Starting phenix.real_space_refine on Sun Aug 24 21:20:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i1v_35123/08_2025/8i1v_35123.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i1v_35123/08_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_35123/08_2025/8i1v_35123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i1v_35123/08_2025/8i1v_35123.map" model { file = "/net/cci-nas-00/data/ceres_data/8i1v_35123/08_2025/8i1v_35123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i1v_35123/08_2025/8i1v_35123.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.37, per 1000 atoms: 0.22 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: 1.94 Conformation dependent library (CDL) restraints added in 936.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.09 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: 4.33 Time building geometry restraints manager: 2.51 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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 20.890 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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:7.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.800 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.008 0.001 ARG G 185 TYR 0.014 0.002 TYR C 175 PHE 0.026 0.002 PHE E 86 TRP 0.058 0.002 TRP F 410 HIS 0.002 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00523 (24259) covalent geometry : angle 0.62296 (32905) hydrogen bonds : bond 0.17765 ( 965) hydrogen bonds : angle 7.26171 ( 2700) *********************** 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 : 0.629 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: 0.7251 time to fit residues: 297.9710 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 : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.090961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.069467 restraints weight = 52452.749| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.67 r_work: 0.2921 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1596 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= 0.163 Angle : 0.573 8.612 32905 Z= 0.302 Chirality : 0.042 0.204 3814 Planarity : 0.004 0.046 4303 Dihedral : 4.541 28.932 3319 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.04 % Allowed : 7.99 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.14), residues: 3085 helix: 2.23 (0.18), residues: 762 sheet: -0.35 (0.19), residues: 719 loop : -1.13 (0.14), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 185 TYR 0.021 0.001 TYR E 411 PHE 0.018 0.002 PHE E 86 TRP 0.029 0.001 TRP F 410 HIS 0.005 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00361 (24259) covalent geometry : angle 0.57294 (32905) hydrogen bonds : bond 0.04737 ( 965) hydrogen bonds : angle 5.30440 ( 2700) *********************** 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 273 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 221 time to evaluate : 0.658 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 208 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.7302 (t80) REVERT: A 72 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7460 (mm-30) REVERT: A 95 ARG cc_start: 0.8191 (ptt-90) cc_final: 0.7718 (mtt180) REVERT: A 267 MET cc_start: 0.8956 (mmm) cc_final: 0.8484 (mtm) REVERT: B 105 GLN cc_start: 0.9092 (tt0) cc_final: 0.8829 (tt0) REVERT: F 162 ARG cc_start: 0.8223 (mtm-85) cc_final: 0.7803 (mtm-85) REVERT: C 323 GLU cc_start: 0.8682 (mp0) cc_final: 0.8452 (pm20) REVERT: E 54 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8487 (mt-10) REVERT: J 279 GLN cc_start: 0.8117 (mt0) cc_final: 0.7892 (mt0) REVERT: K 280 MET cc_start: 0.7244 (mtp) cc_final: 0.6823 (mtp) REVERT: M 280 MET cc_start: 0.7587 (mtm) cc_final: 0.7298 (mtm) outliers start: 52 outliers final: 15 residues processed: 251 average time/residue: 0.7096 time to fit residues: 199.7763 Evaluate side-chains 217 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 ILE 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 8 ILE 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 54 GLU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain H residue 279 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 251 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 210 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 275 optimal weight: 0.9990 chunk 196 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 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** E 41 GLN E 364 GLN ** H 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.088943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.067376 restraints weight = 52595.930| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.64 r_work: 0.2876 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 24259 Z= 0.218 Angle : 0.575 8.966 32905 Z= 0.301 Chirality : 0.042 0.217 3814 Planarity : 0.004 0.052 4303 Dihedral : 4.656 29.939 3319 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.35 % Allowed : 9.40 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.14), residues: 3085 helix: 2.22 (0.18), residues: 774 sheet: -0.50 (0.18), residues: 722 loop : -1.06 (0.14), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 185 TYR 0.016 0.001 TYR E 411 PHE 0.021 0.002 PHE D 86 TRP 0.024 0.001 TRP F 410 HIS 0.004 0.001 HIS C 305 Details of bonding type rmsd covalent geometry : bond 0.00492 (24259) covalent geometry : angle 0.57458 (32905) hydrogen bonds : bond 0.04728 ( 965) hydrogen bonds : angle 4.99427 ( 2700) *********************** 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 264 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 204 time to evaluate : 0.914 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 59 GLU cc_start: 0.3225 (mm-30) cc_final: 0.2533 (mm-30) REVERT: G 81 GLU cc_start: 0.4995 (tm-30) cc_final: 0.3784 (tm-30) REVERT: A 95 ARG cc_start: 0.8281 (ptt-90) cc_final: 0.7799 (mtt180) REVERT: A 267 MET cc_start: 0.9034 (mmm) cc_final: 0.8584 (mtm) REVERT: A 364 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8161 (pt0) REVERT: B 105 GLN cc_start: 0.9113 (tt0) cc_final: 0.8831 (tt0) REVERT: B 356 ASP cc_start: 0.7862 (t0) cc_final: 0.7637 (t0) REVERT: F 40 MET cc_start: 0.8922 (mmm) cc_final: 0.7760 (tmt) REVERT: F 162 ARG cc_start: 0.8351 (mtm-85) cc_final: 0.7934 (mtm-85) REVERT: D 40 MET cc_start: 0.8354 (tpp) cc_final: 0.8119 (tpp) REVERT: E 54 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8459 (mt-10) REVERT: J 279 GLN cc_start: 0.8076 (mt0) cc_final: 0.7855 (mt0) REVERT: K 280 MET cc_start: 0.7330 (mtp) cc_final: 0.6938 (mtp) REVERT: M 280 MET cc_start: 0.7588 (mtm) cc_final: 0.7277 (mtm) outliers start: 60 outliers final: 21 residues processed: 242 average time/residue: 0.7069 time to fit residues: 192.3786 Evaluate side-chains 216 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 141 THR 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 A residue 185 ARG 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 180 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 203 optimal weight: 7.9990 chunk 257 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 153 optimal weight: 0.4980 chunk 50 optimal weight: 6.9990 chunk 217 optimal weight: 7.9990 chunk 287 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- 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 84 ASN F 41 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.089073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.067565 restraints weight = 52175.190| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.64 r_work: 0.2873 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24259 Z= 0.191 Angle : 0.559 10.648 32905 Z= 0.290 Chirality : 0.042 0.207 3814 Planarity : 0.004 0.049 4303 Dihedral : 4.620 28.821 3319 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.12 % Allowed : 11.16 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.14), residues: 3085 helix: 2.22 (0.18), residues: 791 sheet: -0.46 (0.18), residues: 694 loop : -1.10 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 203 TYR 0.011 0.001 TYR D 168 PHE 0.016 0.001 PHE D 86 TRP 0.014 0.001 TRP G 145 HIS 0.003 0.001 HIS C 305 Details of bonding type rmsd covalent geometry : bond 0.00433 (24259) covalent geometry : angle 0.55879 (32905) hydrogen bonds : bond 0.04437 ( 965) hydrogen bonds : angle 4.86306 ( 2700) *********************** 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 258 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 204 time to evaluate : 1.033 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: 0.3244 (OUTLIER) cc_final: 0.2722 (tp30) REVERT: G 81 GLU cc_start: 0.5177 (tm-30) cc_final: 0.4019 (tt0) REVERT: G 83 ASP cc_start: 0.8643 (t0) cc_final: 0.8365 (t0) REVERT: G 114 ASN cc_start: 0.8896 (t0) cc_final: 0.8426 (t0) REVERT: G 117 LEU cc_start: 0.9225 (tp) cc_final: 0.8918 (tm) REVERT: G 208 PHE cc_start: 0.7719 (OUTLIER) cc_final: 0.7376 (t80) REVERT: A 95 ARG cc_start: 0.8292 (ptt-90) cc_final: 0.7813 (mtt180) REVERT: A 267 MET cc_start: 0.9071 (mmm) cc_final: 0.8655 (mtm) REVERT: B 105 GLN cc_start: 0.9111 (tt0) cc_final: 0.8850 (tt0) REVERT: F 40 MET cc_start: 0.8921 (mmm) cc_final: 0.7823 (tmt) REVERT: F 162 ARG cc_start: 0.8368 (mtm-85) cc_final: 0.7993 (mtm-85) REVERT: D 40 MET cc_start: 0.8402 (tpp) cc_final: 0.8153 (tpp) REVERT: J 279 GLN cc_start: 0.8105 (mt0) cc_final: 0.7892 (mt0) REVERT: K 280 MET cc_start: 0.7405 (mtp) cc_final: 0.7035 (mtp) REVERT: M 280 MET cc_start: 0.7616 (mtm) cc_final: 0.7299 (mtm) outliers start: 54 outliers final: 29 residues processed: 239 average time/residue: 0.8553 time to fit residues: 229.4156 Evaluate side-chains 225 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 208 PHE Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 297 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 79 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 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 H residue 279 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 244 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 278 optimal weight: 8.9990 chunk 265 optimal weight: 0.9980 chunk 214 optimal weight: 0.7980 chunk 17 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 297 optimal weight: 1.9990 chunk 205 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.090467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.069033 restraints weight = 52177.900| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.66 r_work: 0.2914 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24259 Z= 0.124 Angle : 0.519 9.066 32905 Z= 0.270 Chirality : 0.041 0.183 3814 Planarity : 0.003 0.048 4303 Dihedral : 4.405 27.710 3319 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.27 % Allowed : 11.71 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.14), residues: 3085 helix: 2.27 (0.18), residues: 791 sheet: -0.33 (0.19), residues: 686 loop : -1.09 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 203 TYR 0.009 0.001 TYR C 168 PHE 0.013 0.001 PHE E 170 TRP 0.013 0.001 TRP G 145 HIS 0.001 0.000 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00274 (24259) covalent geometry : angle 0.51914 (32905) hydrogen bonds : bond 0.03961 ( 965) hydrogen bonds : angle 4.69858 ( 2700) *********************** 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 272 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 214 time to evaluate : 1.014 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 59 GLU cc_start: 0.3125 (mm-30) cc_final: 0.2613 (mm-30) REVERT: G 81 GLU cc_start: 0.5088 (tm-30) cc_final: 0.3835 (tt0) REVERT: G 83 ASP cc_start: 0.8698 (t0) cc_final: 0.8431 (t0) REVERT: G 114 ASN cc_start: 0.8910 (t0) cc_final: 0.8459 (t0) REVERT: G 117 LEU cc_start: 0.9200 (tp) cc_final: 0.8911 (tm) REVERT: G 208 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7389 (t80) REVERT: A 95 ARG cc_start: 0.8328 (ptt-90) cc_final: 0.7874 (mtt180) REVERT: A 267 MET cc_start: 0.9054 (mmm) cc_final: 0.8619 (mtm) REVERT: B 43 SER cc_start: 0.8677 (m) cc_final: 0.8355 (p) REVERT: B 105 GLN cc_start: 0.9086 (tt0) cc_final: 0.8810 (tt0) REVERT: F 40 MET cc_start: 0.8898 (mmm) cc_final: 0.7882 (tmt) REVERT: F 162 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.8010 (mtm-85) REVERT: D 40 MET cc_start: 0.8321 (tpp) cc_final: 0.8042 (tpp) REVERT: E 155 MET cc_start: 0.9376 (tpp) cc_final: 0.9130 (tpp) REVERT: J 279 GLN cc_start: 0.8106 (mt0) cc_final: 0.7852 (mt0) REVERT: K 280 MET cc_start: 0.7343 (mtp) cc_final: 0.6961 (mtp) REVERT: M 280 MET cc_start: 0.7521 (mtm) cc_final: 0.7229 (mtm) outliers start: 58 outliers final: 30 residues processed: 252 average time/residue: 0.7501 time to fit residues: 214.1850 Evaluate side-chains 228 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 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 G residue 425 LEU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain B residue 57 THR 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 119 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 18 optimal weight: 0.2980 chunk 152 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 chunk 210 optimal weight: 0.0770 chunk 105 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 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** ** E 414 ASN ** 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 = 0.3432 r_free = 0.3432 target = 0.090895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.069469 restraints weight = 52166.380| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.66 r_work: 0.2925 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24259 Z= 0.113 Angle : 0.511 9.041 32905 Z= 0.264 Chirality : 0.040 0.178 3814 Planarity : 0.003 0.048 4303 Dihedral : 4.281 27.110 3319 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.88 % Allowed : 12.73 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.14), residues: 3085 helix: 2.26 (0.18), residues: 796 sheet: -0.26 (0.19), residues: 695 loop : -1.09 (0.14), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 203 TYR 0.013 0.001 TYR D 168 PHE 0.012 0.001 PHE E 170 TRP 0.013 0.001 TRP G 145 HIS 0.001 0.000 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00253 (24259) covalent geometry : angle 0.51063 (32905) hydrogen bonds : bond 0.03790 ( 965) hydrogen bonds : angle 4.61693 ( 2700) *********************** 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 254 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 206 time to evaluate : 0.840 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: G 59 GLU cc_start: 0.3161 (mm-30) cc_final: 0.2305 (mm-30) REVERT: G 81 GLU cc_start: 0.5176 (tm-30) cc_final: 0.3609 (tm-30) REVERT: G 83 ASP cc_start: 0.8707 (t0) cc_final: 0.8411 (t0) REVERT: G 114 ASN cc_start: 0.8828 (t0) cc_final: 0.8283 (t0) REVERT: G 117 LEU cc_start: 0.9174 (tp) cc_final: 0.8899 (tm) REVERT: G 208 PHE cc_start: 0.7710 (OUTLIER) cc_final: 0.7389 (t80) REVERT: A 95 ARG cc_start: 0.8340 (ptt-90) cc_final: 0.7892 (mtt180) REVERT: A 267 MET cc_start: 0.9086 (mmm) cc_final: 0.8679 (mtm) REVERT: B 41 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8019 (tm130) REVERT: B 105 GLN cc_start: 0.9080 (tt0) cc_final: 0.8801 (tt0) REVERT: B 299 ARG cc_start: 0.8827 (ttp80) cc_final: 0.7983 (mtt180) REVERT: F 40 MET cc_start: 0.8894 (mmm) cc_final: 0.7977 (tmt) REVERT: F 162 ARG cc_start: 0.8342 (mtm-85) cc_final: 0.8013 (mtm-85) REVERT: D 40 MET cc_start: 0.8291 (tpp) cc_final: 0.8009 (tpp) REVERT: E 62 ASP cc_start: 0.8420 (t70) cc_final: 0.8078 (t0) REVERT: E 155 MET cc_start: 0.9402 (tpp) cc_final: 0.9198 (tpp) REVERT: E 281 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8980 (mp) REVERT: J 279 GLN cc_start: 0.8101 (mt0) cc_final: 0.7828 (mt0) REVERT: K 280 MET cc_start: 0.7345 (mtp) cc_final: 0.6973 (mtp) REVERT: M 280 MET cc_start: 0.7436 (mtm) cc_final: 0.7147 (mtm) outliers start: 48 outliers final: 27 residues processed: 242 average time/residue: 0.7156 time to fit residues: 195.7644 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 : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 132 THR 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 318 VAL 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 216 LYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain B residue 31 LYS 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 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 182 LEU Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain E residue 281 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 108 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 258 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 243 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 130 optimal weight: 0.0020 overall best weight: 3.1794 ------------------------------------------------------------------------------- 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 F 105 GLN 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** D 414 ASN ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.089058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.067493 restraints weight = 52391.061| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.65 r_work: 0.2876 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24259 Z= 0.201 Angle : 0.562 11.947 32905 Z= 0.290 Chirality : 0.041 0.197 3814 Planarity : 0.004 0.050 4303 Dihedral : 4.512 27.031 3319 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.12 % Allowed : 12.93 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.14), residues: 3085 helix: 2.25 (0.18), residues: 804 sheet: -0.34 (0.19), residues: 714 loop : -1.13 (0.14), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 203 TYR 0.015 0.001 TYR F 33 PHE 0.017 0.002 PHE D 86 TRP 0.016 0.001 TRP G 145 HIS 0.003 0.000 HIS C 305 Details of bonding type rmsd covalent geometry : bond 0.00455 (24259) covalent geometry : angle 0.56239 (32905) hydrogen bonds : bond 0.04274 ( 965) hydrogen bonds : angle 4.65847 ( 2700) *********************** 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 250 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 196 time to evaluate : 0.726 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 59 GLU cc_start: 0.2980 (OUTLIER) cc_final: 0.2113 (mm-30) REVERT: G 81 GLU cc_start: 0.4926 (OUTLIER) cc_final: 0.3337 (tm-30) REVERT: G 83 ASP cc_start: 0.8712 (t0) cc_final: 0.8472 (t0) REVERT: G 114 ASN cc_start: 0.8855 (t0) cc_final: 0.8128 (t0) REVERT: G 117 LEU cc_start: 0.9202 (tp) cc_final: 0.8896 (tm) REVERT: A 95 ARG cc_start: 0.8354 (ptt-90) cc_final: 0.7869 (mtt180) REVERT: A 267 MET cc_start: 0.9129 (mmm) cc_final: 0.8707 (mtm) REVERT: B 105 GLN cc_start: 0.9108 (tt0) cc_final: 0.8823 (tt0) REVERT: B 299 ARG cc_start: 0.8859 (ttp80) cc_final: 0.7966 (mtt180) REVERT: F 40 MET cc_start: 0.8932 (mmm) cc_final: 0.7804 (tmt) REVERT: F 70 LEU cc_start: 0.8807 (mm) cc_final: 0.8518 (mt) REVERT: D 40 MET cc_start: 0.8335 (tpp) cc_final: 0.8029 (tpp) REVERT: E 62 ASP cc_start: 0.8557 (t70) cc_final: 0.8261 (t0) REVERT: J 279 GLN cc_start: 0.8089 (mt0) cc_final: 0.7837 (mt0) REVERT: K 280 MET cc_start: 0.7408 (mtp) cc_final: 0.7015 (mtp) REVERT: M 280 MET cc_start: 0.7543 (mtm) cc_final: 0.7217 (mtm) outliers start: 54 outliers final: 34 residues processed: 236 average time/residue: 0.6710 time to fit residues: 179.5895 Evaluate side-chains 222 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 81 GLU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 297 VAL 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 98 optimal weight: 1.9990 chunk 245 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 292 optimal weight: 6.9990 chunk 247 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 154 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.090028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.068577 restraints weight = 52018.634| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.64 r_work: 0.2887 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24259 Z= 0.138 Angle : 0.534 9.229 32905 Z= 0.276 Chirality : 0.041 0.180 3814 Planarity : 0.003 0.053 4303 Dihedral : 4.407 26.616 3319 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.96 % Allowed : 13.40 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.14), residues: 3085 helix: 2.29 (0.18), residues: 797 sheet: -0.27 (0.18), residues: 730 loop : -1.13 (0.14), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 203 TYR 0.013 0.001 TYR F 33 PHE 0.013 0.001 PHE E 170 TRP 0.014 0.001 TRP G 145 HIS 0.002 0.000 HIS C 305 Details of bonding type rmsd covalent geometry : bond 0.00309 (24259) covalent geometry : angle 0.53358 (32905) hydrogen bonds : bond 0.03977 ( 965) hydrogen bonds : angle 4.59809 ( 2700) *********************** 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 243 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 193 time to evaluate : 1.028 Fit side-chains TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 59 GLU cc_start: 0.2782 (mm-30) cc_final: 0.1966 (mm-30) REVERT: G 81 GLU cc_start: 0.4920 (OUTLIER) cc_final: 0.3343 (tm-30) REVERT: G 83 ASP cc_start: 0.8681 (t0) cc_final: 0.8404 (t0) REVERT: G 114 ASN cc_start: 0.8855 (t0) cc_final: 0.8082 (t0) REVERT: G 117 LEU cc_start: 0.9184 (tp) cc_final: 0.8896 (tm) REVERT: G 164 MET cc_start: 0.7065 (mmt) cc_final: 0.6635 (mmm) REVERT: A 95 ARG cc_start: 0.8341 (ptt-90) cc_final: 0.7876 (mtt180) REVERT: A 267 MET cc_start: 0.9110 (mmm) cc_final: 0.8715 (mtm) REVERT: B 105 GLN cc_start: 0.9103 (tt0) cc_final: 0.8813 (tt0) REVERT: B 299 ARG cc_start: 0.8839 (ttp80) cc_final: 0.7975 (mtt180) REVERT: F 40 MET cc_start: 0.8926 (mmm) cc_final: 0.7798 (tmt) REVERT: F 70 LEU cc_start: 0.8811 (mm) cc_final: 0.8518 (mt) REVERT: D 40 MET cc_start: 0.8318 (tpp) cc_final: 0.8016 (tpp) REVERT: E 62 ASP cc_start: 0.8529 (t70) cc_final: 0.8223 (t0) REVERT: J 279 GLN cc_start: 0.8092 (mt0) cc_final: 0.7836 (mt0) REVERT: K 280 MET cc_start: 0.7323 (mtp) cc_final: 0.6954 (mtp) REVERT: M 280 MET cc_start: 0.7514 (mtm) cc_final: 0.7202 (mtm) outliers start: 50 outliers final: 34 residues processed: 233 average time/residue: 0.7622 time to fit residues: 200.6320 Evaluate side-chains 222 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 318 VAL Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 297 VAL 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 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 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 306 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 364 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 114 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 152 optimal weight: 10.0000 chunk 120 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 295 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 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 = 0.3431 r_free = 0.3431 target = 0.090816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.069413 restraints weight = 52454.619| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.66 r_work: 0.2917 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24259 Z= 0.116 Angle : 0.522 9.008 32905 Z= 0.269 Chirality : 0.040 0.172 3814 Planarity : 0.003 0.055 4303 Dihedral : 4.313 26.159 3319 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.84 % Allowed : 13.59 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.14), residues: 3085 helix: 2.26 (0.18), residues: 803 sheet: -0.24 (0.18), residues: 743 loop : -1.11 (0.14), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 203 TYR 0.014 0.001 TYR D 168 PHE 0.016 0.001 PHE G 156 TRP 0.013 0.001 TRP A 354 HIS 0.001 0.000 HIS C 305 Details of bonding type rmsd covalent geometry : bond 0.00258 (24259) covalent geometry : angle 0.52182 (32905) hydrogen bonds : bond 0.03808 ( 965) hydrogen bonds : angle 4.53118 ( 2700) *********************** 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 246 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 0.985 Fit side-chains TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP F 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 59 GLU cc_start: 0.2765 (mm-30) cc_final: 0.1940 (mm-30) REVERT: G 81 GLU cc_start: 0.5234 (OUTLIER) cc_final: 0.3667 (tm-30) REVERT: G 83 ASP cc_start: 0.8654 (t0) cc_final: 0.8391 (t0) REVERT: G 114 ASN cc_start: 0.8874 (t0) cc_final: 0.8117 (t0) REVERT: G 117 LEU cc_start: 0.9175 (tp) cc_final: 0.8895 (tm) REVERT: G 122 MET cc_start: 0.9018 (ttm) cc_final: 0.8811 (tmm) REVERT: G 164 MET cc_start: 0.7148 (mmt) cc_final: 0.6728 (mmm) REVERT: A 72 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7817 (mm-30) REVERT: A 95 ARG cc_start: 0.8318 (ptt-90) cc_final: 0.7880 (mtt180) REVERT: A 267 MET cc_start: 0.9074 (mmm) cc_final: 0.8674 (mtm) REVERT: B 105 GLN cc_start: 0.9100 (tt0) cc_final: 0.8823 (tt0) REVERT: B 299 ARG cc_start: 0.8838 (ttp80) cc_final: 0.7977 (mtt180) REVERT: F 40 MET cc_start: 0.9006 (mmm) cc_final: 0.7833 (tmt) REVERT: F 70 LEU cc_start: 0.8728 (mm) cc_final: 0.8445 (mt) REVERT: D 40 MET cc_start: 0.8305 (tpp) cc_final: 0.8099 (tpp) REVERT: E 62 ASP cc_start: 0.8488 (t70) cc_final: 0.8161 (t0) REVERT: E 281 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8981 (mp) REVERT: J 279 GLN cc_start: 0.8098 (mt0) cc_final: 0.7845 (mt0) REVERT: K 280 MET cc_start: 0.7291 (mtp) cc_final: 0.6922 (mtp) REVERT: M 280 MET cc_start: 0.7425 (mtm) cc_final: 0.7127 (mtm) outliers start: 47 outliers final: 34 residues processed: 237 average time/residue: 0.7975 time to fit residues: 213.6027 Evaluate side-chains 229 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 318 VAL 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 297 VAL 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 B residue 356 ASP 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 182 LEU Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain E residue 61 TRP Chi-restraints excluded: chain E residue 281 LEU 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 255 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 174 optimal weight: 0.8980 chunk 249 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 F 204 GLN ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN C 53 GLN C 364 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 = 0.3412 r_free = 0.3412 target = 0.089670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.068275 restraints weight = 52508.943| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.64 r_work: 0.2896 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24259 Z= 0.171 Angle : 0.558 12.935 32905 Z= 0.287 Chirality : 0.041 0.190 3814 Planarity : 0.004 0.060 4303 Dihedral : 4.407 26.296 3319 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.65 % Allowed : 13.98 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.14), residues: 3085 helix: 2.27 (0.18), residues: 804 sheet: -0.27 (0.18), residues: 744 loop : -1.11 (0.14), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 203 TYR 0.021 0.001 TYR F 33 PHE 0.014 0.001 PHE D 86 TRP 0.015 0.001 TRP G 145 HIS 0.002 0.000 HIS C 305 Details of bonding type rmsd covalent geometry : bond 0.00389 (24259) covalent geometry : angle 0.55839 (32905) hydrogen bonds : bond 0.04058 ( 965) hydrogen bonds : angle 4.55947 ( 2700) ********************** 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 233 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 191 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: G 59 GLU cc_start: 0.2927 (mm-30) cc_final: 0.2081 (mm-30) REVERT: G 81 GLU cc_start: 0.4827 (OUTLIER) cc_final: 0.3289 (tm-30) REVERT: G 83 ASP cc_start: 0.8666 (t0) cc_final: 0.8398 (t0) REVERT: G 114 ASN cc_start: 0.8882 (t0) cc_final: 0.8098 (t0) REVERT: G 117 LEU cc_start: 0.9184 (tp) cc_final: 0.8893 (tm) REVERT: G 164 MET cc_start: 0.7442 (mmt) cc_final: 0.7021 (mmm) REVERT: A 72 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7831 (mm-30) REVERT: A 95 ARG cc_start: 0.8323 (ptt-90) cc_final: 0.7866 (mtt180) REVERT: A 267 MET cc_start: 0.9104 (mmm) cc_final: 0.8718 (mtm) REVERT: B 105 GLN cc_start: 0.9089 (tt0) cc_final: 0.8793 (tt0) REVERT: B 299 ARG cc_start: 0.8832 (ttp80) cc_final: 0.7974 (mtt180) REVERT: F 40 MET cc_start: 0.8883 (mmm) cc_final: 0.7816 (tmt) REVERT: F 70 LEU cc_start: 0.8740 (mm) cc_final: 0.8458 (mt) REVERT: D 40 MET cc_start: 0.8344 (tpp) cc_final: 0.8135 (tpp) REVERT: E 62 ASP cc_start: 0.8551 (t70) cc_final: 0.8229 (t0) REVERT: J 279 GLN cc_start: 0.8095 (mt0) cc_final: 0.7870 (mt0) REVERT: K 280 MET cc_start: 0.7311 (mtp) cc_final: 0.6939 (mtp) REVERT: M 280 MET cc_start: 0.7511 (mtm) cc_final: 0.7197 (mtm) outliers start: 42 outliers final: 35 residues processed: 226 average time/residue: 0.7712 time to fit residues: 196.8104 Evaluate side-chains 222 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 318 VAL Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 297 VAL 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 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 182 LEU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 364 GLN 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 183 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 210 optimal weight: 0.5980 chunk 206 optimal weight: 5.9990 chunk 269 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 227 optimal weight: 0.0570 chunk 76 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.089572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.068153 restraints weight = 52314.499| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.65 r_work: 0.2890 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 24259 Z= 0.176 Angle : 0.568 16.267 32905 Z= 0.293 Chirality : 0.041 0.213 3814 Planarity : 0.004 0.072 4303 Dihedral : 4.425 26.110 3319 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.80 % Allowed : 13.91 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.14), residues: 3085 helix: 2.26 (0.18), residues: 804 sheet: -0.30 (0.18), residues: 746 loop : -1.12 (0.14), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 203 TYR 0.021 0.001 TYR F 33 PHE 0.017 0.001 PHE G 156 TRP 0.014 0.001 TRP G 145 HIS 0.002 0.000 HIS C 305 Details of bonding type rmsd covalent geometry : bond 0.00399 (24259) covalent geometry : angle 0.56762 (32905) hydrogen bonds : bond 0.04076 ( 965) hydrogen bonds : angle 4.57061 ( 2700) =============================================================================== Job complete usr+sys time: 7752.93 seconds wall clock time: 133 minutes 0.80 seconds (7980.80 seconds total)