33 " --> pdb=" O TYR V 49 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TYR V 49 " --> pdb=" O LEU V 33 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP V 35 " --> pdb=" O LEU V 47 " (cutoff:3.500A) 717 hydrogen bonds defined for protein. 1740 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: 4.59 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7309 1.35 - 1.47: 5833 1.47 - 1.60: 9885 1.60 - 1.72: 1 1.72 - 1.84: 162 Bond restraints: 23190 Sorted by residual: bond pdb=" C GLU F 265 " pdb=" N PRO F 266 " ideal model delta sigma weight residual 1.331 1.356 -0.024 7.90e-03 1.60e+04 9.61e+00 bond pdb=" C CYS J 329 " pdb=" N PRO J 330 " ideal model delta sigma weight residual 1.328 1.366 -0.038 1.25e-02 6.40e+03 9.37e+00 bond pdb=" CB PRO J 154 " pdb=" CG PRO J 154 " ideal model delta sigma weight residual 1.492 1.629 -0.137 5.00e-02 4.00e+02 7.48e+00 bond pdb=" C CYS F 329 " pdb=" N PRO F 330 " ideal model delta sigma weight residual 1.328 1.361 -0.033 1.26e-02 6.30e+03 6.78e+00 bond pdb=" C CYS A 329 " pdb=" N PRO A 330 " ideal model delta sigma weight residual 1.328 1.357 -0.029 1.26e-02 6.30e+03 5.20e+00 ... (remaining 23185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 29940 1.82 - 3.63: 1346 3.63 - 5.45: 272 5.45 - 7.27: 16 7.27 - 9.08: 7 Bond angle restraints: 31581 Sorted by residual: angle pdb=" CA PRO J 154 " pdb=" N PRO J 154 " pdb=" CD PRO J 154 " ideal model delta sigma weight residual 112.00 103.40 8.60 1.40e+00 5.10e-01 3.77e+01 angle pdb=" N CYS J 329 " pdb=" CA CYS J 329 " pdb=" C CYS J 329 " ideal model delta sigma weight residual 108.07 112.05 -3.98 8.90e-01 1.26e+00 2.00e+01 angle pdb=" CB LYS H 73 " pdb=" CG LYS H 73 " pdb=" CD LYS H 73 " ideal model delta sigma weight residual 111.30 120.23 -8.93 2.30e+00 1.89e-01 1.51e+01 angle pdb=" N TYR J 89 " pdb=" CA TYR J 89 " pdb=" C TYR J 89 " ideal model delta sigma weight residual 110.43 105.76 4.67 1.31e+00 5.83e-01 1.27e+01 angle pdb=" C CYS A 94 " pdb=" N PHE A 95 " pdb=" CA PHE A 95 " ideal model delta sigma weight residual 121.54 128.32 -6.78 1.91e+00 2.74e-01 1.26e+01 ... (remaining 31576 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 11870 17.94 - 35.88: 1499 35.88 - 53.83: 381 53.83 - 71.77: 78 71.77 - 89.71: 23 Dihedral angle restraints: 13851 sinusoidal: 5454 harmonic: 8397 Sorted by residual: dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 27 " pdb=" CB CYS G 27 " ideal model delta sinusoidal sigma weight residual -86.00 -175.48 89.48 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS J 68 " pdb=" SG CYS J 68 " pdb=" SG CYS J 78 " pdb=" CB CYS J 78 " ideal model delta sinusoidal sigma weight residual -86.00 -170.51 84.51 1 1.00e+01 1.00e-02 8.68e+01 dihedral pdb=" CA CYS A 62 " pdb=" C CYS A 62 " pdb=" N CYS A 63 " pdb=" CA CYS A 63 " ideal model delta harmonic sigma weight residual -180.00 -137.84 -42.16 0 5.00e+00 4.00e-02 7.11e+01 ... (remaining 13848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2110 0.037 - 0.075: 927 0.075 - 0.112: 289 0.112 - 0.150: 132 0.150 - 0.187: 13 Chirality restraints: 3471 Sorted by residual: chirality pdb=" CG LEU V 33 " pdb=" CB LEU V 33 " pdb=" CD1 LEU V 33 " pdb=" CD2 LEU V 33 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.74e-01 chirality pdb=" CA ILE G 16 " pdb=" N ILE G 16 " pdb=" C ILE G 16 " pdb=" CB ILE G 16 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.38e-01 chirality pdb=" CA ILE J 163 " pdb=" N ILE J 163 " pdb=" C ILE J 163 " pdb=" CB ILE J 163 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 3468 not shown) Planarity restraints: 4080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 116 " 0.063 5.00e-02 4.00e+02 9.79e-02 1.53e+01 pdb=" N PRO B 117 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO B 117 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 117 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 265 " 0.054 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO A 266 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 266 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 266 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 117 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" CG ASP A 117 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASP A 117 " 0.021 2.00e-02 2.50e+03 pdb=" OD2 ASP A 117 " 0.019 2.00e-02 2.50e+03 ... (remaining 4077 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 358 2.62 - 3.19: 19740 3.19 - 3.76: 33611 3.76 - 4.33: 46389 4.33 - 4.90: 79624 Nonbonded interactions: 179722 Sorted by model distance: nonbonded pdb=" OD2 ASP J 75 " pdb=" OG1 THR J 218 " model vdw 2.054 3.040 nonbonded pdb=" OG1 THR L 31 " pdb=" O GLY L 50 " model vdw 2.075 3.040 nonbonded pdb=" OG SER A 211 " pdb=" OD1 ASP A 213 " model vdw 2.076 3.040 nonbonded pdb=" OG1 THR S 30 " pdb=" OD1 ASP S 53 " model vdw 2.077 3.040 nonbonded pdb=" OE1 GLU G 34 " pdb=" OG SER G 237 " model vdw 2.080 3.040 ... (remaining 179717 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'L' selection = chain 'T' selection = chain 'V' } 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 group one per residue 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: 36.310 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: 0.030 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.410 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 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 : 0.005 0.137 23231 Z= 0.226 Angle : 0.888 9.085 31663 Z= 0.499 Chirality : 0.049 0.187 3471 Planarity : 0.007 0.098 4080 Dihedral : 17.091 89.709 8364 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.36 % Allowed : 26.62 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.41 (0.15), residues: 2886 helix: -0.89 (0.72), residues: 54 sheet: -1.13 (0.16), residues: 951 loop : -1.97 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 224 TYR 0.039 0.002 TYR F 137 PHE 0.034 0.002 PHE F 95 TRP 0.022 0.002 TRP K 233 HIS 0.008 0.001 HIS G 95 Details of bonding type rmsd covalent geometry : bond 0.00460 (23190) covalent geometry : angle 0.88464 (31581) SS BOND : bond 0.00442 ( 41) SS BOND : angle 1.80527 ( 82) hydrogen bonds : bond 0.13322 ( 678) hydrogen bonds : angle 7.52987 ( 1740) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 397 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 ARG cc_start: 0.7423 (mmt90) cc_final: 0.7221 (mmt90) REVERT: B 165 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7252 (mt-10) REVERT: B 177 LEU cc_start: 0.7624 (pt) cc_final: 0.7386 (pp) REVERT: B 228 ILE cc_start: 0.7667 (pt) cc_final: 0.7335 (pt) REVERT: B 326 THR cc_start: 0.9280 (t) cc_final: 0.8968 (p) REVERT: F 103 MET cc_start: 0.7262 (tpp) cc_final: 0.6877 (tpt) REVERT: F 207 ARG cc_start: 0.7010 (mmt180) cc_final: 0.6476 (mpt180) REVERT: F 213 ASP cc_start: 0.7610 (t70) cc_final: 0.7367 (t70) REVERT: F 214 LEU cc_start: 0.8832 (pt) cc_final: 0.8567 (pp) REVERT: G 302 ASN cc_start: 0.8757 (t0) cc_final: 0.8252 (t0) REVERT: H 27 TYR cc_start: 0.8200 (t80) cc_final: 0.7419 (t80) REVERT: H 100 TRP cc_start: 0.8022 (p90) cc_final: 0.7558 (p90) REVERT: K 35 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7165 (tm-30) REVERT: K 68 MET cc_start: 0.9089 (tpt) cc_final: 0.8865 (tpt) REVERT: K 194 GLN cc_start: 0.8293 (pm20) cc_final: 0.8077 (pm20) REVERT: K 222 GLN cc_start: 0.8221 (pt0) cc_final: 0.7901 (pt0) REVERT: K 339 GLU cc_start: 0.5192 (mm-30) cc_final: 0.4841 (tt0) REVERT: L 30 ASN cc_start: 0.8030 (m110) cc_final: 0.7661 (m110) REVERT: L 54 ARG cc_start: 0.7688 (tpp80) cc_final: 0.6995 (tpp80) REVERT: L 86 TYR cc_start: 0.7234 (m-10) cc_final: 0.6820 (m-10) REVERT: U 52 TYR cc_start: 0.8570 (t80) cc_final: 0.8108 (t80) REVERT: U 63 PHE cc_start: 0.7661 (m-80) cc_final: 0.7096 (m-10) REVERT: U 69 ILE cc_start: 0.6296 (mt) cc_final: 0.6043 (mt) REVERT: V 70 ASP cc_start: 0.7682 (p0) cc_final: 0.7388 (p0) REVERT: V 102 THR cc_start: 0.8194 (t) cc_final: 0.7934 (m) outliers start: 9 outliers final: 6 residues processed: 399 average time/residue: 0.1789 time to fit residues: 107.7718 Evaluate side-chains 352 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 346 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain K residue 138 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.1980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 236 GLN G 213 HIS K 94 HIS K 344 ASN L 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.141892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.118416 restraints weight = 31632.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.117171 restraints weight = 59196.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.117079 restraints weight = 62214.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.116280 restraints weight = 43617.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.116757 restraints weight = 38585.025| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 23231 Z= 0.181 Angle : 0.698 11.471 31663 Z= 0.363 Chirality : 0.048 0.213 3471 Planarity : 0.006 0.076 4080 Dihedral : 6.263 73.797 3163 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 4.16 % Allowed : 24.10 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.24 (0.15), residues: 2886 helix: -0.66 (0.70), residues: 54 sheet: -1.03 (0.16), residues: 1020 loop : -1.86 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG T 61 TYR 0.022 0.002 TYR F 309 PHE 0.021 0.002 PHE G 248 TRP 0.019 0.002 TRP L 35 HIS 0.009 0.001 HIS F 231 Details of bonding type rmsd covalent geometry : bond 0.00435 (23190) covalent geometry : angle 0.69359 (31581) SS BOND : bond 0.00449 ( 41) SS BOND : angle 1.70092 ( 82) hydrogen bonds : bond 0.03697 ( 678) hydrogen bonds : angle 6.43212 ( 1740) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 369 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7900 (tp) REVERT: B 291 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9106 (tp) REVERT: F 175 ASP cc_start: 0.7294 (m-30) cc_final: 0.6948 (m-30) REVERT: F 207 ARG cc_start: 0.7393 (mmt180) cc_final: 0.6842 (mpt180) REVERT: F 213 ASP cc_start: 0.7631 (t70) cc_final: 0.7294 (t70) REVERT: F 290 ARG cc_start: 0.8401 (mmm-85) cc_final: 0.8130 (mmm-85) REVERT: G 92 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.7907 (p) REVERT: G 200 LYS cc_start: 0.4754 (OUTLIER) cc_final: 0.4273 (pttp) REVERT: G 302 ASN cc_start: 0.8858 (t0) cc_final: 0.8181 (t0) REVERT: H 32 ILE cc_start: 0.8438 (tt) cc_final: 0.8227 (tt) REVERT: J 107 TYR cc_start: 0.5950 (t80) cc_final: 0.5356 (t80) REVERT: J 399 PHE cc_start: 0.4718 (OUTLIER) cc_final: 0.4485 (m-80) REVERT: K 27 CYS cc_start: 0.6548 (m) cc_final: 0.6248 (m) REVERT: K 222 GLN cc_start: 0.8171 (pt0) cc_final: 0.7965 (pt0) REVERT: K 306 GLN cc_start: 0.8969 (pm20) cc_final: 0.8297 (pt0) REVERT: K 339 GLU cc_start: 0.5456 (mm-30) cc_final: 0.5081 (tt0) REVERT: L 54 ARG cc_start: 0.7780 (tpp80) cc_final: 0.7226 (tpp80) REVERT: S 94 ARG cc_start: 0.7500 (tmm-80) cc_final: 0.7164 (tmm160) REVERT: U 52 TYR cc_start: 0.8603 (t80) cc_final: 0.8033 (t80) REVERT: U 63 PHE cc_start: 0.7727 (m-80) cc_final: 0.7514 (m-10) REVERT: U 69 ILE cc_start: 0.6487 (mt) cc_final: 0.6218 (mt) REVERT: V 70 ASP cc_start: 0.7853 (p0) cc_final: 0.7498 (p0) outliers start: 104 outliers final: 69 residues processed: 436 average time/residue: 0.1803 time to fit residues: 118.1870 Evaluate side-chains 414 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 340 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain F residue 1 TYR Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 371 CYS Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 118 ASN Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 295 ARG Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain J residue 95 PHE Chi-restraints excluded: chain J residue 142 TRP Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 307 CYS Chi-restraints excluded: chain J residue 321 TYR Chi-restraints excluded: chain J residue 369 GLN Chi-restraints excluded: chain J residue 371 CYS Chi-restraints excluded: chain J residue 399 PHE Chi-restraints excluded: chain K residue 8 GLN Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 138 TYR Chi-restraints excluded: chain K residue 148 LEU Chi-restraints excluded: chain K residue 213 HIS Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain S residue 59 PHE Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 48 ILE Chi-restraints excluded: chain V residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 83 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 chunk 245 optimal weight: 0.6980 chunk 233 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 42 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 HIS F 176 ASN F 231 HIS ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.137027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.111671 restraints weight = 31669.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.109736 restraints weight = 71359.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.110316 restraints weight = 58221.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.110688 restraints weight = 40794.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.110795 restraints weight = 38750.232| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 23231 Z= 0.233 Angle : 0.724 13.029 31663 Z= 0.374 Chirality : 0.048 0.244 3471 Planarity : 0.006 0.067 4080 Dihedral : 6.144 43.998 3155 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 6.51 % Allowed : 23.70 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.11 % 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: -2.27 (0.15), residues: 2886 helix: -0.90 (0.69), residues: 54 sheet: -1.02 (0.15), residues: 1107 loop : -1.91 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 119 TYR 0.024 0.002 TYR F 309 PHE 0.025 0.002 PHE G 248 TRP 0.013 0.002 TRP H 33 HIS 0.013 0.001 HIS F 231 Details of bonding type rmsd covalent geometry : bond 0.00558 (23190) covalent geometry : angle 0.71920 (31581) SS BOND : bond 0.00491 ( 41) SS BOND : angle 1.81553 ( 82) hydrogen bonds : bond 0.03718 ( 678) hydrogen bonds : angle 6.32649 ( 1740) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 343 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.9013 (mmm) cc_final: 0.8566 (mmm) REVERT: A 197 LYS cc_start: 0.7282 (tppp) cc_final: 0.6952 (mmtm) REVERT: A 378 LYS cc_start: 0.8181 (tmtt) cc_final: 0.7862 (tptt) REVERT: B 55 LEU cc_start: 0.8814 (mt) cc_final: 0.8601 (mp) REVERT: B 110 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8878 (p) REVERT: F 207 ARG cc_start: 0.7573 (mmt180) cc_final: 0.7006 (mpt180) REVERT: F 245 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.8745 (ttmt) REVERT: F 301 GLU cc_start: 0.7199 (pp20) cc_final: 0.6623 (pt0) REVERT: G 92 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8310 (p) REVERT: G 168 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.7780 (tp-100) REVERT: G 177 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8646 (pp) REVERT: G 200 LYS cc_start: 0.5011 (OUTLIER) cc_final: 0.4672 (pttp) REVERT: G 302 ASN cc_start: 0.9012 (t0) cc_final: 0.8283 (t0) REVERT: K 27 CYS cc_start: 0.6342 (m) cc_final: 0.6021 (m) REVERT: K 128 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8973 (t) REVERT: K 222 GLN cc_start: 0.8462 (pt0) cc_final: 0.8174 (pt0) REVERT: K 306 GLN cc_start: 0.8990 (pm20) cc_final: 0.8442 (pt0) REVERT: L 54 ARG cc_start: 0.7869 (tpp80) cc_final: 0.7280 (tpp80) REVERT: S 27 TYR cc_start: 0.8803 (t80) cc_final: 0.8406 (t80) REVERT: T 90 GLN cc_start: 0.8862 (pp30) cc_final: 0.8576 (pp30) REVERT: U 46 GLU cc_start: 0.7449 (pt0) cc_final: 0.7035 (pt0) REVERT: V 70 ASP cc_start: 0.7814 (p0) cc_final: 0.7514 (p0) outliers start: 163 outliers final: 107 residues processed: 457 average time/residue: 0.1679 time to fit residues: 116.8516 Evaluate side-chains 441 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 327 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain F residue 1 TYR Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 371 CYS Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 118 ASN Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 168 GLN Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 295 ARG Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 118 HIS Chi-restraints excluded: chain J residue 142 TRP Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 307 CYS Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain J residue 369 GLN Chi-restraints excluded: chain J residue 371 CYS Chi-restraints excluded: chain K residue 8 GLN Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 84 ARG Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 119 ARG Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 148 LEU Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 299 SER Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain S residue 59 PHE Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 251 optimal weight: 4.9990 chunk 175 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 245 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 121 optimal weight: 0.3980 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 GLN G 41 HIS H 3 GLN ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.137802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.113564 restraints weight = 31762.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.112379 restraints weight = 60212.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.112881 restraints weight = 50867.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.111940 restraints weight = 42406.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.112317 restraints weight = 39325.137| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23231 Z= 0.188 Angle : 0.679 11.732 31663 Z= 0.351 Chirality : 0.047 0.188 3471 Planarity : 0.006 0.106 4080 Dihedral : 6.010 44.790 3153 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 6.16 % Allowed : 24.78 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.11 % 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 (0.15), residues: 2886 helix: -0.88 (0.68), residues: 54 sheet: -0.97 (0.15), residues: 1107 loop : -1.87 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 224 TYR 0.023 0.002 TYR L 49 PHE 0.023 0.002 PHE G 248 TRP 0.014 0.001 TRP U 100D HIS 0.006 0.001 HIS J 231 Details of bonding type rmsd covalent geometry : bond 0.00453 (23190) covalent geometry : angle 0.67498 (31581) SS BOND : bond 0.00449 ( 41) SS BOND : angle 1.66290 ( 82) hydrogen bonds : bond 0.03429 ( 678) hydrogen bonds : angle 6.20907 ( 1740) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 345 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.9045 (mmm) cc_final: 0.8505 (mmm) REVERT: A 189 ASP cc_start: 0.5381 (OUTLIER) cc_final: 0.5122 (t0) REVERT: A 197 LYS cc_start: 0.7232 (tppp) cc_final: 0.6870 (mmtm) REVERT: A 264 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7912 (tp) REVERT: A 277 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8620 (mt) REVERT: A 378 LYS cc_start: 0.8168 (tmtt) cc_final: 0.7925 (tptt) REVERT: B 52 MET cc_start: 0.9019 (mtp) cc_final: 0.8633 (mtp) REVERT: B 110 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8833 (p) REVERT: B 119 ARG cc_start: 0.8122 (mmt-90) cc_final: 0.7904 (mmp80) REVERT: B 224 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8095 (ptp-110) REVERT: B 228 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8302 (pt) REVERT: B 326 THR cc_start: 0.9354 (OUTLIER) cc_final: 0.8970 (p) REVERT: B 327 TRP cc_start: 0.9457 (OUTLIER) cc_final: 0.8982 (t-100) REVERT: F 88 MET cc_start: 0.8623 (tpp) cc_final: 0.7930 (mmt) REVERT: F 130 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8484 (pt0) REVERT: F 207 ARG cc_start: 0.7504 (mmt180) cc_final: 0.7010 (mpt180) REVERT: F 245 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.8832 (ttmt) REVERT: F 301 GLU cc_start: 0.7061 (pp20) cc_final: 0.6480 (pt0) REVERT: G 92 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8336 (p) REVERT: G 302 ASN cc_start: 0.9002 (t0) cc_final: 0.8234 (t0) REVERT: K 27 CYS cc_start: 0.6270 (m) cc_final: 0.5940 (m) REVERT: K 35 GLU cc_start: 0.8405 (tm-30) cc_final: 0.7979 (tm-30) REVERT: K 222 GLN cc_start: 0.8440 (pt0) cc_final: 0.8171 (pt0) REVERT: K 306 GLN cc_start: 0.8975 (pm20) cc_final: 0.8588 (pt0) REVERT: K 326 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8834 (p) REVERT: L 54 ARG cc_start: 0.7810 (tpp80) cc_final: 0.7244 (tpp80) REVERT: S 27 TYR cc_start: 0.8860 (t80) cc_final: 0.8434 (t80) REVERT: T 90 GLN cc_start: 0.8868 (pp30) cc_final: 0.8410 (pp30) REVERT: U 46 GLU cc_start: 0.7507 (pt0) cc_final: 0.7076 (pt0) REVERT: U 52 TYR cc_start: 0.8825 (t80) cc_final: 0.8227 (t80) REVERT: V 70 ASP cc_start: 0.7749 (p0) cc_final: 0.7451 (p0) REVERT: V 79 GLU cc_start: 0.7051 (mp0) cc_final: 0.6581 (mp0) outliers start: 154 outliers final: 108 residues processed: 458 average time/residue: 0.1697 time to fit residues: 118.1617 Evaluate side-chains 452 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 332 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 327 TRP Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 95 PHE Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 371 CYS Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 118 ASN Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 295 ARG Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 95 PHE Chi-restraints excluded: chain J residue 118 HIS Chi-restraints excluded: chain J residue 142 TRP Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 243 ARG Chi-restraints excluded: chain J residue 277 ILE Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 307 CYS Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain J residue 371 CYS Chi-restraints excluded: chain K residue 8 GLN Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 84 ARG Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 148 LEU Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 214 THR Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 309 GLU Chi-restraints excluded: chain K residue 314 VAL Chi-restraints excluded: chain K residue 326 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain S residue 59 PHE Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 61 ARG Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain U residue 89 THR Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 224 optimal weight: 0.0770 chunk 1 optimal weight: 0.9990 chunk 285 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 257 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 197 optimal weight: 0.8980 chunk 249 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN A 369 GLN ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.137701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.112907 restraints weight = 31510.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.111200 restraints weight = 65248.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.111212 restraints weight = 63278.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.110453 restraints weight = 43595.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.110908 restraints weight = 39056.939| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 23231 Z= 0.187 Angle : 0.669 10.751 31663 Z= 0.345 Chirality : 0.047 0.257 3471 Planarity : 0.005 0.096 4080 Dihedral : 5.919 44.897 3153 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 7.23 % Allowed : 24.18 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.07 % 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: -2.12 (0.15), residues: 2886 helix: -0.70 (0.68), residues: 54 sheet: -0.88 (0.15), residues: 1104 loop : -1.85 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 224 TYR 0.026 0.002 TYR L 49 PHE 0.024 0.002 PHE K 248 TRP 0.027 0.002 TRP K 233 HIS 0.005 0.001 HIS J 231 Details of bonding type rmsd covalent geometry : bond 0.00451 (23190) covalent geometry : angle 0.66444 (31581) SS BOND : bond 0.00417 ( 41) SS BOND : angle 1.59624 ( 82) hydrogen bonds : bond 0.03368 ( 678) hydrogen bonds : angle 6.13585 ( 1740) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 348 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8773 (ptm160) REVERT: A 88 MET cc_start: 0.9057 (mmm) cc_final: 0.8715 (mmm) REVERT: A 189 ASP cc_start: 0.5447 (OUTLIER) cc_final: 0.5152 (t0) REVERT: A 197 LYS cc_start: 0.7219 (tppp) cc_final: 0.6880 (tppt) REVERT: A 277 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8694 (mt) REVERT: A 378 LYS cc_start: 0.8272 (tmtt) cc_final: 0.8057 (tptt) REVERT: B 52 MET cc_start: 0.9006 (mtp) cc_final: 0.8634 (mtp) REVERT: B 68 MET cc_start: 0.8875 (tpt) cc_final: 0.8290 (tpt) REVERT: B 74 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8402 (ptmt) REVERT: B 110 THR cc_start: 0.9058 (OUTLIER) cc_final: 0.8855 (p) REVERT: B 224 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7999 (ptp-110) REVERT: B 228 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8341 (pt) REVERT: B 302 ASN cc_start: 0.9002 (t0) cc_final: 0.8451 (t0) REVERT: B 326 THR cc_start: 0.9352 (OUTLIER) cc_final: 0.8946 (p) REVERT: B 327 TRP cc_start: 0.9481 (OUTLIER) cc_final: 0.9067 (t-100) REVERT: F 75 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.7833 (m-30) REVERT: F 88 MET cc_start: 0.8568 (tpp) cc_final: 0.7882 (mmt) REVERT: F 130 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8474 (pt0) REVERT: F 207 ARG cc_start: 0.7469 (mmt180) cc_final: 0.6986 (mpt180) REVERT: F 245 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8795 (ttmt) REVERT: F 301 GLU cc_start: 0.7046 (pp20) cc_final: 0.6486 (pt0) REVERT: G 9 TYR cc_start: 0.8056 (t80) cc_final: 0.7705 (t80) REVERT: G 168 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7709 (tp-100) REVERT: G 302 ASN cc_start: 0.8969 (t0) cc_final: 0.8145 (t0) REVERT: J 110 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8732 (ttp-170) REVERT: J 137 TYR cc_start: 0.6674 (p90) cc_final: 0.6265 (p90) REVERT: K 27 CYS cc_start: 0.6437 (m) cc_final: 0.6035 (m) REVERT: K 35 GLU cc_start: 0.8441 (tm-30) cc_final: 0.7973 (tm-30) REVERT: K 60 VAL cc_start: 0.8437 (m) cc_final: 0.8232 (m) REVERT: K 128 VAL cc_start: 0.9266 (OUTLIER) cc_final: 0.9053 (t) REVERT: K 306 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8525 (pt0) REVERT: S 27 TYR cc_start: 0.8829 (t80) cc_final: 0.8420 (t80) REVERT: T 90 GLN cc_start: 0.8914 (pp30) cc_final: 0.8366 (pp30) REVERT: U 32 ILE cc_start: 0.8931 (tp) cc_final: 0.8301 (tt) REVERT: U 46 GLU cc_start: 0.7513 (pt0) cc_final: 0.7042 (pt0) REVERT: V 70 ASP cc_start: 0.7860 (p0) cc_final: 0.7581 (p0) REVERT: V 79 GLU cc_start: 0.6980 (mp0) cc_final: 0.6665 (mp0) outliers start: 181 outliers final: 136 residues processed: 482 average time/residue: 0.1747 time to fit residues: 127.6678 Evaluate side-chains 480 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 328 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 327 TRP Chi-restraints excluded: chain F residue 1 TYR Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 95 PHE Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 371 CYS Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 118 ASN Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 168 GLN Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 295 ARG Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 95 PHE Chi-restraints excluded: chain J residue 110 ARG Chi-restraints excluded: chain J residue 118 HIS Chi-restraints excluded: chain J residue 142 TRP Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 243 ARG Chi-restraints excluded: chain J residue 277 ILE Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 307 CYS Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain J residue 369 GLN Chi-restraints excluded: chain J residue 371 CYS Chi-restraints excluded: chain K residue 8 GLN Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 84 ARG Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 148 LEU Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 214 THR Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 299 SER Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 306 GLN Chi-restraints excluded: chain K residue 309 GLU Chi-restraints excluded: chain K residue 314 VAL Chi-restraints excluded: chain K residue 326 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain S residue 59 PHE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 61 ARG Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain U residue 89 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 212 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN T 6 GLN U 66 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.137185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.112643 restraints weight = 31555.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.111242 restraints weight = 60662.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.111803 restraints weight = 54948.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.111296 restraints weight = 39130.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.111553 restraints weight = 37615.817| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23231 Z= 0.194 Angle : 0.668 10.507 31663 Z= 0.345 Chirality : 0.047 0.187 3471 Planarity : 0.005 0.090 4080 Dihedral : 5.912 44.689 3153 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 7.19 % Allowed : 24.78 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.07 % 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: -2.06 (0.15), residues: 2886 helix: -0.57 (0.69), residues: 54 sheet: -0.80 (0.16), residues: 1089 loop : -1.84 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 224 TYR 0.022 0.002 TYR F 309 PHE 0.025 0.002 PHE K 248 TRP 0.024 0.002 TRP L 35 HIS 0.005 0.001 HIS B 5 Details of bonding type rmsd covalent geometry : bond 0.00469 (23190) covalent geometry : angle 0.66416 (31581) SS BOND : bond 0.00405 ( 41) SS BOND : angle 1.53486 ( 82) hydrogen bonds : bond 0.03358 ( 678) hydrogen bonds : angle 6.10031 ( 1740) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 339 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8622 (ptm160) REVERT: A 61 LYS cc_start: 0.8043 (tptp) cc_final: 0.7537 (tptp) REVERT: A 189 ASP cc_start: 0.5325 (OUTLIER) cc_final: 0.5090 (t0) REVERT: A 197 LYS cc_start: 0.7309 (tppp) cc_final: 0.6964 (tppt) REVERT: A 277 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8705 (mt) REVERT: B 52 MET cc_start: 0.8999 (mtp) cc_final: 0.8620 (mtp) REVERT: B 68 MET cc_start: 0.8930 (tpt) cc_final: 0.8395 (tpt) REVERT: B 74 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8604 (ptmt) REVERT: B 110 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8663 (p) REVERT: B 228 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8389 (pt) REVERT: B 302 ASN cc_start: 0.9042 (t0) cc_final: 0.8489 (t0) REVERT: B 326 THR cc_start: 0.9371 (OUTLIER) cc_final: 0.8964 (p) REVERT: B 327 TRP cc_start: 0.9486 (OUTLIER) cc_final: 0.9043 (t-100) REVERT: F 75 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.7865 (m-30) REVERT: F 88 MET cc_start: 0.8608 (tpp) cc_final: 0.7991 (mmt) REVERT: F 207 ARG cc_start: 0.7336 (mmt180) cc_final: 0.7056 (mpt180) REVERT: F 245 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.8803 (ttmt) REVERT: F 301 GLU cc_start: 0.7081 (pp20) cc_final: 0.6587 (pt0) REVERT: G 9 TYR cc_start: 0.8037 (t80) cc_final: 0.7683 (t80) REVERT: G 168 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7724 (tp-100) REVERT: G 302 ASN cc_start: 0.9040 (t0) cc_final: 0.8168 (t0) REVERT: J 110 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8752 (ttp-170) REVERT: K 27 CYS cc_start: 0.6430 (m) cc_final: 0.6006 (m) REVERT: K 35 GLU cc_start: 0.8475 (tm-30) cc_final: 0.7971 (tm-30) REVERT: K 60 VAL cc_start: 0.8485 (m) cc_final: 0.8189 (m) REVERT: K 128 VAL cc_start: 0.9259 (OUTLIER) cc_final: 0.9057 (t) REVERT: K 205 ARG cc_start: 0.4709 (OUTLIER) cc_final: 0.4241 (mpp80) REVERT: K 306 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8565 (pt0) REVERT: L 6 GLN cc_start: 0.7545 (mt0) cc_final: 0.7338 (mt0) REVERT: S 27 TYR cc_start: 0.8885 (t80) cc_final: 0.8490 (t80) REVERT: T 90 GLN cc_start: 0.8942 (pp30) cc_final: 0.8367 (pp30) REVERT: U 32 ILE cc_start: 0.8960 (tp) cc_final: 0.8376 (tt) REVERT: U 46 GLU cc_start: 0.7537 (pt0) cc_final: 0.7017 (pt0) REVERT: U 94 ARG cc_start: 0.7580 (ttt-90) cc_final: 0.7226 (ttt-90) REVERT: V 70 ASP cc_start: 0.7629 (p0) cc_final: 0.7249 (p0) outliers start: 180 outliers final: 145 residues processed: 475 average time/residue: 0.1761 time to fit residues: 127.5731 Evaluate side-chains 488 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 328 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 327 TRP Chi-restraints excluded: chain F residue 13 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 95 PHE Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 371 CYS Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 118 ASN Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 168 GLN Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 295 ARG Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain J residue 54 LYS Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 95 PHE Chi-restraints excluded: chain J residue 110 ARG Chi-restraints excluded: chain J residue 118 HIS Chi-restraints excluded: chain J residue 142 TRP Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 243 ARG Chi-restraints excluded: chain J residue 277 ILE Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 307 CYS Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain J residue 371 CYS Chi-restraints excluded: chain J residue 396 THR Chi-restraints excluded: chain K residue 8 GLN Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 84 ARG Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 148 LEU Chi-restraints excluded: chain K residue 165 GLU Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 205 ARG Chi-restraints excluded: chain K residue 214 THR Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain K residue 299 SER Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 306 GLN Chi-restraints excluded: chain K residue 309 GLU Chi-restraints excluded: chain K residue 314 VAL Chi-restraints excluded: chain K residue 326 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain S residue 59 PHE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 61 ARG Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain U residue 89 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 114 optimal weight: 1.9990 chunk 230 optimal weight: 0.9990 chunk 8 optimal weight: 0.0040 chunk 282 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 chunk 126 optimal weight: 0.0050 chunk 276 optimal weight: 2.9990 chunk 277 optimal weight: 0.3980 chunk 82 optimal weight: 0.7980 chunk 154 optimal weight: 7.9990 overall best weight: 0.3806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN K 80 ASN V 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.140076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.115048 restraints weight = 31518.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.113698 restraints weight = 63233.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.114106 restraints weight = 59717.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.113597 restraints weight = 40609.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.113907 restraints weight = 34811.792| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23231 Z= 0.131 Angle : 0.633 9.142 31663 Z= 0.326 Chirality : 0.045 0.177 3471 Planarity : 0.005 0.111 4080 Dihedral : 5.697 44.344 3153 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 6.43 % Allowed : 25.74 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.98 (0.15), residues: 2886 helix: -0.24 (0.70), residues: 54 sheet: -0.77 (0.16), residues: 1095 loop : -1.77 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 224 TYR 0.018 0.001 TYR F 309 PHE 0.020 0.001 PHE K 6 TRP 0.039 0.002 TRP L 35 HIS 0.004 0.001 HIS B 114 Details of bonding type rmsd covalent geometry : bond 0.00316 (23190) covalent geometry : angle 0.63007 (31581) SS BOND : bond 0.00338 ( 41) SS BOND : angle 1.38489 ( 82) hydrogen bonds : bond 0.03194 ( 678) hydrogen bonds : angle 5.95874 ( 1740) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 349 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8878 (mmm) cc_final: 0.8441 (mmm) REVERT: A 189 ASP cc_start: 0.5065 (OUTLIER) cc_final: 0.4782 (t0) REVERT: B 52 MET cc_start: 0.8977 (mtp) cc_final: 0.8525 (mmm) REVERT: B 68 MET cc_start: 0.8889 (tpt) cc_final: 0.8368 (tpt) REVERT: B 74 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8474 (ptmt) REVERT: B 291 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9155 (tp) REVERT: B 302 ASN cc_start: 0.8966 (t0) cc_final: 0.8439 (t0) REVERT: B 326 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.8927 (p) REVERT: F 75 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.7830 (m-30) REVERT: F 88 MET cc_start: 0.8514 (tpp) cc_final: 0.7774 (mmt) REVERT: F 207 ARG cc_start: 0.7286 (mmt180) cc_final: 0.6976 (mpt180) REVERT: F 245 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8704 (ttmt) REVERT: F 301 GLU cc_start: 0.6999 (pp20) cc_final: 0.6523 (pt0) REVERT: G 168 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7613 (tp-100) REVERT: G 302 ASN cc_start: 0.8811 (t0) cc_final: 0.7952 (t0) REVERT: J 54 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8879 (ptmt) REVERT: J 110 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8788 (ttp-170) REVERT: J 176 ASN cc_start: 0.7435 (t0) cc_final: 0.7083 (t0) REVERT: K 27 CYS cc_start: 0.6399 (m) cc_final: 0.5999 (m) REVERT: K 35 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8021 (tm-30) REVERT: K 205 ARG cc_start: 0.4636 (OUTLIER) cc_final: 0.4191 (mpp80) REVERT: K 221 LYS cc_start: 0.8961 (ttmm) cc_final: 0.8708 (ttmm) REVERT: K 306 GLN cc_start: 0.8887 (pm20) cc_final: 0.8611 (pt0) REVERT: L 37 LEU cc_start: 0.7829 (tp) cc_final: 0.7580 (tt) REVERT: S 27 TYR cc_start: 0.8809 (t80) cc_final: 0.8352 (t80) REVERT: T 90 GLN cc_start: 0.8925 (pp30) cc_final: 0.8355 (pp30) REVERT: U 32 ILE cc_start: 0.8910 (tp) cc_final: 0.8355 (tt) REVERT: U 46 GLU cc_start: 0.7478 (pt0) cc_final: 0.6971 (pt0) REVERT: U 52 TYR cc_start: 0.8777 (t80) cc_final: 0.8230 (t80) REVERT: V 70 ASP cc_start: 0.7512 (p0) cc_final: 0.7115 (p0) outliers start: 161 outliers final: 117 residues processed: 471 average time/residue: 0.1678 time to fit residues: 120.3025 Evaluate side-chains 460 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 333 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain F residue 13 ILE Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 95 PHE Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 371 CYS Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 118 ASN Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 168 GLN Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain J residue 54 LYS Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 95 PHE Chi-restraints excluded: chain J residue 110 ARG Chi-restraints excluded: chain J residue 118 HIS Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 243 ARG Chi-restraints excluded: chain J residue 277 ILE Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain J residue 371 CYS Chi-restraints excluded: chain J residue 396 THR Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 84 ARG Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 148 LEU Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 205 ARG Chi-restraints excluded: chain K residue 214 THR Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 309 GLU Chi-restraints excluded: chain K residue 314 VAL Chi-restraints excluded: chain K residue 326 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain S residue 59 PHE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 27 SER Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 216 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 272 optimal weight: 0.4980 chunk 198 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN F 176 ASN K 80 ASN T 77 ASN V 77 ASN ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.137979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.108616 restraints weight = 31658.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.107626 restraints weight = 50970.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.109114 restraints weight = 41851.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.108603 restraints weight = 29594.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.108987 restraints weight = 29046.120| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23231 Z= 0.172 Angle : 0.655 9.801 31663 Z= 0.337 Chirality : 0.046 0.183 3471 Planarity : 0.005 0.110 4080 Dihedral : 5.733 44.133 3153 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 6.95 % Allowed : 25.34 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.07 % 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: -1.96 (0.15), residues: 2886 helix: -0.24 (0.70), residues: 54 sheet: -0.71 (0.16), residues: 1089 loop : -1.78 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG U 28 TYR 0.026 0.002 TYR G 9 PHE 0.021 0.002 PHE K 248 TRP 0.041 0.002 TRP L 35 HIS 0.005 0.001 HIS B 114 Details of bonding type rmsd covalent geometry : bond 0.00417 (23190) covalent geometry : angle 0.65124 (31581) SS BOND : bond 0.00413 ( 41) SS BOND : angle 1.55357 ( 82) hydrogen bonds : bond 0.03273 ( 678) hydrogen bonds : angle 5.94953 ( 1740) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 335 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8965 (mmm) cc_final: 0.8491 (mmm) REVERT: A 189 ASP cc_start: 0.5066 (OUTLIER) cc_final: 0.4790 (t0) REVERT: A 219 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8194 (m-40) REVERT: A 277 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8755 (mt) REVERT: B 52 MET cc_start: 0.8789 (mtp) cc_final: 0.8384 (mmm) REVERT: B 68 MET cc_start: 0.8912 (tpt) cc_final: 0.8421 (tpt) REVERT: B 74 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8517 (ptmt) REVERT: B 201 CYS cc_start: 0.4879 (OUTLIER) cc_final: 0.3939 (m) REVERT: B 228 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8510 (pt) REVERT: B 291 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8930 (tp) REVERT: B 302 ASN cc_start: 0.8998 (t0) cc_final: 0.8440 (t0) REVERT: B 326 THR cc_start: 0.9343 (OUTLIER) cc_final: 0.8933 (p) REVERT: B 327 TRP cc_start: 0.9452 (OUTLIER) cc_final: 0.9014 (t-100) REVERT: F 75 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8280 (m-30) REVERT: F 88 MET cc_start: 0.8563 (tpp) cc_final: 0.7841 (mmt) REVERT: F 207 ARG cc_start: 0.7325 (mmt180) cc_final: 0.6992 (mpt180) REVERT: F 245 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8709 (ttmt) REVERT: F 301 GLU cc_start: 0.7266 (pp20) cc_final: 0.6680 (pt0) REVERT: G 5 HIS cc_start: 0.8990 (OUTLIER) cc_final: 0.8209 (m-70) REVERT: G 168 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7645 (tp-100) REVERT: G 302 ASN cc_start: 0.8980 (t0) cc_final: 0.8148 (t0) REVERT: H 52 TYR cc_start: 0.8382 (t80) cc_final: 0.7805 (t80) REVERT: J 54 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8366 (tttm) REVERT: J 110 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8838 (ttp-170) REVERT: J 176 ASN cc_start: 0.7534 (t0) cc_final: 0.7181 (t0) REVERT: K 27 CYS cc_start: 0.6422 (m) cc_final: 0.6008 (m) REVERT: K 35 GLU cc_start: 0.8493 (tm-30) cc_final: 0.7979 (tm-30) REVERT: K 205 ARG cc_start: 0.4783 (OUTLIER) cc_final: 0.4332 (mpp80) REVERT: K 221 LYS cc_start: 0.8997 (ttmm) cc_final: 0.8738 (ttmm) REVERT: K 306 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8618 (pt0) REVERT: S 27 TYR cc_start: 0.8863 (t80) cc_final: 0.8428 (t80) REVERT: S 32 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7507 (tt) REVERT: T 90 GLN cc_start: 0.8879 (pp30) cc_final: 0.8208 (pp30) REVERT: U 32 ILE cc_start: 0.8953 (tp) cc_final: 0.8307 (tt) REVERT: U 46 GLU cc_start: 0.7407 (pt0) cc_final: 0.6898 (pt0) REVERT: U 52 TYR cc_start: 0.8858 (t80) cc_final: 0.8291 (t80) REVERT: V 70 ASP cc_start: 0.7585 (p0) cc_final: 0.7171 (p0) outliers start: 174 outliers final: 131 residues processed: 469 average time/residue: 0.1660 time to fit residues: 119.4663 Evaluate side-chains 478 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 329 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 327 TRP Chi-restraints excluded: chain F residue 13 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 95 PHE Chi-restraints excluded: chain F residue 118 HIS Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 371 CYS Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain G residue 5 HIS Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 118 ASN Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 168 GLN Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain J residue 54 LYS Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 95 PHE Chi-restraints excluded: chain J residue 110 ARG Chi-restraints excluded: chain J residue 118 HIS Chi-restraints excluded: chain J residue 142 TRP Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 243 ARG Chi-restraints excluded: chain J residue 277 ILE Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain J residue 371 CYS Chi-restraints excluded: chain J residue 396 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 8 GLN Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 84 ARG Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 148 LEU Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 205 ARG Chi-restraints excluded: chain K residue 214 THR Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 306 GLN Chi-restraints excluded: chain K residue 309 GLU Chi-restraints excluded: chain K residue 314 VAL Chi-restraints excluded: chain K residue 326 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain S residue 59 PHE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain U residue 89 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 27 SER Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 137 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 285 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 157 optimal weight: 0.8980 chunk 23 optimal weight: 0.0980 chunk 187 optimal weight: 5.9990 chunk 189 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN K 80 ASN U 81 GLN ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.138919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.109130 restraints weight = 31717.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.107821 restraints weight = 53776.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.108962 restraints weight = 50606.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.108963 restraints weight = 31555.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.109345 restraints weight = 29890.426| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23231 Z= 0.151 Angle : 0.645 9.244 31663 Z= 0.332 Chirality : 0.046 0.171 3471 Planarity : 0.005 0.117 4080 Dihedral : 5.677 44.529 3153 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 6.00 % Allowed : 26.14 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.91 (0.15), residues: 2886 helix: -0.19 (0.69), residues: 54 sheet: -0.66 (0.16), residues: 1089 loop : -1.76 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG U 28 TYR 0.021 0.002 TYR T 32 PHE 0.020 0.002 PHE K 248 TRP 0.031 0.002 TRP L 35 HIS 0.004 0.001 HIS B 114 Details of bonding type rmsd covalent geometry : bond 0.00365 (23190) covalent geometry : angle 0.64203 (31581) SS BOND : bond 0.00372 ( 41) SS BOND : angle 1.43611 ( 82) hydrogen bonds : bond 0.03181 ( 678) hydrogen bonds : angle 5.89218 ( 1740) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 339 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9074 (ttpt) cc_final: 0.8863 (tttm) REVERT: A 189 ASP cc_start: 0.5066 (OUTLIER) cc_final: 0.4784 (t0) REVERT: A 277 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8753 (mt) REVERT: B 52 MET cc_start: 0.8791 (mtp) cc_final: 0.8416 (mmm) REVERT: B 68 MET cc_start: 0.8891 (tpt) cc_final: 0.8463 (tpt) REVERT: B 74 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8528 (ptmt) REVERT: B 228 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8406 (pt) REVERT: B 291 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9098 (tp) REVERT: B 302 ASN cc_start: 0.8987 (t0) cc_final: 0.8450 (t0) REVERT: B 326 THR cc_start: 0.9348 (OUTLIER) cc_final: 0.8926 (p) REVERT: F 75 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.7822 (m-30) REVERT: F 88 MET cc_start: 0.8512 (tpp) cc_final: 0.7785 (mmt) REVERT: F 207 ARG cc_start: 0.7438 (mmt180) cc_final: 0.7033 (mpt180) REVERT: F 245 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8675 (ttmt) REVERT: F 301 GLU cc_start: 0.7280 (pp20) cc_final: 0.6721 (pt0) REVERT: G 5 HIS cc_start: 0.8965 (OUTLIER) cc_final: 0.8111 (m-70) REVERT: G 168 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7626 (tp-100) REVERT: G 302 ASN cc_start: 0.8955 (t0) cc_final: 0.8108 (t0) REVERT: H 52 TYR cc_start: 0.8393 (t80) cc_final: 0.7773 (t80) REVERT: J 54 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8873 (ptmt) REVERT: J 110 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8789 (ttp-170) REVERT: J 176 ASN cc_start: 0.7535 (t0) cc_final: 0.7163 (t0) REVERT: K 27 CYS cc_start: 0.6419 (m) cc_final: 0.6025 (m) REVERT: K 35 GLU cc_start: 0.8441 (tm-30) cc_final: 0.7869 (tm-30) REVERT: K 205 ARG cc_start: 0.4753 (OUTLIER) cc_final: 0.4260 (mpp80) REVERT: K 221 LYS cc_start: 0.9003 (ttmm) cc_final: 0.8750 (ttmm) REVERT: K 292 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8786 (tp) REVERT: K 306 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8625 (pt0) REVERT: K 339 GLU cc_start: 0.4255 (tt0) cc_final: 0.3679 (tt0) REVERT: L 35 TRP cc_start: 0.8289 (m100) cc_final: 0.8003 (m100) REVERT: L 37 LEU cc_start: 0.7855 (tp) cc_final: 0.7598 (tt) REVERT: S 27 TYR cc_start: 0.8844 (t80) cc_final: 0.8470 (t80) REVERT: S 32 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7525 (tt) REVERT: T 79 GLU cc_start: 0.6158 (mp0) cc_final: 0.5864 (mp0) REVERT: T 90 GLN cc_start: 0.8868 (pp30) cc_final: 0.8195 (pp30) REVERT: U 32 ILE cc_start: 0.8921 (tp) cc_final: 0.8295 (tt) REVERT: U 46 GLU cc_start: 0.7271 (pt0) cc_final: 0.6662 (pt0) REVERT: U 52 TYR cc_start: 0.8784 (t80) cc_final: 0.8210 (t80) REVERT: V 70 ASP cc_start: 0.7678 (p0) cc_final: 0.7260 (p0) outliers start: 150 outliers final: 126 residues processed: 456 average time/residue: 0.1710 time to fit residues: 119.6946 Evaluate side-chains 471 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 329 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain F residue 13 ILE Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 95 PHE Chi-restraints excluded: chain F residue 118 HIS Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 371 CYS Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain G residue 5 HIS Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 118 ASN Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 168 GLN Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain J residue 54 LYS Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 95 PHE Chi-restraints excluded: chain J residue 110 ARG Chi-restraints excluded: chain J residue 118 HIS Chi-restraints excluded: chain J residue 142 TRP Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 243 ARG Chi-restraints excluded: chain J residue 277 ILE Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 307 CYS Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain J residue 371 CYS Chi-restraints excluded: chain J residue 396 THR Chi-restraints excluded: chain K residue 8 GLN Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 84 ARG Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 148 LEU Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 205 ARG Chi-restraints excluded: chain K residue 214 THR Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 306 GLN Chi-restraints excluded: chain K residue 309 GLU Chi-restraints excluded: chain K residue 314 VAL Chi-restraints excluded: chain K residue 326 THR Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain S residue 59 PHE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain U residue 89 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 27 SER Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 109 optimal weight: 0.9990 chunk 264 optimal weight: 4.9990 chunk 15 optimal weight: 0.0060 chunk 113 optimal weight: 0.5980 chunk 103 optimal weight: 0.0970 chunk 90 optimal weight: 0.4980 chunk 77 optimal weight: 0.5980 chunk 274 optimal weight: 6.9990 chunk 262 optimal weight: 4.9990 chunk 199 optimal weight: 0.9990 chunk 276 optimal weight: 1.9990 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN G 151 ASN J 30 GLN K 80 ASN U 66 HIS ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.140523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.110382 restraints weight = 31727.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.108289 restraints weight = 58038.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.109785 restraints weight = 45784.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.109848 restraints weight = 30951.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.110136 restraints weight = 28617.694| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23231 Z= 0.127 Angle : 0.628 9.345 31663 Z= 0.324 Chirality : 0.045 0.172 3471 Planarity : 0.005 0.116 4080 Dihedral : 5.551 43.843 3153 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 5.68 % Allowed : 26.66 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.87 (0.15), residues: 2886 helix: -0.01 (0.69), residues: 54 sheet: -0.64 (0.16), residues: 1092 loop : -1.74 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 28 TYR 0.022 0.001 TYR G 9 PHE 0.017 0.001 PHE K 248 TRP 0.031 0.002 TRP L 35 HIS 0.004 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00307 (23190) covalent geometry : angle 0.62535 (31581) SS BOND : bond 0.00338 ( 41) SS BOND : angle 1.33299 ( 82) hydrogen bonds : bond 0.03068 ( 678) hydrogen bonds : angle 5.80597 ( 1740) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 350 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASP cc_start: 0.5047 (OUTLIER) cc_final: 0.4632 (t0) REVERT: A 277 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8753 (mt) REVERT: B 52 MET cc_start: 0.8762 (mtp) cc_final: 0.8360 (mmt) REVERT: B 68 MET cc_start: 0.8903 (tpt) cc_final: 0.8477 (tpt) REVERT: B 74 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8478 (ptmt) REVERT: B 99 ILE cc_start: 0.9119 (mt) cc_final: 0.8866 (mt) REVERT: B 201 CYS cc_start: 0.4298 (OUTLIER) cc_final: 0.3515 (t) REVERT: B 228 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8395 (pt) REVERT: B 291 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9146 (tp) REVERT: B 302 ASN cc_start: 0.8985 (t0) cc_final: 0.8471 (t0) REVERT: B 326 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.8895 (p) REVERT: F 4 THR cc_start: 0.9138 (m) cc_final: 0.8482 (p) REVERT: F 38 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8631 (mt) REVERT: F 75 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.7715 (m-30) REVERT: F 82 SER cc_start: 0.9222 (m) cc_final: 0.8395 (p) REVERT: F 88 MET cc_start: 0.8487 (tpp) cc_final: 0.7720 (mmt) REVERT: F 207 ARG cc_start: 0.7601 (mmt180) cc_final: 0.7357 (mpt180) REVERT: F 245 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8665 (ttmt) REVERT: F 301 GLU cc_start: 0.7280 (pp20) cc_final: 0.6747 (pt0) REVERT: G 5 HIS cc_start: 0.8929 (OUTLIER) cc_final: 0.8031 (m-70) REVERT: G 168 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7510 (tp-100) REVERT: G 302 ASN cc_start: 0.8820 (t0) cc_final: 0.8030 (t0) REVERT: H 52 TYR cc_start: 0.8402 (t80) cc_final: 0.7726 (t80) REVERT: J 54 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8899 (ptmt) REVERT: J 110 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8752 (ttp-170) REVERT: K 4 THR cc_start: 0.7980 (p) cc_final: 0.7711 (p) REVERT: K 27 CYS cc_start: 0.6413 (m) cc_final: 0.5993 (m) REVERT: K 205 ARG cc_start: 0.4724 (OUTLIER) cc_final: 0.4177 (mpp80) REVERT: K 221 LYS cc_start: 0.9004 (ttmm) cc_final: 0.8746 (ttmm) REVERT: K 292 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8741 (tp) REVERT: K 306 GLN cc_start: 0.8868 (pm20) cc_final: 0.8666 (pt0) REVERT: K 309 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: K 339 GLU cc_start: 0.4375 (tt0) cc_final: 0.4113 (tt0) REVERT: L 35 TRP cc_start: 0.8247 (m100) cc_final: 0.8032 (m100) REVERT: L 37 LEU cc_start: 0.7853 (tp) cc_final: 0.7614 (tt) REVERT: S 27 TYR cc_start: 0.8884 (t80) cc_final: 0.8458 (t80) REVERT: S 32 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7516 (tt) REVERT: T 79 GLU cc_start: 0.6010 (mp0) cc_final: 0.5047 (mp0) REVERT: T 90 GLN cc_start: 0.8838 (pp30) cc_final: 0.8206 (pp30) REVERT: U 32 ILE cc_start: 0.8818 (tp) cc_final: 0.8170 (tt) REVERT: U 46 GLU cc_start: 0.7223 (pt0) cc_final: 0.6596 (pt0) REVERT: U 52 TYR cc_start: 0.8763 (t80) cc_final: 0.8159 (t80) REVERT: V 70 ASP cc_start: 0.7650 (p0) cc_final: 0.7245 (p0) outliers start: 142 outliers final: 121 residues processed: 457 average time/residue: 0.1722 time to fit residues: 120.2745 Evaluate side-chains 477 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 338 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain F residue 13 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 95 PHE Chi-restraints excluded: chain F residue 118 HIS Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 371 CYS Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain G residue 5 HIS Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 118 ASN Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 168 GLN Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain J residue 54 LYS Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 95 PHE Chi-restraints excluded: chain J residue 110 ARG Chi-restraints excluded: chain J residue 118 HIS Chi-restraints excluded: chain J residue 142 TRP Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 243 ARG Chi-restraints excluded: chain J residue 277 ILE Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 307 CYS Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain J residue 371 CYS Chi-restraints excluded: chain J residue 396 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 8 GLN Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 84 ARG Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 148 LEU Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 205 ARG Chi-restraints excluded: chain K residue 214 THR Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain K residue 309 GLU Chi-restraints excluded: chain K residue 314 VAL Chi-restraints excluded: chain K residue 326 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain S residue 59 PHE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain U residue 89 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 27 SER Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 189 optimal weight: 0.7980 chunk 207 optimal weight: 0.0970 chunk 261 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 223 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN H 66 HIS J 30 GLN ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.140433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.110521 restraints weight = 31738.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.108052 restraints weight = 59186.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.109202 restraints weight = 45544.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.110362 restraints weight = 30940.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.110458 restraints weight = 28812.677| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 23231 Z= 0.173 Angle : 0.771 59.183 31663 Z= 0.426 Chirality : 0.047 0.669 3471 Planarity : 0.005 0.114 4080 Dihedral : 5.581 43.799 3153 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 5.92 % Allowed : 26.50 % Favored : 67.59 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.86 (0.15), residues: 2886 helix: -0.01 (0.69), residues: 54 sheet: -0.63 (0.16), residues: 1092 loop : -1.73 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 28 TYR 0.018 0.001 TYR F 309 PHE 0.017 0.001 PHE K 248 TRP 0.026 0.002 TRP L 35 HIS 0.005 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00392 (23190) covalent geometry : angle 0.76495 (31581) SS BOND : bond 0.00699 ( 41) SS BOND : angle 1.97019 ( 82) hydrogen bonds : bond 0.03083 ( 678) hydrogen bonds : angle 5.80638 ( 1740) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4721.74 seconds wall clock time: 82 minutes 31.17 seconds (4951.17 seconds total)