Starting phenix.real_space_refine on Thu Jun 19 23:26:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i1v_35123/06_2025/8i1v_35123.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i1v_35123/06_2025/8i1v_35123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i1v_35123/06_2025/8i1v_35123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i1v_35123/06_2025/8i1v_35123.map" model { file = "/net/cci-nas-00/data/ceres_data/8i1v_35123/06_2025/8i1v_35123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i1v_35123/06_2025/8i1v_35123.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.007 sd= 0.825 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 98 5.16 5 C 14961 2.51 5 N 4163 2.21 5 O 4648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23870 Number of models: 1 Model: "" Number of chains: 14 Chain: "G" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3203 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3162 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 20, 'TRANS': 394} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3156 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3220 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 20, 'TRANS': 401} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3220 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 20, 'TRANS': 401} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3139 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 20, 'TRANS': 391} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3139 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 20, 'TRANS': 391} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "I" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "J" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "K" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "L" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "M" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "N" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Time building chain proxies: 14.99, per 1000 atoms: 0.63 Number of scatterers: 23870 At special positions: 0 Unit cell: (102.82, 182.32, 161.12, 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 98 16.00 O 4648 8.00 N 4163 7.00 C 14961 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.47 Conformation dependent library (CDL) restraints added in 3.1 seconds 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5868 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 56 sheets defined 26.6% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'G' and resid 4 through 24 removed outlier: 3.656A pdb=" N THR G 24 " --> pdb=" O ILE G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 30 Processing helix chain 'G' and resid 96 through 127 removed outlier: 3.526A pdb=" N TYR G 100 " --> pdb=" O ASP G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 159 Processing helix chain 'G' and resid 171 through 178 Processing helix chain 'G' and resid 321 through 326 Processing helix chain 'G' and resid 417 through 419 No H-bonds generated for 'chain 'G' and resid 417 through 419' Processing helix chain 'A' and resid 4 through 23 Processing helix chain 'A' and resid 24 through 30 removed outlier: 3.929A pdb=" N GLN A 28 " --> pdb=" O THR A 24 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 30 " --> pdb=" O MET A 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 24 through 30' Processing helix chain 'A' and resid 90 through 95 Processing helix chain 'A' and resid 96 through 126 removed outlier: 3.502A pdb=" N LYS A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 159 Processing helix chain 'A' and resid 171 through 178 Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'B' and resid 4 through 23 Processing helix chain 'B' and resid 90 through 95 Processing helix chain 'B' and resid 96 through 127 Processing helix chain 'B' and resid 146 through 159 Processing helix chain 'B' and resid 171 through 178 Processing helix chain 'B' and resid 321 through 326 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'F' and resid 4 through 23 removed outlier: 3.593A pdb=" N ALA F 12 " --> pdb=" O ILE F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 95 Processing helix chain 'F' and resid 96 through 127 Processing helix chain 'F' and resid 146 through 159 Processing helix chain 'F' and resid 171 through 178 Processing helix chain 'F' and resid 202 through 207 Processing helix chain 'F' and resid 321 through 326 Processing helix chain 'F' and resid 417 through 419 No H-bonds generated for 'chain 'F' and resid 417 through 419' Processing helix chain 'C' and resid 4 through 23 Processing helix chain 'C' and resid 92 through 95 Processing helix chain 'C' and resid 96 through 127 Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 202 through 207 Processing helix chain 'C' and resid 321 through 326 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'D' and resid 4 through 24 removed outlier: 3.718A pdb=" N ALA D 12 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR D 24 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 127 Processing helix chain 'D' and resid 146 through 158 Processing helix chain 'D' and resid 171 through 178 Processing helix chain 'D' and resid 186 through 190 removed outlier: 3.921A pdb=" N ARG D 190 " --> pdb=" O ILE D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 326 Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'E' and resid 4 through 23 Processing helix chain 'E' and resid 96 through 127 Processing helix chain 'E' and resid 146 through 158 Processing helix chain 'E' and resid 171 through 179 removed outlier: 3.559A pdb=" N GLY E 179 " --> pdb=" O TYR E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 326 Processing helix chain 'E' and resid 417 through 419 No H-bonds generated for 'chain 'E' and resid 417 through 419' Processing helix chain 'H' and resid 272 through 287 Processing helix chain 'H' and resid 288 through 300 Processing helix chain 'I' and resid 272 through 287 Processing helix chain 'I' and resid 288 through 300 Processing helix chain 'J' and resid 272 through 287 Processing helix chain 'J' and resid 288 through 300 Processing helix chain 'K' and resid 272 through 287 Processing helix chain 'K' and resid 288 through 300 Processing helix chain 'L' and resid 272 through 287 Processing helix chain 'L' and resid 288 through 300 Processing helix chain 'M' and resid 272 through 287 Processing helix chain 'M' and resid 288 through 300 Processing helix chain 'N' and resid 272 through 287 Processing helix chain 'N' and resid 288 through 300 removed outlier: 3.848A pdb=" N TYR N 292 " --> pdb=" O ASP N 288 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 31 through 33 Processing sheet with id=AA2, first strand: chain 'G' and resid 47 through 51 removed outlier: 4.503A pdb=" N LEU G 73 " --> pdb=" O VAL G 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 83 through 89 removed outlier: 3.670A pdb=" N GLY G 403 " --> pdb=" O LEU G 89 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN G 389 " --> pdb=" O TRP G 410 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 129 through 131 removed outlier: 5.746A pdb=" N LEU G 129 " --> pdb=" O VAL G 423 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR G 168 " --> pdb=" O LEU G 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 136 through 137 removed outlier: 7.536A pdb=" N ALA G 136 " --> pdb=" O TRP G 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 219 through 220 removed outlier: 3.605A pdb=" N ALA G 348 " --> pdb=" O LEU G 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 241 through 243 Processing sheet with id=AA8, first strand: chain 'G' and resid 257 through 260 removed outlier: 4.070A pdb=" N ARG G 299 " --> pdb=" O GLU G 307 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 279 through 281 removed outlier: 4.343A pdb=" N PHE G 280 " --> pdb=" O LEU G 289 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 31 through 33 Processing sheet with id=AB2, first strand: chain 'A' and resid 46 through 50 Processing sheet with id=AB3, first strand: chain 'A' and resid 376 through 383 removed outlier: 3.942A pdb=" N LEU A 388 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN A 389 " --> pdb=" O TRP A 410 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN F 58 " --> pdb=" O ASN A 84 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 129 through 133 Processing sheet with id=AB5, first strand: chain 'A' and resid 219 through 220 removed outlier: 3.760A pdb=" N ALA A 348 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 241 through 243 Processing sheet with id=AB7, first strand: chain 'A' and resid 257 through 260 removed outlier: 6.993A pdb=" N HIS A 305 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N VAL A 300 " --> pdb=" O HIS A 305 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLU A 307 " --> pdb=" O VAL A 298 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 279 through 281 removed outlier: 6.420A pdb=" N GLN A 291 " --> pdb=" O PHE A 280 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 31 through 33 removed outlier: 6.542A pdb=" N LYS B 31 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 46 through 50 Processing sheet with id=AC2, first strand: chain 'B' and resid 58 through 59 removed outlier: 4.604A pdb=" N GLN B 58 " --> pdb=" O ASN C 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 89 removed outlier: 3.516A pdb=" N ILE B 407 " --> pdb=" O ASP B 85 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASN B 389 " --> pdb=" O TRP B 410 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 129 through 133 removed outlier: 6.210A pdb=" N LEU B 129 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU B 425 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE B 131 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 219 through 220 removed outlier: 3.725A pdb=" N ALA B 348 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 241 through 243 Processing sheet with id=AC7, first strand: chain 'B' and resid 257 through 260 removed outlier: 7.309A pdb=" N HIS B 305 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL B 300 " --> pdb=" O HIS B 305 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLU B 307 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU B 289 " --> pdb=" O LYS B 279 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS B 279 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N GLN B 291 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 9.468A pdb=" N GLY B 277 " --> pdb=" O GLN B 291 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ALA B 293 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE B 275 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 31 through 33 removed outlier: 6.271A pdb=" N LYS F 31 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N SER F 363 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N TYR F 33 " --> pdb=" O SER F 363 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN F 389 " --> pdb=" O TRP F 410 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 31 through 33 removed outlier: 6.271A pdb=" N LYS F 31 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N SER F 363 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N TYR F 33 " --> pdb=" O SER F 363 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY F 403 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLN E 58 " --> pdb=" O ASN F 84 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 47 through 51 removed outlier: 4.488A pdb=" N LEU F 73 " --> pdb=" O VAL F 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 129 through 133 removed outlier: 3.500A pdb=" N SER F 133 " --> pdb=" O LEU F 425 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N THR F 166 " --> pdb=" O ASP F 210 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU F 212 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR F 168 " --> pdb=" O LEU F 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 219 through 220 removed outlier: 3.578A pdb=" N ALA F 348 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 241 through 243 Processing sheet with id=AD5, first strand: chain 'F' and resid 257 through 260 removed outlier: 6.950A pdb=" N GLU F 307 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU F 289 " --> pdb=" O LYS F 279 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LYS F 279 " --> pdb=" O LEU F 289 " (cutoff:3.500A) removed outlier: 10.145A pdb=" N GLN F 291 " --> pdb=" O GLY F 277 " (cutoff:3.500A) removed outlier: 9.365A pdb=" N GLY F 277 " --> pdb=" O GLN F 291 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ALA F 293 " --> pdb=" O PHE F 275 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE F 275 " --> pdb=" O ALA F 293 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 31 through 33 removed outlier: 6.471A pdb=" N LYS C 31 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 50 Processing sheet with id=AD8, first strand: chain 'C' and resid 86 through 89 removed outlier: 3.808A pdb=" N GLY C 403 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN C 389 " --> pdb=" O TRP C 410 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 131 through 133 removed outlier: 3.525A pdb=" N SER C 133 " --> pdb=" O LEU C 425 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 219 through 220 removed outlier: 3.623A pdb=" N ALA C 348 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 242 through 243 Processing sheet with id=AE3, first strand: chain 'C' and resid 257 through 260 removed outlier: 6.963A pdb=" N HIS C 305 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL C 300 " --> pdb=" O HIS C 305 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLU C 307 " --> pdb=" O VAL C 298 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 279 through 281 removed outlier: 4.563A pdb=" N PHE C 280 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 31 through 33 removed outlier: 6.593A pdb=" N LYS D 31 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N SER D 363 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR D 33 " --> pdb=" O SER D 363 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY D 403 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 31 through 33 removed outlier: 6.593A pdb=" N LYS D 31 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N SER D 363 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR D 33 " --> pdb=" O SER D 363 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN D 389 " --> pdb=" O TRP D 410 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 47 through 50 Processing sheet with id=AE8, first strand: chain 'D' and resid 58 through 59 removed outlier: 4.425A pdb=" N GLN D 58 " --> pdb=" O ASN E 84 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY E 403 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN E 389 " --> pdb=" O TRP E 410 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 129 through 133 Processing sheet with id=AF1, first strand: chain 'D' and resid 219 through 220 removed outlier: 3.564A pdb=" N ALA D 348 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 241 through 243 Processing sheet with id=AF3, first strand: chain 'D' and resid 257 through 260 removed outlier: 6.781A pdb=" N GLU D 307 " --> pdb=" O VAL D 298 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 279 through 281 removed outlier: 4.894A pdb=" N PHE D 280 " --> pdb=" O LEU D 289 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 31 through 33 removed outlier: 6.275A pdb=" N LYS E 31 " --> pdb=" O ILE E 361 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 47 through 50 Processing sheet with id=AF7, first strand: chain 'E' and resid 129 through 133 removed outlier: 3.545A pdb=" N SER E 133 " --> pdb=" O LEU E 425 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LEU E 212 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR E 168 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 219 through 220 removed outlier: 3.540A pdb=" N ALA E 348 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 241 through 243 Processing sheet with id=AG1, first strand: chain 'E' and resid 257 through 260 removed outlier: 6.896A pdb=" N GLU E 307 " --> pdb=" O VAL E 298 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 279 through 281 removed outlier: 6.468A pdb=" N GLN E 291 " --> pdb=" O PHE E 280 " (cutoff:3.500A) 973 hydrogen bonds defined for protein. 2700 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.05 Time building geometry restraints manager: 6.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4180 1.31 - 1.44: 5879 1.44 - 1.56: 14010 1.56 - 1.69: 1 1.69 - 1.81: 189 Bond restraints: 24259 Sorted by residual: bond pdb=" CA GLN B 395 " pdb=" C GLN B 395 " ideal model delta sigma weight residual 1.521 1.467 0.054 1.21e-02 6.83e+03 1.96e+01 bond pdb=" CA PRO A 25 " pdb=" CB PRO A 25 " ideal model delta sigma weight residual 1.533 1.475 0.058 1.42e-02 4.96e+03 1.68e+01 bond pdb=" C THR A 19 " pdb=" O THR A 19 " ideal model delta sigma weight residual 1.237 1.191 0.046 1.19e-02 7.06e+03 1.47e+01 bond pdb=" CA SER A 21 " pdb=" C SER A 21 " ideal model delta sigma weight residual 1.522 1.470 0.052 1.39e-02 5.18e+03 1.40e+01 bond pdb=" C GLN B 395 " pdb=" O GLN B 395 " ideal model delta sigma weight residual 1.234 1.191 0.043 1.20e-02 6.94e+03 1.28e+01 ... (remaining 24254 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 32395 2.07 - 4.15: 439 4.15 - 6.22: 57 6.22 - 8.30: 13 8.30 - 10.37: 1 Bond angle restraints: 32905 Sorted by residual: angle pdb=" C SER A 44 " pdb=" CA SER A 44 " pdb=" CB SER A 44 " ideal model delta sigma weight residual 116.54 111.02 5.52 1.15e+00 7.56e-01 2.30e+01 angle pdb=" N ALA A 22 " pdb=" CA ALA A 22 " pdb=" C ALA A 22 " ideal model delta sigma weight residual 112.04 118.81 -6.77 1.44e+00 4.82e-01 2.21e+01 angle pdb=" C PRO A 25 " pdb=" CA PRO A 25 " pdb=" CB PRO A 25 " ideal model delta sigma weight residual 111.56 104.19 7.37 1.65e+00 3.67e-01 2.00e+01 angle pdb=" N MET A 164 " pdb=" CA MET A 164 " pdb=" C MET A 164 " ideal model delta sigma weight residual 114.75 109.84 4.91 1.26e+00 6.30e-01 1.52e+01 angle pdb=" N SER B 399 " pdb=" CA SER B 399 " pdb=" C SER B 399 " ideal model delta sigma weight residual 113.18 108.57 4.61 1.21e+00 6.83e-01 1.45e+01 ... (remaining 32900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 13594 17.98 - 35.96: 1011 35.96 - 53.94: 159 53.94 - 71.92: 31 71.92 - 89.90: 14 Dihedral angle restraints: 14809 sinusoidal: 5779 harmonic: 9030 Sorted by residual: dihedral pdb=" CA ARG A 162 " pdb=" C ARG A 162 " pdb=" N ASP A 163 " pdb=" CA ASP A 163 " ideal model delta harmonic sigma weight residual 180.00 -150.41 -29.59 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA ARG B 162 " pdb=" C ARG B 162 " pdb=" N ASP B 163 " pdb=" CA ASP B 163 " ideal model delta harmonic sigma weight residual 180.00 -152.40 -27.60 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA TRP G 145 " pdb=" C TRP G 145 " pdb=" N ASN G 146 " pdb=" CA ASN G 146 " ideal model delta harmonic sigma weight residual 180.00 158.18 21.82 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 14806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3379 0.068 - 0.137: 418 0.137 - 0.205: 10 0.205 - 0.273: 5 0.273 - 0.341: 2 Chirality restraints: 3814 Sorted by residual: chirality pdb=" CA ALA A 22 " pdb=" N ALA A 22 " pdb=" C ALA A 22 " pdb=" CB ALA A 22 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA ILE A 20 " pdb=" N ILE A 20 " pdb=" C ILE A 20 " pdb=" CB ILE A 20 " both_signs ideal model delta sigma weight residual False 2.43 2.15 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA ASN E 161 " pdb=" N ASN E 161 " pdb=" C ASN E 161 " pdb=" CB ASN E 161 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 3811 not shown) Planarity restraints: 4303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 410 " 0.027 2.00e-02 2.50e+03 2.15e-02 1.16e+01 pdb=" CG TRP F 410 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP F 410 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP F 410 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 410 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 410 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 410 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 410 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 410 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP F 410 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER G 55 " 0.045 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO G 56 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO G 56 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 56 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 24 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO D 25 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 25 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 25 " -0.036 5.00e-02 4.00e+02 ... (remaining 4300 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 257 2.63 - 3.19: 21241 3.19 - 3.76: 35498 3.76 - 4.33: 51339 4.33 - 4.90: 87002 Nonbonded interactions: 195337 Sorted by model distance: nonbonded pdb=" O ASN E 161 " pdb=" ND2 ASN E 161 " model vdw 2.058 3.120 nonbonded pdb=" OE1 GLU B 52 " pdb=" NH2 ARG C 109 " model vdw 2.196 3.120 nonbonded pdb=" NH2 ARG C 158 " pdb=" OE1 GLN C 283 " model vdw 2.214 3.120 nonbonded pdb=" NH2 ARG F 213 " pdb=" OE2 GLU E 152 " model vdw 2.222 3.120 nonbonded pdb=" OE2 GLU A 152 " pdb=" NH2 ARG B 213 " model vdw 2.225 3.120 ... (remaining 195332 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 192 or resid 210 through 430)) selection = (chain 'B' and (resid 2 through 192 or resid 210 through 430)) selection = (chain 'C' and (resid 2 through 192 or resid 210 through 430)) selection = chain 'D' selection = chain 'E' selection = (chain 'F' and (resid 2 through 192 or resid 210 through 430)) selection = (chain 'G' and (resid 2 through 192 or resid 210 through 430)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 53.490 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 0.070 24259 Z= 0.246 Angle : 0.623 10.373 32905 Z= 0.345 Chirality : 0.044 0.341 3814 Planarity : 0.004 0.067 4303 Dihedral : 13.195 89.903 8941 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.04 % Allowed : 0.51 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3085 helix: 1.97 (0.18), residues: 747 sheet: -0.61 (0.19), residues: 725 loop : -1.09 (0.14), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP F 410 HIS 0.002 0.001 HIS B 305 PHE 0.026 0.002 PHE E 86 TYR 0.014 0.002 TYR C 175 ARG 0.008 0.001 ARG G 185 Details of bonding type rmsd hydrogen bonds : bond 0.17765 ( 965) hydrogen bonds : angle 7.26171 ( 2700) covalent geometry : bond 0.00523 (24259) covalent geometry : angle 0.62296 (32905) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 368 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. REVERT: K 280 MET cc_start: 0.7667 (mtp) cc_final: 0.7424 (mtt) REVERT: M 280 MET cc_start: 0.8344 (mtm) cc_final: 0.8020 (mtm) outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 1.7386 time to fit residues: 714.0369 Evaluate side-chains 208 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 7.9990 chunk 235 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 243 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 282 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 305 HIS ** G 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN B 7 GLN F 204 GLN ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 369 ASN C 53 GLN D 84 ASN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 ASN E 7 GLN E 41 GLN E 88 GLN E 305 HIS E 364 GLN ** H 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.092166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.070965 restraints weight = 52165.793| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.66 r_work: 0.2952 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24259 Z= 0.130 Angle : 0.559 8.316 32905 Z= 0.295 Chirality : 0.042 0.196 3814 Planarity : 0.004 0.044 4303 Dihedral : 4.448 28.170 3319 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.76 % Allowed : 8.11 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3085 helix: 2.21 (0.18), residues: 764 sheet: -0.34 (0.19), residues: 713 loop : -1.15 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 410 HIS 0.001 0.000 HIS E 305 PHE 0.016 0.001 PHE E 170 TYR 0.019 0.001 TYR E 411 ARG 0.007 0.001 ARG F 185 Details of bonding type rmsd hydrogen bonds : bond 0.04755 ( 965) hydrogen bonds : angle 5.35492 ( 2700) covalent geometry : bond 0.00282 (24259) covalent geometry : angle 0.55894 (32905) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 229 time to evaluate : 2.535 Fit side-chains TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. REVERT: G 117 LEU cc_start: 0.9234 (tp) cc_final: 0.8964 (tm) REVERT: G 208 PHE cc_start: 0.7505 (OUTLIER) cc_final: 0.7242 (t80) REVERT: A 72 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7351 (mm-30) REVERT: A 95 ARG cc_start: 0.8179 (ptt-90) cc_final: 0.7713 (mtt180) REVERT: A 267 MET cc_start: 0.8926 (mmm) cc_final: 0.8423 (mtm) REVERT: B 105 GLN cc_start: 0.9032 (tt0) cc_final: 0.8725 (tt0) REVERT: E 246 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8756 (t0) REVERT: J 279 GLN cc_start: 0.8103 (mt0) cc_final: 0.7880 (mt0) REVERT: K 280 MET cc_start: 0.7259 (mtp) cc_final: 0.6740 (mtt) REVERT: M 280 MET cc_start: 0.7698 (mtm) cc_final: 0.7400 (mtm) outliers start: 45 outliers final: 12 residues processed: 254 average time/residue: 1.6946 time to fit residues: 483.2063 Evaluate side-chains 220 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 206 time to evaluate : 2.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 208 PHE Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 301 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 14 optimal weight: 10.0000 chunk 301 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 291 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 213 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 281 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 305 HIS ** G 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A 341 ASN A 364 GLN F 53 GLN F 204 GLN F 283 GLN F 305 HIS ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN D 114 ASN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 ASN E 41 GLN E 364 GLN ** H 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.088535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.067001 restraints weight = 52174.745| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.62 r_work: 0.2869 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 24259 Z= 0.260 Angle : 0.605 9.142 32905 Z= 0.316 Chirality : 0.043 0.219 3814 Planarity : 0.004 0.055 4303 Dihedral : 4.719 30.047 3319 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.35 % Allowed : 9.28 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3085 helix: 2.22 (0.18), residues: 774 sheet: -0.49 (0.18), residues: 715 loop : -1.07 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 410 HIS 0.005 0.001 HIS C 305 PHE 0.023 0.002 PHE A 86 TYR 0.017 0.002 TYR E 411 ARG 0.007 0.001 ARG F 185 Details of bonding type rmsd hydrogen bonds : bond 0.04866 ( 965) hydrogen bonds : angle 5.05489 ( 2700) covalent geometry : bond 0.00588 (24259) covalent geometry : angle 0.60456 (32905) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 202 time to evaluate : 2.948 Fit side-chains TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 59 GLU cc_start: 0.3320 (mm-30) cc_final: 0.2510 (mm-30) REVERT: G 81 GLU cc_start: 0.5196 (tm-30) cc_final: 0.3815 (tt0) REVERT: G 164 MET cc_start: 0.7296 (mmt) cc_final: 0.6961 (mmm) REVERT: G 208 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.7318 (t80) REVERT: A 95 ARG cc_start: 0.8303 (ptt-90) cc_final: 0.7805 (mtt180) REVERT: A 267 MET cc_start: 0.9035 (mmm) cc_final: 0.8614 (mtm) REVERT: A 364 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8349 (pt0) REVERT: B 105 GLN cc_start: 0.9124 (tt0) cc_final: 0.8852 (tt0) REVERT: F 40 MET cc_start: 0.8903 (mmm) cc_final: 0.7752 (tmt) REVERT: F 162 ARG cc_start: 0.8313 (mtm-85) cc_final: 0.7680 (mtm-85) REVERT: D 40 MET cc_start: 0.8407 (tpp) cc_final: 0.8202 (tpp) REVERT: E 54 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8466 (mt-10) REVERT: E 62 ASP cc_start: 0.8663 (t70) cc_final: 0.8463 (t0) REVERT: J 279 GLN cc_start: 0.8075 (mt0) cc_final: 0.7849 (mt0) REVERT: K 280 MET cc_start: 0.7300 (mtp) cc_final: 0.6804 (mtt) REVERT: M 280 MET cc_start: 0.7646 (mtm) cc_final: 0.7337 (mtm) outliers start: 60 outliers final: 19 residues processed: 240 average time/residue: 1.8682 time to fit residues: 504.0102 Evaluate side-chains 214 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 208 PHE Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 364 GLN Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain H residue 279 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 212 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 269 optimal weight: 20.0000 chunk 245 optimal weight: 2.9990 chunk 170 optimal weight: 0.0870 chunk 263 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 278 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN A 364 GLN F 204 GLN F 283 GLN ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN C 53 GLN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.090358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.068966 restraints weight = 52579.035| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.65 r_work: 0.2905 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24259 Z= 0.127 Angle : 0.526 9.182 32905 Z= 0.274 Chirality : 0.041 0.191 3814 Planarity : 0.004 0.047 4303 Dihedral : 4.477 27.916 3319 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.08 % Allowed : 10.97 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3085 helix: 2.31 (0.18), residues: 775 sheet: -0.43 (0.19), residues: 703 loop : -1.08 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 145 HIS 0.001 0.000 HIS C 305 PHE 0.013 0.001 PHE E 170 TYR 0.011 0.001 TYR D 168 ARG 0.008 0.000 ARG F 203 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 965) hydrogen bonds : angle 4.83374 ( 2700) covalent geometry : bond 0.00279 (24259) covalent geometry : angle 0.52550 (32905) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 210 time to evaluate : 2.789 Fit side-chains TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 59 GLU cc_start: 0.2933 (OUTLIER) cc_final: 0.2146 (mm-30) REVERT: G 81 GLU cc_start: 0.4927 (tm-30) cc_final: 0.3553 (tm-30) REVERT: G 83 ASP cc_start: 0.8648 (t0) cc_final: 0.8372 (t0) REVERT: G 114 ASN cc_start: 0.8855 (t0) cc_final: 0.8384 (t0) REVERT: G 117 LEU cc_start: 0.9208 (tp) cc_final: 0.8919 (tm) REVERT: G 208 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7377 (t80) REVERT: A 95 ARG cc_start: 0.8317 (ptt-90) cc_final: 0.7866 (mtt180) REVERT: A 267 MET cc_start: 0.9021 (mmm) cc_final: 0.8582 (mtm) REVERT: B 105 GLN cc_start: 0.9106 (tt0) cc_final: 0.8843 (tt0) REVERT: F 40 MET cc_start: 0.8906 (mmm) cc_final: 0.7833 (tmt) REVERT: F 122 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8440 (ttm) REVERT: D 40 MET cc_start: 0.8401 (tpp) cc_final: 0.8159 (tpp) REVERT: E 62 ASP cc_start: 0.8472 (t70) cc_final: 0.8203 (t0) REVERT: J 279 GLN cc_start: 0.8101 (mt0) cc_final: 0.7858 (mt0) REVERT: K 280 MET cc_start: 0.7390 (mtp) cc_final: 0.6999 (mtp) REVERT: M 280 MET cc_start: 0.7597 (mtm) cc_final: 0.7294 (mtm) outliers start: 53 outliers final: 23 residues processed: 240 average time/residue: 1.8342 time to fit residues: 495.5777 Evaluate side-chains 220 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 208 PHE Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain H residue 279 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 239 optimal weight: 0.6980 chunk 227 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 310 optimal weight: 8.9990 chunk 305 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 41 GLN ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN C 53 GLN ** D 351 ASN ** 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 = 0.3398 r_free = 0.3398 target = 0.088902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.067416 restraints weight = 52645.412| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.65 r_work: 0.2873 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24259 Z= 0.193 Angle : 0.557 9.287 32905 Z= 0.289 Chirality : 0.041 0.194 3814 Planarity : 0.004 0.053 4303 Dihedral : 4.574 28.102 3319 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.19 % Allowed : 11.67 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3085 helix: 2.26 (0.18), residues: 791 sheet: -0.37 (0.19), residues: 687 loop : -1.10 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 145 HIS 0.003 0.000 HIS C 305 PHE 0.017 0.001 PHE D 86 TYR 0.011 0.001 TYR F 33 ARG 0.008 0.000 ARG F 203 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 965) hydrogen bonds : angle 4.78225 ( 2700) covalent geometry : bond 0.00436 (24259) covalent geometry : angle 0.55665 (32905) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 200 time to evaluate : 3.387 Fit side-chains TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 59 GLU cc_start: 0.2718 (mm-30) cc_final: 0.1884 (mm-30) REVERT: G 81 GLU cc_start: 0.5015 (tm-30) cc_final: 0.3377 (tp30) REVERT: G 83 ASP cc_start: 0.8629 (t0) cc_final: 0.8342 (t0) REVERT: G 114 ASN cc_start: 0.8791 (t0) cc_final: 0.8286 (t0) REVERT: G 117 LEU cc_start: 0.9219 (tp) cc_final: 0.8900 (tm) REVERT: A 95 ARG cc_start: 0.8339 (ptt-90) cc_final: 0.7858 (mtt180) REVERT: A 267 MET cc_start: 0.9099 (mmm) cc_final: 0.8716 (mtm) REVERT: B 105 GLN cc_start: 0.9103 (tt0) cc_final: 0.8829 (tt0) REVERT: F 40 MET cc_start: 0.8910 (mmm) cc_final: 0.7838 (tmt) REVERT: F 52 GLU cc_start: 0.7665 (pp20) cc_final: 0.7351 (pp20) REVERT: F 59 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7310 (mm-30) REVERT: F 70 LEU cc_start: 0.8737 (mm) cc_final: 0.8428 (mt) REVERT: F 83 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8459 (t0) REVERT: D 40 MET cc_start: 0.8346 (tpp) cc_final: 0.8063 (tpp) REVERT: J 279 GLN cc_start: 0.8103 (mt0) cc_final: 0.7839 (mt0) REVERT: K 280 MET cc_start: 0.7397 (mtp) cc_final: 0.7018 (mtp) REVERT: M 280 MET cc_start: 0.7616 (mtm) cc_final: 0.7296 (mtm) outliers start: 56 outliers final: 30 residues processed: 238 average time/residue: 1.7526 time to fit residues: 470.3192 Evaluate side-chains 222 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain H residue 279 GLN Chi-restraints excluded: chain H residue 280 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 177 optimal weight: 0.9980 chunk 157 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 223 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 260 optimal weight: 5.9990 chunk 205 optimal weight: 0.5980 chunk 263 optimal weight: 0.0970 chunk 66 optimal weight: 3.9990 overall best weight: 2.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN F 84 ASN F 204 GLN ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN C 53 GLN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 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 = 0.3407 r_free = 0.3407 target = 0.089455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.067955 restraints weight = 52156.108| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.65 r_work: 0.2886 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24259 Z= 0.162 Angle : 0.537 9.309 32905 Z= 0.278 Chirality : 0.041 0.200 3814 Planarity : 0.004 0.046 4303 Dihedral : 4.496 26.827 3319 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.08 % Allowed : 12.57 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3085 helix: 2.27 (0.18), residues: 791 sheet: -0.36 (0.19), residues: 706 loop : -1.10 (0.14), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 145 HIS 0.002 0.000 HIS C 305 PHE 0.013 0.001 PHE D 86 TYR 0.013 0.001 TYR D 168 ARG 0.010 0.000 ARG F 203 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 965) hydrogen bonds : angle 4.70066 ( 2700) covalent geometry : bond 0.00364 (24259) covalent geometry : angle 0.53683 (32905) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 204 time to evaluate : 2.575 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 59 GLU cc_start: 0.2489 (mm-30) cc_final: 0.1655 (mm-30) REVERT: G 81 GLU cc_start: 0.4902 (OUTLIER) cc_final: 0.3429 (tm-30) REVERT: G 83 ASP cc_start: 0.8709 (t0) cc_final: 0.8469 (t0) REVERT: G 114 ASN cc_start: 0.8797 (t0) cc_final: 0.8271 (t0) REVERT: G 117 LEU cc_start: 0.9201 (tp) cc_final: 0.8894 (tm) REVERT: A 18 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8675 (mm-30) REVERT: A 95 ARG cc_start: 0.8326 (ptt-90) cc_final: 0.7861 (mtt180) REVERT: A 267 MET cc_start: 0.9092 (mmm) cc_final: 0.8679 (mtm) REVERT: B 41 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7974 (tm130) REVERT: B 105 GLN cc_start: 0.9092 (tt0) cc_final: 0.8798 (tt0) REVERT: F 40 MET cc_start: 0.8886 (mmm) cc_final: 0.7804 (tmt) REVERT: F 52 GLU cc_start: 0.7625 (pp20) cc_final: 0.7313 (pp20) REVERT: F 70 LEU cc_start: 0.8769 (mm) cc_final: 0.8448 (mt) REVERT: D 40 MET cc_start: 0.8371 (tpp) cc_final: 0.8072 (tpp) REVERT: E 62 ASP cc_start: 0.8476 (t70) cc_final: 0.8194 (t0) REVERT: J 279 GLN cc_start: 0.8101 (mt0) cc_final: 0.7855 (mt0) REVERT: K 280 MET cc_start: 0.7431 (mtp) cc_final: 0.7036 (mtp) REVERT: M 280 MET cc_start: 0.7591 (mtm) cc_final: 0.7259 (mtm) outliers start: 53 outliers final: 31 residues processed: 242 average time/residue: 1.5730 time to fit residues: 431.7624 Evaluate side-chains 228 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain H residue 279 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 122 optimal weight: 4.9990 chunk 270 optimal weight: 0.9980 chunk 199 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 230 optimal weight: 6.9990 chunk 288 optimal weight: 7.9990 chunk 282 optimal weight: 5.9990 chunk 222 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN C 53 GLN D 78 ASN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 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 = 0.3375 r_free = 0.3375 target = 0.087662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.066030 restraints weight = 52749.069| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.65 r_work: 0.2849 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 24259 Z= 0.272 Angle : 0.604 9.657 32905 Z= 0.312 Chirality : 0.043 0.210 3814 Planarity : 0.004 0.050 4303 Dihedral : 4.735 27.196 3319 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.12 % Allowed : 12.77 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3085 helix: 2.22 (0.18), residues: 785 sheet: -0.41 (0.18), residues: 736 loop : -1.14 (0.14), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 145 HIS 0.005 0.001 HIS C 305 PHE 0.020 0.002 PHE D 86 TYR 0.012 0.002 TYR A 180 ARG 0.010 0.001 ARG F 203 Details of bonding type rmsd hydrogen bonds : bond 0.04638 ( 965) hydrogen bonds : angle 4.80005 ( 2700) covalent geometry : bond 0.00620 (24259) covalent geometry : angle 0.60357 (32905) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 191 time to evaluate : 2.759 Fit side-chains TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 59 GLU cc_start: 0.2934 (mm-30) cc_final: 0.2045 (mm-30) REVERT: G 81 GLU cc_start: 0.5095 (OUTLIER) cc_final: 0.3569 (tm-30) REVERT: G 83 ASP cc_start: 0.8687 (t0) cc_final: 0.8464 (t0) REVERT: G 114 ASN cc_start: 0.8852 (t0) cc_final: 0.8133 (t0) REVERT: A 95 ARG cc_start: 0.8322 (ptt-90) cc_final: 0.7806 (mtt180) REVERT: A 185 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8072 (mtt-85) REVERT: A 267 MET cc_start: 0.9122 (mmm) cc_final: 0.8729 (mtm) REVERT: B 105 GLN cc_start: 0.9134 (tt0) cc_final: 0.8857 (tt0) REVERT: F 40 MET cc_start: 0.8878 (mmm) cc_final: 0.7738 (tmt) REVERT: F 52 GLU cc_start: 0.7707 (pp20) cc_final: 0.7373 (pp20) REVERT: F 70 LEU cc_start: 0.8792 (mm) cc_final: 0.8461 (mt) REVERT: D 40 MET cc_start: 0.8351 (tpp) cc_final: 0.8053 (tpp) REVERT: E 164 MET cc_start: 0.7522 (mpp) cc_final: 0.7287 (tmm) REVERT: J 279 GLN cc_start: 0.8091 (mt0) cc_final: 0.7875 (mt0) REVERT: K 280 MET cc_start: 0.7426 (mtp) cc_final: 0.7042 (mtp) REVERT: M 280 MET cc_start: 0.7537 (mtm) cc_final: 0.7207 (mtm) outliers start: 54 outliers final: 33 residues processed: 232 average time/residue: 1.5973 time to fit residues: 418.5907 Evaluate side-chains 218 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain H residue 279 GLN Chi-restraints excluded: chain H residue 280 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 222 optimal weight: 2.9990 chunk 249 optimal weight: 7.9990 chunk 187 optimal weight: 0.0970 chunk 173 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 chunk 208 optimal weight: 10.0000 chunk 240 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 263 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN B 41 GLN B 389 ASN ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN C 53 GLN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.089007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.067577 restraints weight = 52343.614| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.63 r_work: 0.2880 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24259 Z= 0.168 Angle : 0.551 9.269 32905 Z= 0.285 Chirality : 0.041 0.201 3814 Planarity : 0.004 0.051 4303 Dihedral : 4.597 27.092 3319 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.84 % Allowed : 13.47 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3085 helix: 2.19 (0.18), residues: 797 sheet: -0.37 (0.18), residues: 730 loop : -1.18 (0.14), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 145 HIS 0.001 0.000 HIS C 305 PHE 0.015 0.001 PHE G 156 TYR 0.010 0.001 TYR C 327 ARG 0.012 0.000 ARG F 203 Details of bonding type rmsd hydrogen bonds : bond 0.04205 ( 965) hydrogen bonds : angle 4.67921 ( 2700) covalent geometry : bond 0.00376 (24259) covalent geometry : angle 0.55094 (32905) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 198 time to evaluate : 2.648 Fit side-chains TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 59 GLU cc_start: 0.2932 (mm-30) cc_final: 0.2035 (mm-30) REVERT: G 81 GLU cc_start: 0.5011 (OUTLIER) cc_final: 0.3388 (tm-30) REVERT: G 83 ASP cc_start: 0.8698 (t0) cc_final: 0.8458 (t0) REVERT: G 114 ASN cc_start: 0.8853 (t0) cc_final: 0.8098 (t0) REVERT: G 117 LEU cc_start: 0.9219 (tp) cc_final: 0.8906 (tm) REVERT: G 164 MET cc_start: 0.7130 (mmt) cc_final: 0.6703 (mmm) REVERT: A 95 ARG cc_start: 0.8289 (ptt-90) cc_final: 0.7800 (mtt180) REVERT: A 185 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8066 (mtt-85) REVERT: A 267 MET cc_start: 0.9101 (mmm) cc_final: 0.8704 (mtm) REVERT: B 41 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8022 (tm-30) REVERT: B 105 GLN cc_start: 0.9100 (tt0) cc_final: 0.8810 (tt0) REVERT: F 40 MET cc_start: 0.8888 (mmm) cc_final: 0.7784 (tmt) REVERT: F 41 GLN cc_start: 0.9016 (mt0) cc_final: 0.8799 (tt0) REVERT: F 52 GLU cc_start: 0.7638 (pp20) cc_final: 0.7330 (pp20) REVERT: F 70 LEU cc_start: 0.8760 (mm) cc_final: 0.8450 (mt) REVERT: F 162 ARG cc_start: 0.8341 (mtm-85) cc_final: 0.7952 (mtm-85) REVERT: D 40 MET cc_start: 0.8366 (tpp) cc_final: 0.8073 (tpp) REVERT: E 62 ASP cc_start: 0.8547 (t70) cc_final: 0.8264 (t0) REVERT: J 279 GLN cc_start: 0.8110 (mt0) cc_final: 0.7853 (mt0) REVERT: K 280 MET cc_start: 0.7439 (mtp) cc_final: 0.7062 (mtp) REVERT: M 280 MET cc_start: 0.7591 (mtm) cc_final: 0.7263 (mtm) outliers start: 47 outliers final: 31 residues processed: 234 average time/residue: 1.6014 time to fit residues: 430.9234 Evaluate side-chains 218 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain H residue 279 GLN Chi-restraints excluded: chain H residue 280 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 217 optimal weight: 3.9990 chunk 308 optimal weight: 0.7980 chunk 207 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 218 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 28 optimal weight: 0.2980 chunk 188 optimal weight: 2.9990 chunk 292 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN C 53 GLN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 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 = 0.3420 r_free = 0.3420 target = 0.090259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.068934 restraints weight = 52018.556| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.62 r_work: 0.2911 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 24259 Z= 0.112 Angle : 0.537 8.960 32905 Z= 0.277 Chirality : 0.041 0.195 3814 Planarity : 0.003 0.054 4303 Dihedral : 4.435 26.856 3319 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.53 % Allowed : 14.06 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3085 helix: 2.20 (0.18), residues: 797 sheet: -0.26 (0.19), residues: 716 loop : -1.15 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 354 HIS 0.001 0.000 HIS A 305 PHE 0.012 0.001 PHE E 170 TYR 0.009 0.001 TYR C 168 ARG 0.013 0.000 ARG F 203 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 965) hydrogen bonds : angle 4.59205 ( 2700) covalent geometry : bond 0.00247 (24259) covalent geometry : angle 0.53706 (32905) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 2.545 Fit side-chains TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 59 GLU cc_start: 0.2550 (mm-30) cc_final: 0.1683 (mm-30) REVERT: G 81 GLU cc_start: 0.4849 (OUTLIER) cc_final: 0.3214 (tp30) REVERT: G 83 ASP cc_start: 0.8650 (t0) cc_final: 0.8398 (t0) REVERT: G 114 ASN cc_start: 0.8845 (t0) cc_final: 0.8093 (t0) REVERT: G 117 LEU cc_start: 0.9194 (tp) cc_final: 0.8906 (tm) REVERT: G 164 MET cc_start: 0.7188 (mmt) cc_final: 0.6766 (mmm) REVERT: G 370 HIS cc_start: 0.8776 (m-70) cc_final: 0.8475 (m-70) REVERT: A 72 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7805 (mm-30) REVERT: A 95 ARG cc_start: 0.8257 (ptt-90) cc_final: 0.7821 (mtt180) REVERT: A 185 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.8035 (mtt-85) REVERT: A 267 MET cc_start: 0.9057 (mmm) cc_final: 0.8675 (mtm) REVERT: B 105 GLN cc_start: 0.9109 (tt0) cc_final: 0.8832 (tt0) REVERT: B 356 ASP cc_start: 0.7699 (t0) cc_final: 0.7483 (m-30) REVERT: F 40 MET cc_start: 0.8946 (mmm) cc_final: 0.7825 (tmt) REVERT: F 41 GLN cc_start: 0.8984 (mt0) cc_final: 0.8758 (tt0) REVERT: F 52 GLU cc_start: 0.7623 (pp20) cc_final: 0.7299 (pp20) REVERT: F 70 LEU cc_start: 0.8754 (mm) cc_final: 0.8446 (mt) REVERT: D 85 ASP cc_start: 0.8498 (t0) cc_final: 0.8223 (p0) REVERT: E 62 ASP cc_start: 0.8494 (t70) cc_final: 0.8193 (t0) REVERT: E 164 MET cc_start: 0.7500 (mpp) cc_final: 0.7194 (tmm) REVERT: E 356 ASP cc_start: 0.8703 (t0) cc_final: 0.8369 (t0) REVERT: J 279 GLN cc_start: 0.8116 (mt0) cc_final: 0.7860 (mt0) REVERT: K 280 MET cc_start: 0.7311 (mtp) cc_final: 0.6944 (mtp) REVERT: M 280 MET cc_start: 0.7501 (mtm) cc_final: 0.7162 (mtm) outliers start: 39 outliers final: 28 residues processed: 236 average time/residue: 1.7583 time to fit residues: 470.3319 Evaluate side-chains 225 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 61 TRP Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain H residue 279 GLN Chi-restraints excluded: chain H residue 280 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 169 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 236 optimal weight: 5.9990 chunk 281 optimal weight: 0.9980 chunk 293 optimal weight: 20.0000 chunk 232 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN C 53 GLN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 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 = 0.3375 r_free = 0.3375 target = 0.087616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.066062 restraints weight = 52812.014| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.64 r_work: 0.2850 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 24259 Z= 0.277 Angle : 0.626 9.417 32905 Z= 0.323 Chirality : 0.043 0.208 3814 Planarity : 0.004 0.056 4303 Dihedral : 4.736 28.245 3319 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.68 % Allowed : 14.26 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3085 helix: 2.13 (0.18), residues: 801 sheet: -0.33 (0.18), residues: 724 loop : -1.20 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 145 HIS 0.004 0.001 HIS C 305 PHE 0.020 0.002 PHE D 86 TYR 0.017 0.002 TYR D 168 ARG 0.012 0.001 ARG F 203 Details of bonding type rmsd hydrogen bonds : bond 0.04590 ( 965) hydrogen bonds : angle 4.74140 ( 2700) covalent geometry : bond 0.00631 (24259) covalent geometry : angle 0.62620 (32905) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 3.001 Fit side-chains TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 81 GLU cc_start: 0.5140 (OUTLIER) cc_final: 0.3246 (tp30) REVERT: G 83 ASP cc_start: 0.8694 (t0) cc_final: 0.8426 (t0) REVERT: G 114 ASN cc_start: 0.8886 (t0) cc_final: 0.8126 (t0) REVERT: G 117 LEU cc_start: 0.9227 (tp) cc_final: 0.8914 (tm) REVERT: G 164 MET cc_start: 0.7220 (mmt) cc_final: 0.6794 (mmm) REVERT: A 72 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7987 (mm-30) REVERT: A 267 MET cc_start: 0.9120 (mmm) cc_final: 0.8770 (mtm) REVERT: B 105 GLN cc_start: 0.9134 (tt0) cc_final: 0.8846 (tt0) REVERT: B 299 ARG cc_start: 0.8903 (ttp80) cc_final: 0.7946 (mtt180) REVERT: F 40 MET cc_start: 0.8926 (mmm) cc_final: 0.7741 (tmt) REVERT: F 41 GLN cc_start: 0.9030 (mt0) cc_final: 0.8787 (tt0) REVERT: F 52 GLU cc_start: 0.7665 (pp20) cc_final: 0.7309 (pp20) REVERT: F 70 LEU cc_start: 0.8771 (mm) cc_final: 0.8467 (mt) REVERT: E 338 MET cc_start: 0.8914 (ptt) cc_final: 0.8687 (ptt) REVERT: J 279 GLN cc_start: 0.8133 (mt0) cc_final: 0.7912 (mt0) REVERT: K 280 MET cc_start: 0.7433 (mtp) cc_final: 0.7065 (mtp) REVERT: M 280 MET cc_start: 0.7572 (mtm) cc_final: 0.7243 (mtm) outliers start: 43 outliers final: 32 residues processed: 214 average time/residue: 1.7083 time to fit residues: 410.7799 Evaluate side-chains 207 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain H residue 279 GLN Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain I residue 290 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 255 optimal weight: 0.7980 chunk 185 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 263 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 270 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 154 optimal weight: 7.9990 chunk 253 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 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 = 0.3397 r_free = 0.3397 target = 0.088845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.067445 restraints weight = 52208.381| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.61 r_work: 0.2870 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24259 Z= 0.163 Angle : 0.577 9.308 32905 Z= 0.298 Chirality : 0.041 0.190 3814 Planarity : 0.004 0.058 4303 Dihedral : 4.640 27.486 3319 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.37 % Allowed : 14.69 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.14), residues: 3085 helix: 2.11 (0.18), residues: 804 sheet: -0.30 (0.18), residues: 725 loop : -1.23 (0.14), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 145 HIS 0.002 0.000 HIS C 305 PHE 0.013 0.001 PHE D 86 TYR 0.009 0.001 TYR B 100 ARG 0.013 0.000 ARG F 203 Details of bonding type rmsd hydrogen bonds : bond 0.04256 ( 965) hydrogen bonds : angle 4.68969 ( 2700) covalent geometry : bond 0.00365 (24259) covalent geometry : angle 0.57660 (32905) =============================================================================== Job complete usr+sys time: 18953.82 seconds wall clock time: 331 minutes 52.68 seconds (19912.68 seconds total)