Starting phenix.real_space_refine on Sun Sep 29 17:27:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1v_35123/09_2024/8i1v_35123.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1v_35123/09_2024/8i1v_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1v_35123/09_2024/8i1v_35123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1v_35123/09_2024/8i1v_35123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1v_35123/09_2024/8i1v_35123.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1v_35123/09_2024/8i1v_35123.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.825 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 14961 2.51 5 N 4163 2.21 5 O 4648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23870 Number of models: 1 Model: "" Number of chains: 14 Chain: "G" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3203 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3162 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 20, 'TRANS': 394} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3156 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3220 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 20, 'TRANS': 401} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3220 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 20, 'TRANS': 401} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3139 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 20, 'TRANS': 391} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3139 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 20, 'TRANS': 391} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "I" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "J" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "K" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "L" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "M" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "N" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Time building chain proxies: 14.20, per 1000 atoms: 0.59 Number of scatterers: 23870 At special positions: 0 Unit cell: (102.82, 182.32, 161.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 4648 8.00 N 4163 7.00 C 14961 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.55 Conformation dependent library (CDL) restraints added in 2.9 seconds 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5868 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 56 sheets defined 26.6% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 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: 7.69 Time building geometry restraints manager: 6.48 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 50.940 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.410 ------------------------------------------------------------------------------- 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= 0.344 Angle : 0.623 10.373 32905 Z= 0.345 Chirality : 0.044 0.341 3814 Planarity : 0.004 0.067 4303 Dihedral : 13.195 89.903 8941 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.04 % Allowed : 0.51 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3085 helix: 1.97 (0.18), residues: 747 sheet: -0.61 (0.19), residues: 725 loop : -1.09 (0.14), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP F 410 HIS 0.002 0.001 HIS B 305 PHE 0.026 0.002 PHE E 86 TYR 0.014 0.002 TYR C 175 ARG 0.008 0.001 ARG G 185 *********************** 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 fitting. rotamer outliers: 1 poor density : 368 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. REVERT: K 280 MET cc_start: 0.7667 (mtp) cc_final: 0.7424 (mtt) REVERT: M 280 MET cc_start: 0.8344 (mtm) cc_final: 0.8020 (mtm) outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 1.6333 time to fit residues: 673.7828 Evaluate side-chains 208 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 7.9990 chunk 235 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 243 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 282 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 305 HIS ** G 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN B 7 GLN F 204 GLN ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 369 ASN C 53 GLN D 84 ASN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 ASN E 7 GLN E 41 GLN E 88 GLN E 305 HIS E 364 GLN ** H 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24259 Z= 0.186 Angle : 0.559 8.316 32905 Z= 0.295 Chirality : 0.042 0.196 3814 Planarity : 0.004 0.044 4303 Dihedral : 4.448 28.170 3319 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.76 % Allowed : 8.11 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3085 helix: 2.21 (0.18), residues: 764 sheet: -0.34 (0.19), residues: 713 loop : -1.15 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 410 HIS 0.001 0.000 HIS E 305 PHE 0.016 0.001 PHE E 170 TYR 0.019 0.001 TYR E 411 ARG 0.007 0.001 ARG F 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 229 time to evaluate : 2.872 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: A 267 MET cc_start: 0.7110 (mmm) cc_final: 0.6745 (mtm) REVERT: K 280 MET cc_start: 0.7538 (mtp) cc_final: 0.7204 (mtt) REVERT: M 280 MET cc_start: 0.8358 (mtm) cc_final: 0.8072 (mtm) outliers start: 45 outliers final: 12 residues processed: 254 average time/residue: 1.6046 time to fit residues: 458.6028 Evaluate side-chains 216 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 204 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain E residue 301 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 156 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 282 optimal weight: 4.9990 chunk 305 optimal weight: 4.9990 chunk 251 optimal weight: 5.9990 chunk 280 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 226 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 B 105 GLN F 53 GLN F 204 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 Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 24259 Z= 0.340 Angle : 0.585 9.153 32905 Z= 0.306 Chirality : 0.042 0.213 3814 Planarity : 0.004 0.054 4303 Dihedral : 4.662 29.792 3319 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.31 % Allowed : 9.52 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3085 helix: 2.22 (0.18), residues: 774 sheet: -0.48 (0.18), residues: 724 loop : -1.06 (0.14), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 410 HIS 0.004 0.001 HIS C 305 PHE 0.022 0.002 PHE A 86 TYR 0.016 0.002 TYR E 411 ARG 0.005 0.001 ARG F 162 *********************** 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 260 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 201 time to evaluate : 3.005 Fit side-chains TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 59 GLU cc_start: 0.4259 (mm-30) cc_final: 0.3087 (mm-30) REVERT: G 81 GLU cc_start: 0.5435 (tm-30) cc_final: 0.3835 (tm-30) REVERT: A 95 ARG cc_start: 0.5906 (OUTLIER) cc_final: 0.4312 (ttt180) REVERT: A 267 MET cc_start: 0.7311 (mmm) cc_final: 0.6981 (mtm) REVERT: A 364 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6709 (pt0) REVERT: F 162 ARG cc_start: 0.6463 (mtm-85) cc_final: 0.6111 (mtm-85) REVERT: E 54 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.7043 (mt-10) REVERT: K 280 MET cc_start: 0.7569 (mtp) cc_final: 0.7277 (mtt) REVERT: M 280 MET cc_start: 0.8340 (mtm) cc_final: 0.8041 (mtm) outliers start: 59 outliers final: 19 residues processed: 239 average time/residue: 1.6217 time to fit residues: 436.2595 Evaluate side-chains 208 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 186 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain A residue 95 ARG 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 E residue 54 GLU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain H residue 279 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 279 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 189 optimal weight: 0.0170 chunk 283 optimal weight: 1.9990 chunk 300 optimal weight: 20.0000 chunk 148 optimal weight: 6.9990 chunk 269 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24259 Z= 0.265 Angle : 0.554 9.492 32905 Z= 0.288 Chirality : 0.042 0.202 3814 Planarity : 0.004 0.049 4303 Dihedral : 4.585 28.517 3319 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.15 % Allowed : 11.28 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3085 helix: 2.23 (0.18), residues: 785 sheet: -0.45 (0.19), residues: 697 loop : -1.08 (0.14), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 145 HIS 0.002 0.000 HIS C 305 PHE 0.015 0.001 PHE D 86 TYR 0.010 0.001 TYR D 168 ARG 0.008 0.000 ARG F 203 *********************** 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 253 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 198 time to evaluate : 2.512 Fit side-chains TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 59 GLU cc_start: 0.3710 (OUTLIER) cc_final: 0.2486 (mm-30) REVERT: G 81 GLU cc_start: 0.5375 (tm-30) cc_final: 0.3665 (tm-30) REVERT: A 95 ARG cc_start: 0.5920 (OUTLIER) cc_final: 0.4323 (ttt180) REVERT: A 267 MET cc_start: 0.7316 (mmm) cc_final: 0.7040 (mtm) REVERT: C 284 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.6476 (mtp) REVERT: M 280 MET cc_start: 0.8276 (mtm) cc_final: 0.7985 (mtm) outliers start: 55 outliers final: 27 residues processed: 229 average time/residue: 1.5485 time to fit residues: 401.0698 Evaluate side-chains 215 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 185 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain A residue 95 ARG 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 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 297 VAL Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 284 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 139 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain H residue 279 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 250 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 223 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 256 optimal weight: 0.6980 chunk 207 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 269 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 overall best weight: 1.7402 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24259 Z= 0.202 Angle : 0.527 9.451 32905 Z= 0.273 Chirality : 0.041 0.184 3814 Planarity : 0.003 0.048 4303 Dihedral : 4.435 27.597 3319 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.62 % Allowed : 11.63 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3085 helix: 2.22 (0.18), residues: 797 sheet: -0.32 (0.19), residues: 689 loop : -1.10 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 145 HIS 0.002 0.000 HIS C 305 PHE 0.013 0.001 PHE E 170 TYR 0.009 0.001 TYR B 100 ARG 0.009 0.000 ARG F 203 *********************** 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 273 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 206 time to evaluate : 2.859 Fit side-chains TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 59 GLU cc_start: 0.3699 (OUTLIER) cc_final: 0.2503 (mm-30) REVERT: G 81 GLU cc_start: 0.5182 (OUTLIER) cc_final: 0.3439 (tm-30) REVERT: A 267 MET cc_start: 0.7332 (mmm) cc_final: 0.7065 (mtm) REVERT: F 122 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6510 (ttm) REVERT: E 246 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.7003 (m-30) REVERT: M 280 MET cc_start: 0.8225 (mtm) cc_final: 0.7926 (mtm) outliers start: 67 outliers final: 29 residues processed: 249 average time/residue: 1.4842 time to fit residues: 420.0656 Evaluate side-chains 220 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 187 time to evaluate : 2.652 ------------------------------------------------------------------------------- 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 132 THR Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain 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 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 122 MET Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain C residue 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 376 MET Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain H residue 279 GLN Chi-restraints excluded: chain H residue 280 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 101 optimal weight: 5.9990 chunk 270 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 300 optimal weight: 3.9990 chunk 249 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 99 optimal weight: 20.0000 chunk 157 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN F 41 GLN ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN F 204 GLN F 283 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** J 279 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 24259 Z= 0.397 Angle : 0.607 9.742 32905 Z= 0.314 Chirality : 0.043 0.208 3814 Planarity : 0.004 0.050 4303 Dihedral : 4.724 27.973 3319 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.66 % Allowed : 12.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3085 helix: 2.16 (0.18), residues: 798 sheet: -0.37 (0.19), residues: 700 loop : -1.13 (0.14), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 145 HIS 0.005 0.001 HIS C 305 PHE 0.021 0.002 PHE D 86 TYR 0.013 0.002 TYR D 168 ARG 0.009 0.001 ARG F 203 *********************** 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 260 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 192 time to evaluate : 2.577 Fit side-chains TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 59 GLU cc_start: 0.4036 (mm-30) cc_final: 0.2744 (mm-30) REVERT: G 81 GLU cc_start: 0.5474 (OUTLIER) cc_final: 0.3669 (tm-30) REVERT: A 95 ARG cc_start: 0.5803 (OUTLIER) cc_final: 0.5581 (mtt180) REVERT: A 267 MET cc_start: 0.7447 (mmm) cc_final: 0.7206 (mtm) REVERT: E 54 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.7064 (mt-10) REVERT: E 246 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.7120 (m-30) REVERT: M 280 MET cc_start: 0.8282 (mtm) cc_final: 0.7987 (mtm) outliers start: 68 outliers final: 36 residues processed: 238 average time/residue: 1.5384 time to fit residues: 414.9362 Evaluate side-chains 221 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 181 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain A residue 95 ARG 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 376 MET 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 219 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain C residue 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 54 GLU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 246 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 290 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 219 optimal weight: 0.8980 chunk 170 optimal weight: 7.9990 chunk 253 optimal weight: 0.4980 chunk 168 optimal weight: 0.0980 chunk 299 optimal weight: 30.0000 chunk 187 optimal weight: 0.9990 chunk 182 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN B 389 ASN F 41 GLN ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN F 283 GLN ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 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** J 279 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24259 Z= 0.176 Angle : 0.530 9.200 32905 Z= 0.274 Chirality : 0.041 0.182 3814 Planarity : 0.003 0.043 4303 Dihedral : 4.425 27.050 3319 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.80 % Allowed : 13.40 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3085 helix: 2.17 (0.18), residues: 804 sheet: -0.31 (0.19), residues: 705 loop : -1.11 (0.14), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 145 HIS 0.001 0.000 HIS A 305 PHE 0.013 0.001 PHE E 170 TYR 0.009 0.001 TYR F 33 ARG 0.011 0.000 ARG F 203 *********************** 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 242 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 196 time to evaluate : 2.678 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: 0.3637 (mm-30) cc_final: 0.2377 (mm-30) REVERT: G 81 GLU cc_start: 0.5317 (tm-30) cc_final: 0.3487 (tm-30) REVERT: A 267 MET cc_start: 0.7355 (mmm) cc_final: 0.7132 (mtm) REVERT: F 122 MET cc_start: 0.6995 (ttm) cc_final: 0.6528 (ttm) REVERT: M 280 MET cc_start: 0.8242 (mtm) cc_final: 0.7924 (mtm) outliers start: 46 outliers final: 24 residues processed: 229 average time/residue: 1.4608 time to fit residues: 382.0150 Evaluate side-chains 208 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 184 time to evaluate : 2.480 ------------------------------------------------------------------------------- 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 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 306 VAL Chi-restraints excluded: chain A residue 416 THR 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 297 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 61 TRP Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain 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 185 optimal weight: 0.3980 chunk 119 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 chunk 204 optimal weight: 0.0270 chunk 148 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 235 optimal weight: 4.9990 chunk 272 optimal weight: 6.9990 overall best weight: 1.2440 ------------------------------------------------------------------------------- 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 ** 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** J 279 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24259 Z= 0.180 Angle : 0.528 8.843 32905 Z= 0.273 Chirality : 0.040 0.180 3814 Planarity : 0.003 0.049 4303 Dihedral : 4.318 26.469 3319 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.65 % Allowed : 13.87 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3085 helix: 2.20 (0.18), residues: 803 sheet: -0.24 (0.18), residues: 724 loop : -1.11 (0.14), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 145 HIS 0.001 0.000 HIS C 305 PHE 0.013 0.001 PHE G 156 TYR 0.014 0.001 TYR D 168 ARG 0.012 0.000 ARG F 203 *********************** 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 234 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 192 time to evaluate : 2.770 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: 0.3689 (mm-30) cc_final: 0.2452 (mm-30) REVERT: G 81 GLU cc_start: 0.5016 (OUTLIER) cc_final: 0.3186 (tm-30) REVERT: M 280 MET cc_start: 0.8238 (mtm) cc_final: 0.7923 (mtm) outliers start: 42 outliers final: 26 residues processed: 224 average time/residue: 1.4942 time to fit residues: 379.9070 Evaluate side-chains 211 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 184 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain B residue 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 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 I residue 290 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 287 optimal weight: 0.3980 chunk 262 optimal weight: 3.9990 chunk 279 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 219 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 252 optimal weight: 4.9990 chunk 264 optimal weight: 4.9990 chunk 278 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN F 41 GLN F 84 ASN F 204 GLN ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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= 0.266 Angle : 0.554 10.935 32905 Z= 0.285 Chirality : 0.041 0.186 3814 Planarity : 0.004 0.056 4303 Dihedral : 4.406 26.654 3319 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.57 % Allowed : 14.10 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3085 helix: 2.20 (0.18), residues: 803 sheet: -0.26 (0.18), residues: 731 loop : -1.13 (0.14), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 145 HIS 0.002 0.000 HIS C 305 PHE 0.013 0.001 PHE D 86 TYR 0.009 0.001 TYR C 168 ARG 0.013 0.000 ARG F 203 *********************** 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 227 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 187 time to evaluate : 2.444 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: 0.3839 (mm-30) cc_final: 0.2557 (mm-30) REVERT: G 81 GLU cc_start: 0.5119 (OUTLIER) cc_final: 0.3237 (tm-30) REVERT: G 164 MET cc_start: 0.7189 (mmm) cc_final: 0.6921 (mmt) REVERT: M 280 MET cc_start: 0.8268 (mtm) cc_final: 0.7951 (mtm) outliers start: 40 outliers final: 29 residues processed: 222 average time/residue: 1.5585 time to fit residues: 394.9714 Evaluate side-chains 211 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 181 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain B residue 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 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 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 I residue 290 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 295 optimal weight: 3.9990 chunk 180 optimal weight: 8.9990 chunk 140 optimal weight: 0.9990 chunk 205 optimal weight: 0.8980 chunk 309 optimal weight: 50.0000 chunk 285 optimal weight: 7.9990 chunk 246 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 190 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN F 41 GLN F 84 ASN F 204 GLN ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24259 Z= 0.233 Angle : 0.554 8.855 32905 Z= 0.287 Chirality : 0.041 0.205 3814 Planarity : 0.004 0.059 4303 Dihedral : 4.408 26.122 3319 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.49 % Allowed : 14.38 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3085 helix: 2.19 (0.18), residues: 803 sheet: -0.27 (0.18), residues: 732 loop : -1.13 (0.14), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 145 HIS 0.002 0.000 HIS A 305 PHE 0.012 0.001 PHE D 86 TYR 0.016 0.001 TYR D 168 ARG 0.013 0.000 ARG F 203 ********************** 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 224 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 186 time to evaluate : 2.776 Fit side-chains revert: symmetry clash REVERT: G 59 GLU cc_start: 0.3815 (mm-30) cc_final: 0.2565 (mm-30) REVERT: G 81 GLU cc_start: 0.5050 (OUTLIER) cc_final: 0.3411 (tm-30) REVERT: G 164 MET cc_start: 0.7217 (mmm) cc_final: 0.6965 (mmt) REVERT: K 280 MET cc_start: 0.7940 (tpp) cc_final: 0.7522 (mtt) REVERT: M 280 MET cc_start: 0.8264 (mtm) cc_final: 0.7948 (mtm) outliers start: 38 outliers final: 30 residues processed: 214 average time/residue: 1.5467 time to fit residues: 375.2257 Evaluate side-chains 210 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 179 time to evaluate : 2.670 ------------------------------------------------------------------------------- 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 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 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 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 I residue 290 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 227 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 247 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 253 optimal weight: 0.0270 chunk 31 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 overall best weight: 2.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS B 41 GLN F 41 GLN F 84 ASN F 204 GLN ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.090008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.068525 restraints weight = 52367.373| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.66 r_work: 0.2900 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24259 Z= 0.248 Angle : 0.558 9.024 32905 Z= 0.289 Chirality : 0.041 0.200 3814 Planarity : 0.004 0.059 4303 Dihedral : 4.444 25.772 3319 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.61 % Allowed : 14.53 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3085 helix: 2.18 (0.18), residues: 804 sheet: -0.27 (0.18), residues: 732 loop : -1.13 (0.14), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 145 HIS 0.002 0.000 HIS C 305 PHE 0.019 0.001 PHE G 156 TYR 0.016 0.001 TYR D 168 ARG 0.014 0.000 ARG F 203 =============================================================================== Job complete usr+sys time: 7757.18 seconds wall clock time: 137 minutes 0.41 seconds (8220.41 seconds total)