Starting phenix.real_space_refine on Sun Aug 24 08:25:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hao_34598/08_2025/8hao_34598_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hao_34598/08_2025/8hao_34598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hao_34598/08_2025/8hao_34598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hao_34598/08_2025/8hao_34598.map" model { file = "/net/cci-nas-00/data/ceres_data/8hao_34598/08_2025/8hao_34598_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hao_34598/08_2025/8hao_34598_neut.cif" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.027 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 120 5.16 5 C 11745 2.51 5 N 3242 2.21 5 O 3372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 18479 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1950 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2614 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1950 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "D" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2614 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "F" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "H" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 288 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "I" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2977 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain breaks: 4 Chain: "N" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "P" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 288 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "R" Number of atoms: 2960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2960 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 11, 'TRANS': 348} Chain breaks: 4 Time building chain proxies: 4.66, per 1000 atoms: 0.25 Number of scatterers: 18479 At special positions: 0 Unit cell: (168.92, 143.376, 206, 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 120 16.00 O 3372 8.00 N 3242 7.00 C 11745 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 99 " - pdb=" SG CYS F 107 " distance=2.05 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 117 " distance=2.03 Simple disulfide: pdb=" SG CYS I 108 " - pdb=" SG CYS I 148 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 170 " distance=2.03 Simple disulfide: pdb=" SG CYS I 281 " - pdb=" SG CYS I 351 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.04 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 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: 1.73 Conformation dependent library (CDL) restraints added in 887.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4352 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 21 sheets defined 42.1% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 5 through 33 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.509A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.762A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.449A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 298 through 320 removed outlier: 4.407A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 6 through 33 Processing helix chain 'C' and resid 45 through 54 Processing helix chain 'C' and resid 212 through 216 removed outlier: 3.504A pdb=" N PHE C 215 " --> pdb=" O ILE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 246 Processing helix chain 'C' and resid 260 through 271 removed outlier: 3.756A pdb=" N LEU C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 279 removed outlier: 4.399A pdb=" N TYR C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 Processing helix chain 'C' and resid 298 through 320 removed outlier: 4.061A pdb=" N SER C 319 " --> pdb=" O ILE C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 358 Processing helix chain 'D' and resid 4 through 25 removed outlier: 3.548A pdb=" N GLU D 10 " --> pdb=" O GLN D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'E' and resid 7 through 24 Processing helix chain 'E' and resid 29 through 44 removed outlier: 3.569A pdb=" N ASP E 36 " --> pdb=" O LYS E 32 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 48 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.802A pdb=" N THR F 91 " --> pdb=" O PRO F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.512A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'H' and resid 2 through 33 Processing helix chain 'I' and resid 33 through 51 Processing helix chain 'I' and resid 178 through 212 Processing helix chain 'I' and resid 217 through 246 Processing helix chain 'I' and resid 278 through 312 Processing helix chain 'I' and resid 316 through 347 removed outlier: 4.146A pdb=" N TRP I 322 " --> pdb=" O LYS I 318 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU I 331 " --> pdb=" O PHE I 327 " (cutoff:3.500A) Proline residue: I 332 - end of helix Processing helix chain 'I' and resid 357 through 359 No H-bonds generated for 'chain 'I' and resid 357 through 359' Processing helix chain 'I' and resid 360 through 392 Proline residue: I 366 - end of helix Processing helix chain 'I' and resid 400 through 418 Proline residue: I 415 - end of helix Processing helix chain 'I' and resid 419 through 425 removed outlier: 3.589A pdb=" N PHE I 424 " --> pdb=" O TYR I 421 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET I 425 " --> pdb=" O ILE I 422 " (cutoff:3.500A) Processing helix chain 'I' and resid 434 through 460 removed outlier: 3.913A pdb=" N SER I 449 " --> pdb=" O MET I 445 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY I 452 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE I 453 " --> pdb=" O SER I 449 " (cutoff:3.500A) Processing helix chain 'I' and resid 463 through 481 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.656A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 33 Processing helix chain 'R' and resid 33 through 51 Processing helix chain 'R' and resid 179 through 212 removed outlier: 3.531A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 246 Processing helix chain 'R' and resid 278 through 312 Processing helix chain 'R' and resid 316 through 347 removed outlier: 4.231A pdb=" N TRP R 322 " --> pdb=" O LYS R 318 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 357 through 359 No H-bonds generated for 'chain 'R' and resid 357 through 359' Processing helix chain 'R' and resid 360 through 392 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 400 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 419 through 423 Processing helix chain 'R' and resid 434 through 460 removed outlier: 4.053A pdb=" N SER R 449 " --> pdb=" O MET R 445 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 481 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.852A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 52 removed outlier: 6.789A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.833A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.870A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.666A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.696A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.660A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.514A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 184 through 191 removed outlier: 4.817A pdb=" N VAL C 201 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ARG C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILE C 222 " --> pdb=" O ARG C 35 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU C 39 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ASP C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 45 through 52 removed outlier: 5.692A pdb=" N THR D 47 " --> pdb=" O ASN D 340 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN D 340 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG D 49 " --> pdb=" O ILE D 338 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N PHE D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER D 331 " --> pdb=" O PHE D 335 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.942A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP D 83 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS D 89 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.470A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 146 through 151 removed outlier: 6.695A pdb=" N CYS D 166 " --> pdb=" O THR D 179 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N THR D 179 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU D 168 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN D 175 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 187 through 192 removed outlier: 3.708A pdb=" N SER D 189 " --> pdb=" O GLY D 202 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN D 220 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 229 through 234 removed outlier: 3.523A pdb=" N SER D 245 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.537A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.245A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'N' and resid 10 through 12 removed outlier: 7.235A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'R' and resid 148 through 149 987 hydrogen bonds defined for protein. 2847 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: 3.59 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6030 1.35 - 1.47: 4785 1.47 - 1.59: 7905 1.59 - 1.72: 1 1.72 - 1.84: 172 Bond restraints: 18893 Sorted by residual: bond pdb=" CB PRO F 41 " pdb=" CG PRO F 41 " ideal model delta sigma weight residual 1.492 1.624 -0.132 5.00e-02 4.00e+02 6.93e+00 bond pdb=" N PHE I 173 " pdb=" CA PHE I 173 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.41e-02 5.03e+03 5.52e+00 bond pdb=" N GLU D 3 " pdb=" CA GLU D 3 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 bond pdb=" N GLU B 3 " pdb=" CA GLU B 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N LEU C 5 " pdb=" CA LEU C 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 ... (remaining 18888 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 25339 2.16 - 4.32: 212 4.32 - 6.48: 19 6.48 - 8.63: 2 8.63 - 10.79: 1 Bond angle restraints: 25573 Sorted by residual: angle pdb=" CA PRO F 41 " pdb=" N PRO F 41 " pdb=" CD PRO F 41 " ideal model delta sigma weight residual 112.00 101.21 10.79 1.40e+00 5.10e-01 5.94e+01 angle pdb=" N PHE I 173 " pdb=" CA PHE I 173 " pdb=" C PHE I 173 " ideal model delta sigma weight residual 108.86 114.77 -5.91 1.41e+00 5.03e-01 1.76e+01 angle pdb=" C LYS I 172 " pdb=" N PHE I 173 " pdb=" CA PHE I 173 " ideal model delta sigma weight residual 122.53 116.44 6.09 1.61e+00 3.86e-01 1.43e+01 angle pdb=" N CYS R 108 " pdb=" CA CYS R 108 " pdb=" CB CYS R 108 " ideal model delta sigma weight residual 114.17 109.98 4.19 1.14e+00 7.69e-01 1.35e+01 angle pdb=" CA CYS R 48 " pdb=" CB CYS R 48 " pdb=" SG CYS R 48 " ideal model delta sigma weight residual 114.40 121.81 -7.41 2.30e+00 1.89e-01 1.04e+01 ... (remaining 25568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 9723 17.61 - 35.21: 1133 35.21 - 52.82: 259 52.82 - 70.42: 47 70.42 - 88.03: 29 Dihedral angle restraints: 11191 sinusoidal: 4457 harmonic: 6734 Sorted by residual: dihedral pdb=" CB CYS F 99 " pdb=" SG CYS F 99 " pdb=" SG CYS F 107 " pdb=" CB CYS F 107 " ideal model delta sinusoidal sigma weight residual -86.00 0.43 -86.43 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CB CYS I 131 " pdb=" SG CYS I 131 " pdb=" SG CYS I 170 " pdb=" CB CYS I 170 " ideal model delta sinusoidal sigma weight residual 93.00 170.66 -77.66 1 1.00e+01 1.00e-02 7.55e+01 dihedral pdb=" CB CYS R 131 " pdb=" SG CYS R 131 " pdb=" SG CYS R 170 " pdb=" CB CYS R 170 " ideal model delta sinusoidal sigma weight residual 93.00 170.32 -77.32 1 1.00e+01 1.00e-02 7.49e+01 ... (remaining 11188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1795 0.027 - 0.053: 652 0.053 - 0.080: 209 0.080 - 0.106: 82 0.106 - 0.133: 79 Chirality restraints: 2817 Sorted by residual: chirality pdb=" CA ILE D 58 " pdb=" N ILE D 58 " pdb=" C ILE D 58 " pdb=" CB ILE D 58 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE D 93 " pdb=" N ILE D 93 " pdb=" C ILE D 93 " pdb=" CB ILE D 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA VAL I 31 " pdb=" N VAL I 31 " pdb=" C VAL I 31 " pdb=" CB VAL I 31 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 2814 not shown) Planarity restraints: 3251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS I 172 " -0.027 2.00e-02 2.50e+03 5.37e-02 2.88e+01 pdb=" C LYS I 172 " 0.093 2.00e-02 2.50e+03 pdb=" O LYS I 172 " -0.035 2.00e-02 2.50e+03 pdb=" N PHE I 173 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA F 40 " -0.073 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO F 41 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO F 41 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO F 41 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 106 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO D 107 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 107 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 107 " 0.028 5.00e-02 4.00e+02 ... (remaining 3248 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 58 2.41 - 3.03: 11629 3.03 - 3.65: 27455 3.65 - 4.28: 40609 4.28 - 4.90: 70071 Nonbonded interactions: 149822 Sorted by model distance: nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU E 58 " model vdw 1.785 3.040 nonbonded pdb=" OE2 GLU A 266 " pdb=" OG1 THR C 48 " model vdw 1.899 3.040 nonbonded pdb=" O ALA I 242 " pdb=" OG SER I 246 " model vdw 1.974 3.040 nonbonded pdb=" OD2 ASP D 163 " pdb=" OG1 THR D 165 " model vdw 2.081 3.040 nonbonded pdb=" NE2 GLN D 75 " pdb=" O VAL D 100 " model vdw 2.188 3.120 ... (remaining 149817 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' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'P' } ncs_group { reference = (chain 'I' and (resid 31 through 173 or resid 178 through 481)) selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.210 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: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 18.410 Find NCS groups from input model: 0.280 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5232 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 : 0.003 0.132 18905 Z= 0.116 Angle : 0.505 10.793 25597 Z= 0.283 Chirality : 0.037 0.133 2817 Planarity : 0.004 0.103 3251 Dihedral : 15.904 88.026 6803 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.91 % Favored : 96.92 % Rotamer: Outliers : 0.40 % Allowed : 17.19 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.91 (0.18), residues: 2270 helix: 3.33 (0.17), residues: 915 sheet: 0.82 (0.25), residues: 452 loop : -0.76 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 20 TYR 0.021 0.001 TYR R 191 PHE 0.015 0.001 PHE C 196 TRP 0.011 0.001 TRP I 164 HIS 0.003 0.000 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00251 (18893) covalent geometry : angle 0.50331 (25573) SS BOND : bond 0.00567 ( 12) SS BOND : angle 1.58495 ( 24) hydrogen bonds : bond 0.16588 ( 987) hydrogen bonds : angle 5.84100 ( 2847) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 646 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASN cc_start: 0.7348 (t0) cc_final: 0.7126 (t0) REVERT: A 238 ASN cc_start: 0.7077 (m-40) cc_final: 0.6716 (m-40) REVERT: A 308 ILE cc_start: 0.8531 (mt) cc_final: 0.8297 (mt) REVERT: B 16 ASN cc_start: 0.7383 (m-40) cc_final: 0.7050 (m110) REVERT: B 146 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7403 (tp) REVERT: B 237 ASN cc_start: 0.6806 (p0) cc_final: 0.6257 (t0) REVERT: C 263 LEU cc_start: 0.7316 (mp) cc_final: 0.6742 (mp) REVERT: D 192 LEU cc_start: 0.5644 (OUTLIER) cc_final: 0.5435 (mm) REVERT: D 232 ILE cc_start: 0.5833 (tt) cc_final: 0.5394 (mt) REVERT: E 38 MET cc_start: 0.5122 (mmp) cc_final: 0.4792 (mmp) REVERT: F 126 VAL cc_start: 0.6441 (t) cc_final: 0.6051 (t) REVERT: H 5 ILE cc_start: 0.6292 (mt) cc_final: 0.5454 (mt) REVERT: I 457 ILE cc_start: 0.7930 (mm) cc_final: 0.7641 (mm) REVERT: R 403 TYR cc_start: 0.5343 (m-80) cc_final: 0.4915 (m-80) outliers start: 8 outliers final: 0 residues processed: 651 average time/residue: 0.1790 time to fit residues: 165.9340 Evaluate side-chains 481 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 479 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain D residue 192 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.0070 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN C 28 GLN C 43 ASN D 13 GLN ** D 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 HIS F 31 ASN H 9 HIS H 14 HIS H 16 ASN ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 HIS ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 448 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.167781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.143028 restraints weight = 34645.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.147932 restraints weight = 17409.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.151077 restraints weight = 10411.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.153109 restraints weight = 7032.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.154516 restraints weight = 5231.127| |-----------------------------------------------------------------------------| r_work (final): 0.4498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18905 Z= 0.152 Angle : 0.670 10.380 25597 Z= 0.349 Chirality : 0.044 0.285 2817 Planarity : 0.005 0.065 3251 Dihedral : 4.276 44.753 2540 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.35 % Favored : 96.48 % Rotamer: Outliers : 3.97 % Allowed : 22.01 % Favored : 74.02 % 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: 1.50 (0.18), residues: 2270 helix: 2.79 (0.16), residues: 903 sheet: 0.81 (0.25), residues: 432 loop : -0.77 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 43 TYR 0.035 0.002 TYR I 320 PHE 0.033 0.002 PHE I 291 TRP 0.015 0.002 TRP R 154 HIS 0.010 0.001 HIS D 62 Details of bonding type rmsd covalent geometry : bond 0.00322 (18893) covalent geometry : angle 0.66898 (25573) SS BOND : bond 0.00258 ( 12) SS BOND : angle 1.16044 ( 24) hydrogen bonds : bond 0.04553 ( 987) hydrogen bonds : angle 4.47838 ( 2847) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 538 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8389 (mm-40) REVERT: A 198 MET cc_start: 0.7253 (tpp) cc_final: 0.6909 (tpp) REVERT: A 337 GLU cc_start: 0.7216 (mp0) cc_final: 0.6111 (mp0) REVERT: B 17 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7565 (pp30) REVERT: B 124 TYR cc_start: 0.4366 (m-80) cc_final: 0.4074 (m-10) REVERT: B 160 SER cc_start: 0.8099 (t) cc_final: 0.7456 (p) REVERT: B 184 THR cc_start: 0.6773 (OUTLIER) cc_final: 0.6231 (t) REVERT: B 187 VAL cc_start: 0.7723 (t) cc_final: 0.7451 (p) REVERT: C 17 LYS cc_start: 0.8448 (mmtp) cc_final: 0.8198 (mmtp) REVERT: C 267 LYS cc_start: 0.8018 (mttp) cc_final: 0.7797 (mttp) REVERT: D 55 LEU cc_start: 0.7044 (mp) cc_final: 0.6468 (mp) REVERT: D 62 HIS cc_start: 0.6729 (t70) cc_final: 0.6439 (t70) REVERT: D 217 MET cc_start: 0.5665 (ptm) cc_final: 0.5379 (ptm) REVERT: D 232 ILE cc_start: 0.6908 (tt) cc_final: 0.6575 (mt) REVERT: D 289 TYR cc_start: 0.6546 (m-80) cc_final: 0.6325 (m-80) REVERT: E 17 GLU cc_start: 0.7799 (tp30) cc_final: 0.7444 (tp30) REVERT: E 38 MET cc_start: 0.5701 (mmp) cc_final: 0.5402 (mmp) REVERT: F 86 LEU cc_start: 0.7865 (tp) cc_final: 0.7665 (tp) REVERT: F 90 ASP cc_start: 0.6598 (m-30) cc_final: 0.6366 (m-30) REVERT: G 38 MET cc_start: 0.7708 (mmm) cc_final: 0.7386 (mtt) REVERT: I 425 MET cc_start: 0.3988 (tmm) cc_final: 0.3503 (tmm) REVERT: I 457 ILE cc_start: 0.8267 (mm) cc_final: 0.7947 (mm) REVERT: I 473 SER cc_start: 0.7999 (m) cc_final: 0.7742 (p) REVERT: R 40 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.6067 (tp) REVERT: R 186 ARG cc_start: 0.7470 (mtp180) cc_final: 0.7229 (mtp180) REVERT: R 191 TYR cc_start: 0.6088 (OUTLIER) cc_final: 0.5708 (p90) REVERT: R 401 GLN cc_start: 0.8215 (pm20) cc_final: 0.7557 (pm20) REVERT: R 405 LYS cc_start: 0.9066 (tptt) cc_final: 0.8472 (tptt) REVERT: R 425 MET cc_start: 0.5214 (ppp) cc_final: 0.4729 (ppp) REVERT: R 441 MET cc_start: 0.7229 (mmp) cc_final: 0.6678 (mmt) outliers start: 79 outliers final: 39 residues processed: 580 average time/residue: 0.1682 time to fit residues: 141.9543 Evaluate side-chains 515 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 473 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 16 ASN Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 232 LEU Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 238 PHE Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain R residue 336 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 4 optimal weight: 2.9990 chunk 213 optimal weight: 8.9990 chunk 187 optimal weight: 0.6980 chunk 145 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 0.0370 chunk 84 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 261 GLN B 16 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 28 GLN D 119 ASN D 259 GLN ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN G 44 HIS H 6 GLN H 10 ASN ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 ASN ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 10 ASN R 220 ASN R 223 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.155879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.131258 restraints weight = 34929.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.135572 restraints weight = 18006.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.138391 restraints weight = 10987.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.140248 restraints weight = 7550.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.141545 restraints weight = 5678.460| |-----------------------------------------------------------------------------| r_work (final): 0.4365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 18905 Z= 0.189 Angle : 0.692 8.484 25597 Z= 0.371 Chirality : 0.046 0.259 2817 Planarity : 0.005 0.078 3251 Dihedral : 4.526 30.278 2536 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.35 % Favored : 96.48 % Rotamer: Outliers : 5.03 % Allowed : 21.71 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 1.24 (0.18), residues: 2270 helix: 2.42 (0.16), residues: 905 sheet: 0.62 (0.24), residues: 432 loop : -0.71 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 256 TYR 0.021 0.002 TYR I 320 PHE 0.036 0.002 PHE I 447 TRP 0.025 0.002 TRP D 82 HIS 0.007 0.002 HIS I 216 Details of bonding type rmsd covalent geometry : bond 0.00417 (18893) covalent geometry : angle 0.69092 (25573) SS BOND : bond 0.00360 ( 12) SS BOND : angle 1.22219 ( 24) hydrogen bonds : bond 0.04729 ( 987) hydrogen bonds : angle 4.60585 ( 2847) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 590 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8609 (mttt) cc_final: 0.8209 (mtmt) REVERT: A 52 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8421 (mm-40) REVERT: A 250 ARG cc_start: 0.7199 (mmt-90) cc_final: 0.6836 (mmt-90) REVERT: A 310 ASP cc_start: 0.8068 (m-30) cc_final: 0.7708 (m-30) REVERT: A 337 GLU cc_start: 0.7769 (mp0) cc_final: 0.7166 (mp0) REVERT: A 359 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7421 (tt0) REVERT: B 9 GLN cc_start: 0.8940 (mm-40) cc_final: 0.8666 (mm-40) REVERT: B 68 ARG cc_start: 0.5313 (tpt-90) cc_final: 0.5024 (mmm160) REVERT: B 96 ARG cc_start: 0.7537 (mtm-85) cc_final: 0.7052 (ttm110) REVERT: B 237 ASN cc_start: 0.7921 (p0) cc_final: 0.7510 (p0) REVERT: B 307 VAL cc_start: 0.7207 (OUTLIER) cc_final: 0.6888 (t) REVERT: C 13 VAL cc_start: 0.8439 (t) cc_final: 0.7648 (t) REVERT: C 16 SER cc_start: 0.8715 (t) cc_final: 0.8362 (t) REVERT: C 17 LYS cc_start: 0.8601 (mmtp) cc_final: 0.8330 (mmtp) REVERT: C 20 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7569 (mm-30) REVERT: C 35 ARG cc_start: 0.6927 (mtt90) cc_final: 0.6717 (mtt180) REVERT: C 38 LEU cc_start: 0.8103 (tp) cc_final: 0.7822 (tp) REVERT: D 12 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8298 (mm-30) REVERT: D 62 HIS cc_start: 0.7114 (t70) cc_final: 0.5791 (t70) REVERT: D 99 TRP cc_start: 0.8174 (m100) cc_final: 0.7858 (m100) REVERT: D 150 ARG cc_start: 0.7220 (mmt-90) cc_final: 0.6556 (mmt180) REVERT: D 171 ILE cc_start: 0.4657 (OUTLIER) cc_final: 0.4162 (mm) REVERT: D 215 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7462 (pt0) REVERT: D 279 SER cc_start: 0.8492 (m) cc_final: 0.8287 (t) REVERT: D 293 ASN cc_start: 0.7521 (p0) cc_final: 0.7257 (p0) REVERT: D 325 MET cc_start: 0.5816 (mmm) cc_final: 0.5510 (mmt) REVERT: E 17 GLU cc_start: 0.8081 (tp30) cc_final: 0.7864 (tp30) REVERT: E 38 MET cc_start: 0.5821 (mmp) cc_final: 0.5529 (mmp) REVERT: F 29 PHE cc_start: 0.8129 (t80) cc_final: 0.7784 (t80) REVERT: F 33 LYS cc_start: 0.7755 (tttt) cc_final: 0.7538 (tmtt) REVERT: F 90 ASP cc_start: 0.6915 (m-30) cc_final: 0.6564 (m-30) REVERT: G 38 MET cc_start: 0.8176 (mmm) cc_final: 0.7708 (mmm) REVERT: I 42 HIS cc_start: 0.8391 (m170) cc_final: 0.8087 (m170) REVERT: I 425 MET cc_start: 0.4655 (tmm) cc_final: 0.3834 (tmm) REVERT: I 437 TRP cc_start: 0.5843 (t60) cc_final: 0.5238 (t60) REVERT: I 441 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.7165 (mmt) REVERT: I 473 SER cc_start: 0.7989 (m) cc_final: 0.7662 (p) REVERT: N 54 SER cc_start: 0.8283 (p) cc_final: 0.8081 (p) REVERT: R 189 MET cc_start: 0.7382 (ttp) cc_final: 0.7173 (tmm) REVERT: R 237 ILE cc_start: 0.8028 (tp) cc_final: 0.7772 (tt) REVERT: R 400 ARG cc_start: 0.8340 (mmm160) cc_final: 0.7361 (mmm160) REVERT: R 401 GLN cc_start: 0.8379 (pm20) cc_final: 0.7495 (pm20) REVERT: R 405 LYS cc_start: 0.9150 (tptt) cc_final: 0.8875 (tptt) REVERT: R 425 MET cc_start: 0.5066 (ppp) cc_final: 0.4488 (ppp) REVERT: R 466 VAL cc_start: 0.8854 (t) cc_final: 0.8629 (p) outliers start: 100 outliers final: 57 residues processed: 648 average time/residue: 0.1661 time to fit residues: 156.4860 Evaluate side-chains 597 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 537 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 107 CYS Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 154 TRP Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 237 ILE Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain I residue 334 VAL Chi-restraints excluded: chain I residue 387 THR Chi-restraints excluded: chain I residue 441 MET Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 238 PHE Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain R residue 336 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 137 optimal weight: 2.9990 chunk 146 optimal weight: 0.0170 chunk 109 optimal weight: 1.9990 chunk 194 optimal weight: 0.2980 chunk 88 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 83 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN C 22 GLN C 28 GLN D 119 ASN ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS H 16 ASN ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN R 220 ASN R 223 HIS R 438 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.156435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.131476 restraints weight = 34754.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.135873 restraints weight = 17991.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.138734 restraints weight = 11014.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.140635 restraints weight = 7571.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.141735 restraints weight = 5704.700| |-----------------------------------------------------------------------------| r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18905 Z= 0.137 Angle : 0.673 12.258 25597 Z= 0.349 Chirality : 0.044 0.249 2817 Planarity : 0.004 0.041 3251 Dihedral : 4.369 26.747 2536 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.13 % Favored : 96.70 % Rotamer: Outliers : 4.02 % Allowed : 25.28 % Favored : 70.70 % 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: 1.20 (0.18), residues: 2270 helix: 2.48 (0.16), residues: 903 sheet: 0.48 (0.24), residues: 440 loop : -0.78 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 15 TYR 0.028 0.002 TYR I 403 PHE 0.030 0.001 PHE I 447 TRP 0.028 0.002 TRP A 248 HIS 0.011 0.001 HIS I 216 Details of bonding type rmsd covalent geometry : bond 0.00295 (18893) covalent geometry : angle 0.67159 (25573) SS BOND : bond 0.00287 ( 12) SS BOND : angle 1.56643 ( 24) hydrogen bonds : bond 0.04234 ( 987) hydrogen bonds : angle 4.34192 ( 2847) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 578 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8623 (mttt) cc_final: 0.8210 (mtmt) REVERT: A 51 LYS cc_start: 0.7634 (tptt) cc_final: 0.7314 (tptt) REVERT: A 52 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8435 (mt0) REVERT: A 250 ARG cc_start: 0.7136 (mmt-90) cc_final: 0.6537 (mtp85) REVERT: A 310 ASP cc_start: 0.8041 (m-30) cc_final: 0.7628 (m-30) REVERT: A 337 GLU cc_start: 0.7826 (mp0) cc_final: 0.7526 (mp0) REVERT: A 359 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7402 (tt0) REVERT: B 9 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8745 (mm-40) REVERT: B 96 ARG cc_start: 0.7519 (mtm-85) cc_final: 0.7173 (mtm-85) REVERT: B 97 SER cc_start: 0.8327 (t) cc_final: 0.7977 (p) REVERT: B 137 ARG cc_start: 0.7617 (mtt180) cc_final: 0.7369 (mtt180) REVERT: B 237 ASN cc_start: 0.7574 (p0) cc_final: 0.7204 (p0) REVERT: C 13 VAL cc_start: 0.8557 (t) cc_final: 0.7710 (t) REVERT: C 17 LYS cc_start: 0.8539 (mmtp) cc_final: 0.8129 (mmtp) REVERT: C 25 LYS cc_start: 0.8878 (pttp) cc_final: 0.8547 (ptpp) REVERT: C 35 ARG cc_start: 0.6805 (mtt90) cc_final: 0.6603 (mtt180) REVERT: C 53 MET cc_start: 0.3835 (mmt) cc_final: 0.1990 (mmt) REVERT: C 215 PHE cc_start: 0.7062 (m-80) cc_final: 0.6298 (m-80) REVERT: C 267 LYS cc_start: 0.8353 (mttp) cc_final: 0.8078 (mttp) REVERT: C 360 LEU cc_start: 0.7955 (mt) cc_final: 0.7731 (mp) REVERT: D 62 HIS cc_start: 0.7223 (t70) cc_final: 0.5724 (t70) REVERT: D 150 ARG cc_start: 0.7222 (mmt-90) cc_final: 0.6223 (mmt180) REVERT: D 171 ILE cc_start: 0.4709 (OUTLIER) cc_final: 0.4231 (mm) REVERT: D 192 LEU cc_start: 0.7120 (mm) cc_final: 0.6915 (mp) REVERT: D 215 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7518 (pt0) REVERT: D 293 ASN cc_start: 0.7571 (p0) cc_final: 0.7280 (p0) REVERT: F 29 PHE cc_start: 0.8225 (t80) cc_final: 0.8000 (t80) REVERT: F 77 ASN cc_start: 0.6895 (t0) cc_final: 0.6580 (t0) REVERT: G 38 MET cc_start: 0.8294 (mmm) cc_final: 0.7932 (mmm) REVERT: I 42 HIS cc_start: 0.8397 (m170) cc_final: 0.8109 (m170) REVERT: I 216 HIS cc_start: 0.7294 (m-70) cc_final: 0.6257 (m-70) REVERT: I 352 TRP cc_start: 0.6600 (m-10) cc_final: 0.5748 (m-90) REVERT: I 425 MET cc_start: 0.4910 (tmm) cc_final: 0.4082 (tmm) REVERT: I 441 MET cc_start: 0.7776 (mmt) cc_final: 0.7174 (mmt) REVERT: I 469 GLU cc_start: 0.7438 (tp30) cc_final: 0.6504 (tp30) REVERT: N 54 SER cc_start: 0.8394 (p) cc_final: 0.8191 (p) REVERT: P 24 LEU cc_start: 0.4911 (OUTLIER) cc_final: 0.4624 (tt) REVERT: R 189 MET cc_start: 0.7459 (ttp) cc_final: 0.7080 (tmm) REVERT: R 379 ILE cc_start: 0.7512 (mm) cc_final: 0.7083 (tp) REVERT: R 405 LYS cc_start: 0.9224 (tptt) cc_final: 0.8896 (tptt) REVERT: R 425 MET cc_start: 0.5061 (ppp) cc_final: 0.4455 (ppp) REVERT: R 429 TYR cc_start: 0.6907 (m-80) cc_final: 0.6675 (m-80) REVERT: R 441 MET cc_start: 0.7604 (mmp) cc_final: 0.6913 (mmt) outliers start: 80 outliers final: 61 residues processed: 627 average time/residue: 0.1649 time to fit residues: 150.5472 Evaluate side-chains 608 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 545 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 107 CYS Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 154 TRP Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 237 ILE Chi-restraints excluded: chain I residue 457 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain R residue 238 PHE Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 385 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 73 optimal weight: 5.9990 chunk 69 optimal weight: 0.0170 chunk 175 optimal weight: 0.0970 chunk 172 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 193 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 chunk 213 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 0.0670 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN D 119 ASN ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN G 44 HIS ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 467 GLN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 307 HIS R 420 HIS ** R 438 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 = 0.4568 r_free = 0.4568 target = 0.157898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.132894 restraints weight = 35238.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.137069 restraints weight = 18847.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.139767 restraints weight = 11836.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.141606 restraints weight = 8334.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.142864 restraints weight = 6376.560| |-----------------------------------------------------------------------------| r_work (final): 0.4375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.6438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18905 Z= 0.133 Angle : 0.668 14.035 25597 Z= 0.345 Chirality : 0.044 0.278 2817 Planarity : 0.004 0.049 3251 Dihedral : 4.322 23.297 2536 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.17 % Favored : 96.70 % Rotamer: Outliers : 4.42 % Allowed : 27.19 % Favored : 68.39 % 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: 1.11 (0.18), residues: 2270 helix: 2.40 (0.16), residues: 902 sheet: 0.51 (0.25), residues: 424 loop : -0.84 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 19 TYR 0.024 0.001 TYR R 305 PHE 0.032 0.002 PHE N 29 TRP 0.033 0.002 TRP I 437 HIS 0.005 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00291 (18893) covalent geometry : angle 0.66714 (25573) SS BOND : bond 0.00228 ( 12) SS BOND : angle 1.49798 ( 24) hydrogen bonds : bond 0.04134 ( 987) hydrogen bonds : angle 4.28341 ( 2847) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 570 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.7548 (tptt) cc_final: 0.7216 (tptt) REVERT: A 224 VAL cc_start: 0.7716 (m) cc_final: 0.7469 (m) REVERT: A 310 ASP cc_start: 0.7960 (m-30) cc_final: 0.7583 (m-30) REVERT: A 359 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7375 (tt0) REVERT: B 8 ARG cc_start: 0.8353 (ptt-90) cc_final: 0.8106 (ptt-90) REVERT: B 9 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8715 (mm-40) REVERT: B 17 GLN cc_start: 0.8462 (tm-30) cc_final: 0.7744 (pp30) REVERT: B 96 ARG cc_start: 0.7457 (mtm-85) cc_final: 0.6906 (ttm110) REVERT: C 20 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7518 (mm-30) REVERT: C 53 MET cc_start: 0.3687 (mmt) cc_final: 0.2048 (mmt) REVERT: C 267 LYS cc_start: 0.8437 (mttp) cc_final: 0.8192 (mttp) REVERT: D 62 HIS cc_start: 0.7090 (t70) cc_final: 0.5797 (t70) REVERT: D 150 ARG cc_start: 0.7181 (mmt-90) cc_final: 0.6255 (mmt180) REVERT: D 171 ILE cc_start: 0.4715 (OUTLIER) cc_final: 0.4272 (mm) REVERT: D 293 ASN cc_start: 0.7603 (p0) cc_final: 0.7284 (p0) REVERT: F 29 PHE cc_start: 0.8231 (t80) cc_final: 0.7959 (t80) REVERT: F 77 ASN cc_start: 0.6758 (t0) cc_final: 0.6509 (t0) REVERT: G 38 MET cc_start: 0.8211 (mmm) cc_final: 0.7917 (mmm) REVERT: H 20 ARG cc_start: 0.6332 (ttm170) cc_final: 0.5695 (ttm170) REVERT: I 32 MET cc_start: 0.5315 (tmm) cc_final: 0.4858 (tmm) REVERT: I 42 HIS cc_start: 0.8406 (m170) cc_final: 0.8109 (m170) REVERT: I 156 LEU cc_start: 0.2128 (OUTLIER) cc_final: -0.1200 (tt) REVERT: I 164 TRP cc_start: 0.3849 (t60) cc_final: 0.3476 (t60) REVERT: I 352 TRP cc_start: 0.6629 (m-10) cc_final: 0.5936 (m-90) REVERT: I 425 MET cc_start: 0.4974 (tmm) cc_final: 0.4128 (tmm) REVERT: I 437 TRP cc_start: 0.5550 (t60) cc_final: 0.5301 (t60) REVERT: I 469 GLU cc_start: 0.7336 (tp30) cc_final: 0.6566 (tp30) REVERT: I 472 LYS cc_start: 0.8527 (tmmt) cc_final: 0.8004 (tmmt) REVERT: I 476 ARG cc_start: 0.8291 (tmm160) cc_final: 0.8066 (tmm160) REVERT: N 54 SER cc_start: 0.8354 (p) cc_final: 0.8126 (p) REVERT: R 189 MET cc_start: 0.7381 (ttp) cc_final: 0.7082 (tmm) REVERT: R 214 ARG cc_start: 0.7424 (tmt170) cc_final: 0.6717 (tmt170) REVERT: R 379 ILE cc_start: 0.7660 (mm) cc_final: 0.7366 (tp) REVERT: R 400 ARG cc_start: 0.8138 (mmm160) cc_final: 0.7652 (mmm160) REVERT: R 404 ARG cc_start: 0.8245 (ptp90) cc_final: 0.7943 (ptp90) REVERT: R 405 LYS cc_start: 0.9159 (tptt) cc_final: 0.8872 (tptt) REVERT: R 425 MET cc_start: 0.4923 (ppp) cc_final: 0.4281 (ppp) REVERT: R 429 TYR cc_start: 0.6999 (m-80) cc_final: 0.6706 (m-80) REVERT: R 441 MET cc_start: 0.7620 (mmp) cc_final: 0.6915 (mmt) REVERT: R 444 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7364 (mm-30) REVERT: R 469 GLU cc_start: 0.6558 (mm-30) cc_final: 0.6340 (mm-30) outliers start: 88 outliers final: 66 residues processed: 623 average time/residue: 0.1480 time to fit residues: 134.2462 Evaluate side-chains 618 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 550 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 329 HIS Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 107 CYS Chi-restraints excluded: chain F residue 115 TYR Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 9 HIS Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 154 TRP Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 237 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain R residue 225 HIS Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 238 PHE Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 385 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 184 optimal weight: 0.9980 chunk 142 optimal weight: 0.0980 chunk 152 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 168 optimal weight: 0.9980 chunk 133 optimal weight: 0.4980 chunk 181 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN D 142 HIS ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN G 44 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN P 10 ASN R 220 ASN R 307 HIS R 438 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.155369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.130487 restraints weight = 35372.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.134583 restraints weight = 18996.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.137288 restraints weight = 11970.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.139071 restraints weight = 8429.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.140324 restraints weight = 6453.854| |-----------------------------------------------------------------------------| r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.6964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18905 Z= 0.153 Angle : 0.682 13.220 25597 Z= 0.356 Chirality : 0.045 0.315 2817 Planarity : 0.004 0.052 3251 Dihedral : 4.385 21.877 2536 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.79 % Favored : 96.08 % Rotamer: Outliers : 5.08 % Allowed : 27.19 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.99 (0.18), residues: 2270 helix: 2.28 (0.16), residues: 902 sheet: 0.44 (0.24), residues: 432 loop : -0.89 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 15 TYR 0.024 0.002 TYR R 305 PHE 0.027 0.002 PHE I 447 TRP 0.033 0.002 TRP D 99 HIS 0.015 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00335 (18893) covalent geometry : angle 0.68120 (25573) SS BOND : bond 0.00445 ( 12) SS BOND : angle 1.37106 ( 24) hydrogen bonds : bond 0.04193 ( 987) hydrogen bonds : angle 4.29728 ( 2847) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 574 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8467 (mttt) cc_final: 0.8085 (mtmt) REVERT: A 51 LYS cc_start: 0.7538 (tptt) cc_final: 0.7306 (tptt) REVERT: A 247 ARG cc_start: 0.7279 (tpp-160) cc_final: 0.6928 (tpp-160) REVERT: A 310 ASP cc_start: 0.7916 (m-30) cc_final: 0.7528 (m-30) REVERT: A 347 ARG cc_start: 0.7931 (tpp-160) cc_final: 0.7558 (tpp-160) REVERT: A 357 GLN cc_start: 0.8373 (tp-100) cc_final: 0.8146 (tp-100) REVERT: A 359 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7429 (tt0) REVERT: B 8 ARG cc_start: 0.8349 (ptt-90) cc_final: 0.8085 (ptt-90) REVERT: B 9 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8713 (mm-40) REVERT: B 27 ASP cc_start: 0.5168 (m-30) cc_final: 0.4658 (p0) REVERT: B 68 ARG cc_start: 0.5421 (tpt-90) cc_final: 0.5172 (mmm160) REVERT: B 96 ARG cc_start: 0.7430 (mtm-85) cc_final: 0.6907 (ttm110) REVERT: C 17 LYS cc_start: 0.8448 (mmtp) cc_final: 0.8145 (mmtp) REVERT: C 20 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7578 (mm-30) REVERT: C 53 MET cc_start: 0.3863 (mmt) cc_final: 0.2736 (mmt) REVERT: C 267 LYS cc_start: 0.8505 (mttp) cc_final: 0.8261 (mttp) REVERT: C 360 LEU cc_start: 0.7946 (mt) cc_final: 0.7737 (mp) REVERT: D 6 GLN cc_start: 0.8204 (pm20) cc_final: 0.7224 (pm20) REVERT: D 62 HIS cc_start: 0.7110 (t70) cc_final: 0.5876 (t70) REVERT: D 150 ARG cc_start: 0.7164 (mmt-90) cc_final: 0.6283 (mmt180) REVERT: D 171 ILE cc_start: 0.4758 (OUTLIER) cc_final: 0.4339 (mm) REVERT: D 262 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6855 (mpp) REVERT: D 293 ASN cc_start: 0.7692 (p0) cc_final: 0.7361 (p0) REVERT: F 29 PHE cc_start: 0.8246 (t80) cc_final: 0.8031 (t80) REVERT: F 77 ASN cc_start: 0.6686 (t0) cc_final: 0.6373 (t0) REVERT: G 14 LYS cc_start: 0.8835 (pttp) cc_final: 0.8480 (pttm) REVERT: G 38 MET cc_start: 0.8255 (mmm) cc_final: 0.7818 (mmm) REVERT: H 20 ARG cc_start: 0.6302 (ttm170) cc_final: 0.5639 (ttm170) REVERT: I 32 MET cc_start: 0.5320 (tmm) cc_final: 0.4775 (tmm) REVERT: I 42 HIS cc_start: 0.8458 (m170) cc_final: 0.8147 (m170) REVERT: I 156 LEU cc_start: 0.2181 (OUTLIER) cc_final: -0.0620 (tt) REVERT: I 164 TRP cc_start: 0.4042 (t60) cc_final: 0.3683 (t60) REVERT: I 218 THR cc_start: 0.7662 (OUTLIER) cc_final: 0.7341 (t) REVERT: I 348 ASN cc_start: 0.7268 (t0) cc_final: 0.7031 (t0) REVERT: I 352 TRP cc_start: 0.6779 (m-10) cc_final: 0.6229 (m-90) REVERT: I 425 MET cc_start: 0.5097 (tmm) cc_final: 0.4196 (tmm) REVERT: I 469 GLU cc_start: 0.7383 (tp30) cc_final: 0.6452 (tp30) REVERT: I 472 LYS cc_start: 0.8645 (tmmt) cc_final: 0.8069 (tmmt) REVERT: N 11 LEU cc_start: 0.7760 (tp) cc_final: 0.7552 (tp) REVERT: P 24 LEU cc_start: 0.4980 (OUTLIER) cc_final: 0.4699 (tt) REVERT: R 189 MET cc_start: 0.7397 (ttp) cc_final: 0.7118 (tmm) REVERT: R 214 ARG cc_start: 0.7441 (tmt170) cc_final: 0.6850 (tmt170) REVERT: R 379 ILE cc_start: 0.7755 (mm) cc_final: 0.7534 (tp) REVERT: R 385 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8334 (tt) REVERT: R 400 ARG cc_start: 0.8076 (mmm160) cc_final: 0.7428 (mmm160) REVERT: R 404 ARG cc_start: 0.8273 (ptp90) cc_final: 0.7916 (ptt-90) REVERT: R 405 LYS cc_start: 0.9191 (tptt) cc_final: 0.8843 (tptt) REVERT: R 425 MET cc_start: 0.4900 (ppp) cc_final: 0.4272 (ppp) REVERT: R 429 TYR cc_start: 0.7042 (m-80) cc_final: 0.6507 (m-80) REVERT: R 469 GLU cc_start: 0.6656 (mm-30) cc_final: 0.6415 (mm-30) outliers start: 101 outliers final: 69 residues processed: 629 average time/residue: 0.1524 time to fit residues: 138.9029 Evaluate side-chains 623 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 548 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 56 TYR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 107 CYS Chi-restraints excluded: chain F residue 115 TYR Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 9 HIS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 154 TRP Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 237 ILE Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain R residue 225 HIS Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 238 PHE Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 389 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 194 optimal weight: 0.2980 chunk 169 optimal weight: 2.9990 chunk 204 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 177 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 HIS ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS H 16 ASN ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 451 GLN N 3 GLN R 307 HIS ** R 463 ASN ** 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 = 0.4515 r_free = 0.4515 target = 0.153227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.128322 restraints weight = 35687.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.132358 restraints weight = 19199.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.135030 restraints weight = 12119.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.136744 restraints weight = 8559.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.138005 restraints weight = 6606.302| |-----------------------------------------------------------------------------| r_work (final): 0.4320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.7433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18905 Z= 0.159 Angle : 0.716 13.941 25597 Z= 0.372 Chirality : 0.045 0.287 2817 Planarity : 0.004 0.044 3251 Dihedral : 4.462 21.876 2536 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.66 % Favored : 96.21 % Rotamer: Outliers : 5.18 % Allowed : 28.84 % Favored : 65.98 % 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: 0.85 (0.18), residues: 2270 helix: 2.15 (0.17), residues: 903 sheet: 0.30 (0.25), residues: 436 loop : -0.91 (0.21), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 15 TYR 0.027 0.002 TYR I 443 PHE 0.046 0.002 PHE B 199 TRP 0.057 0.002 TRP I 437 HIS 0.009 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00360 (18893) covalent geometry : angle 0.71466 (25573) SS BOND : bond 0.00345 ( 12) SS BOND : angle 1.37516 ( 24) hydrogen bonds : bond 0.04259 ( 987) hydrogen bonds : angle 4.35037 ( 2847) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 591 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8529 (mttt) cc_final: 0.8059 (mtmt) REVERT: A 29 VAL cc_start: 0.9056 (m) cc_final: 0.8819 (p) REVERT: A 51 LYS cc_start: 0.7692 (tptt) cc_final: 0.7422 (tptt) REVERT: A 186 GLU cc_start: 0.7606 (pm20) cc_final: 0.7142 (pm20) REVERT: A 229 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6748 (t70) REVERT: A 247 ARG cc_start: 0.7208 (tpp-160) cc_final: 0.6789 (tpp-160) REVERT: A 310 ASP cc_start: 0.7922 (m-30) cc_final: 0.7510 (m-30) REVERT: A 325 TYR cc_start: 0.6522 (t80) cc_final: 0.6247 (t80) REVERT: A 337 GLU cc_start: 0.8060 (mp0) cc_final: 0.7753 (mp0) REVERT: A 359 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7461 (tt0) REVERT: B 9 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8805 (mm-40) REVERT: B 27 ASP cc_start: 0.5148 (m-30) cc_final: 0.4614 (p0) REVERT: B 62 HIS cc_start: 0.7183 (t-90) cc_final: 0.6923 (t-90) REVERT: B 68 ARG cc_start: 0.5624 (tpt-90) cc_final: 0.5399 (mmm160) REVERT: B 96 ARG cc_start: 0.7331 (mtm-85) cc_final: 0.6912 (ttm110) REVERT: C 17 LYS cc_start: 0.8510 (mmtp) cc_final: 0.8238 (mmtp) REVERT: C 20 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7671 (mm-30) REVERT: C 27 LYS cc_start: 0.8035 (ttmm) cc_final: 0.7800 (ttmm) REVERT: C 53 MET cc_start: 0.4544 (mmt) cc_final: 0.3575 (mmt) REVERT: C 227 SER cc_start: 0.8624 (p) cc_final: 0.8344 (t) REVERT: C 267 LYS cc_start: 0.8497 (mttp) cc_final: 0.8244 (mttp) REVERT: C 316 SER cc_start: 0.8292 (t) cc_final: 0.8081 (p) REVERT: D 6 GLN cc_start: 0.8276 (pm20) cc_final: 0.7159 (pm20) REVERT: D 59 TYR cc_start: 0.7528 (OUTLIER) cc_final: 0.7249 (m-80) REVERT: D 62 HIS cc_start: 0.7081 (t70) cc_final: 0.5785 (t70) REVERT: D 150 ARG cc_start: 0.7119 (mmt-90) cc_final: 0.6237 (mmt180) REVERT: D 151 PHE cc_start: 0.6810 (m-80) cc_final: 0.6506 (m-80) REVERT: D 176 GLN cc_start: 0.8169 (mp10) cc_final: 0.7612 (mt0) REVERT: D 293 ASN cc_start: 0.7854 (p0) cc_final: 0.7539 (p0) REVERT: F 29 PHE cc_start: 0.8213 (t80) cc_final: 0.8000 (t80) REVERT: F 63 SER cc_start: 0.7814 (m) cc_final: 0.7567 (t) REVERT: G 14 LYS cc_start: 0.8871 (pttp) cc_final: 0.8508 (pttm) REVERT: G 38 MET cc_start: 0.8293 (mmm) cc_final: 0.7853 (mmm) REVERT: H 20 ARG cc_start: 0.6376 (ttm170) cc_final: 0.5677 (ttm170) REVERT: I 32 MET cc_start: 0.5077 (tmm) cc_final: 0.4649 (tmm) REVERT: I 42 HIS cc_start: 0.8504 (m170) cc_final: 0.8162 (m170) REVERT: I 156 LEU cc_start: 0.2440 (OUTLIER) cc_final: 0.0317 (tt) REVERT: I 164 TRP cc_start: 0.4265 (t60) cc_final: 0.3933 (t60) REVERT: I 352 TRP cc_start: 0.6883 (m-10) cc_final: 0.6427 (m-90) REVERT: I 380 ASN cc_start: 0.6954 (t0) cc_final: 0.6693 (t0) REVERT: I 425 MET cc_start: 0.5208 (tmm) cc_final: 0.4242 (tmm) REVERT: I 457 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.7700 (mm) REVERT: P 24 LEU cc_start: 0.4985 (OUTLIER) cc_final: 0.4713 (tt) REVERT: R 32 MET cc_start: 0.7242 (tmm) cc_final: 0.6638 (tmm) REVERT: R 36 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8348 (mp0) REVERT: R 189 MET cc_start: 0.7424 (ttp) cc_final: 0.7148 (tmm) REVERT: R 214 ARG cc_start: 0.7534 (tmt170) cc_final: 0.6919 (tmt170) REVERT: R 379 ILE cc_start: 0.7793 (mm) cc_final: 0.7589 (tp) REVERT: R 385 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8270 (tt) REVERT: R 400 ARG cc_start: 0.8068 (mmm160) cc_final: 0.7408 (mmm160) REVERT: R 404 ARG cc_start: 0.8299 (ptp90) cc_final: 0.7979 (ptt-90) REVERT: R 405 LYS cc_start: 0.9201 (tptt) cc_final: 0.8777 (tptt) REVERT: R 425 MET cc_start: 0.4915 (OUTLIER) cc_final: 0.4248 (ppp) REVERT: R 429 TYR cc_start: 0.7028 (m-80) cc_final: 0.6623 (m-80) REVERT: R 441 MET cc_start: 0.7681 (mmp) cc_final: 0.7018 (mmt) REVERT: R 444 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7695 (mm-30) REVERT: R 449 SER cc_start: 0.7816 (OUTLIER) cc_final: 0.7452 (p) REVERT: R 465 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7487 (mt-10) REVERT: R 469 GLU cc_start: 0.6724 (mm-30) cc_final: 0.6418 (mm-30) outliers start: 103 outliers final: 75 residues processed: 655 average time/residue: 0.1420 time to fit residues: 135.3686 Evaluate side-chains 649 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 566 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 107 CYS Chi-restraints excluded: chain F residue 115 TYR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 9 HIS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 117 CYS Chi-restraints excluded: chain I residue 154 TRP Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 311 PHE Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 436 LEU Chi-restraints excluded: chain I residue 457 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 238 PHE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 425 MET Chi-restraints excluded: chain R residue 449 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 58 optimal weight: 0.5980 chunk 134 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS B 183 HIS D 119 ASN D 142 HIS ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 216 HIS R 307 HIS ** R 463 ASN ** 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 = 0.4495 r_free = 0.4495 target = 0.151352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.126604 restraints weight = 35375.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.130612 restraints weight = 19113.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.133260 restraints weight = 12077.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.134984 restraints weight = 8517.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.136223 restraints weight = 6552.820| |-----------------------------------------------------------------------------| r_work (final): 0.4300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.7889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18905 Z= 0.163 Angle : 0.747 14.298 25597 Z= 0.388 Chirality : 0.046 0.285 2817 Planarity : 0.004 0.049 3251 Dihedral : 4.566 21.194 2536 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 4.92 % Allowed : 29.70 % Favored : 65.38 % 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: 0.74 (0.18), residues: 2270 helix: 1.99 (0.17), residues: 917 sheet: 0.24 (0.25), residues: 436 loop : -0.94 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 8 TYR 0.026 0.002 TYR I 443 PHE 0.038 0.002 PHE B 199 TRP 0.047 0.002 TRP I 437 HIS 0.008 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00367 (18893) covalent geometry : angle 0.74582 (25573) SS BOND : bond 0.00327 ( 12) SS BOND : angle 1.34166 ( 24) hydrogen bonds : bond 0.04338 ( 987) hydrogen bonds : angle 4.43516 ( 2847) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 573 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8532 (mttt) cc_final: 0.8156 (mtmt) REVERT: A 51 LYS cc_start: 0.7798 (tptt) cc_final: 0.7575 (tptt) REVERT: A 186 GLU cc_start: 0.7624 (pm20) cc_final: 0.7239 (pm20) REVERT: A 204 GLN cc_start: 0.8058 (tp-100) cc_final: 0.7680 (tp-100) REVERT: A 229 ASP cc_start: 0.7059 (OUTLIER) cc_final: 0.6785 (t70) REVERT: A 247 ARG cc_start: 0.7169 (tpp-160) cc_final: 0.6813 (tpp-160) REVERT: A 255 ILE cc_start: 0.8897 (mp) cc_final: 0.8673 (mt) REVERT: A 310 ASP cc_start: 0.7869 (m-30) cc_final: 0.7474 (m-30) REVERT: A 325 TYR cc_start: 0.6650 (t80) cc_final: 0.6423 (t80) REVERT: A 357 GLN cc_start: 0.8382 (tp-100) cc_final: 0.8162 (tp-100) REVERT: B 9 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8821 (mm-40) REVERT: B 96 ARG cc_start: 0.7320 (mtm-85) cc_final: 0.6901 (ttm110) REVERT: C 17 LYS cc_start: 0.8402 (mmtp) cc_final: 0.8170 (mmtp) REVERT: C 20 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7684 (mm-30) REVERT: C 53 MET cc_start: 0.4469 (mmt) cc_final: 0.3577 (mmt) REVERT: C 214 CYS cc_start: 0.7022 (p) cc_final: 0.6222 (t) REVERT: C 241 LYS cc_start: 0.7458 (tttp) cc_final: 0.7241 (tttp) REVERT: C 316 SER cc_start: 0.8267 (t) cc_final: 0.8045 (p) REVERT: D 59 TYR cc_start: 0.7578 (OUTLIER) cc_final: 0.7260 (m-80) REVERT: D 62 HIS cc_start: 0.7105 (t70) cc_final: 0.5823 (t70) REVERT: D 82 TRP cc_start: 0.7687 (m100) cc_final: 0.7256 (m100) REVERT: D 150 ARG cc_start: 0.7144 (mmt-90) cc_final: 0.6265 (mmt180) REVERT: D 151 PHE cc_start: 0.6865 (m-80) cc_final: 0.6574 (m-80) REVERT: D 176 GLN cc_start: 0.8149 (mp10) cc_final: 0.7606 (mt0) REVERT: D 293 ASN cc_start: 0.7948 (p0) cc_final: 0.7620 (p0) REVERT: F 29 PHE cc_start: 0.8265 (t80) cc_final: 0.8032 (t80) REVERT: F 63 SER cc_start: 0.7904 (m) cc_final: 0.7646 (t) REVERT: G 14 LYS cc_start: 0.8870 (pttp) cc_final: 0.8514 (pttm) REVERT: G 38 MET cc_start: 0.8295 (mmm) cc_final: 0.7837 (mmm) REVERT: H 20 ARG cc_start: 0.6336 (ttm170) cc_final: 0.5629 (ttm170) REVERT: I 32 MET cc_start: 0.5083 (tmm) cc_final: 0.4633 (tmm) REVERT: I 42 HIS cc_start: 0.8473 (m170) cc_final: 0.8166 (m170) REVERT: I 156 LEU cc_start: 0.2157 (OUTLIER) cc_final: 0.0056 (tt) REVERT: I 164 TRP cc_start: 0.4218 (t60) cc_final: 0.3928 (t60) REVERT: I 228 LEU cc_start: 0.7673 (tt) cc_final: 0.7304 (tp) REVERT: I 346 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6723 (tt) REVERT: I 352 TRP cc_start: 0.6879 (m-10) cc_final: 0.6573 (m-90) REVERT: I 380 ASN cc_start: 0.7064 (t0) cc_final: 0.6856 (t0) REVERT: I 425 MET cc_start: 0.5288 (tmm) cc_final: 0.4232 (tmm) REVERT: I 469 GLU cc_start: 0.7608 (tp30) cc_final: 0.7120 (tp30) REVERT: I 472 LYS cc_start: 0.8632 (tmmt) cc_final: 0.8344 (tmmt) REVERT: P 24 LEU cc_start: 0.4955 (OUTLIER) cc_final: 0.4677 (tt) REVERT: R 32 MET cc_start: 0.7236 (tmm) cc_final: 0.6613 (tmm) REVERT: R 189 MET cc_start: 0.7449 (ttp) cc_final: 0.7193 (tmm) REVERT: R 214 ARG cc_start: 0.7566 (tmt170) cc_final: 0.7118 (tmt170) REVERT: R 400 ARG cc_start: 0.8043 (mmm160) cc_final: 0.7841 (mmm160) REVERT: R 405 LYS cc_start: 0.9197 (tptt) cc_final: 0.8783 (tptt) REVERT: R 425 MET cc_start: 0.4965 (OUTLIER) cc_final: 0.4266 (ppp) REVERT: R 429 TYR cc_start: 0.7026 (m-80) cc_final: 0.6555 (m-80) REVERT: R 441 MET cc_start: 0.7731 (mmp) cc_final: 0.7179 (mmt) REVERT: R 469 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6420 (mm-30) outliers start: 98 outliers final: 73 residues processed: 630 average time/residue: 0.1453 time to fit residues: 132.6402 Evaluate side-chains 623 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 544 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 56 TYR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 358 TYR Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 107 CYS Chi-restraints excluded: chain F residue 115 TYR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 9 HIS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 117 CYS Chi-restraints excluded: chain I residue 154 TRP Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 202 LEU Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 311 PHE Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 436 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 238 PHE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 110 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 165 optimal weight: 0.0970 chunk 100 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 HIS ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 HIS ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS H 16 ASN ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.151183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.126244 restraints weight = 35794.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.130289 restraints weight = 19183.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.132960 restraints weight = 12071.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.134758 restraints weight = 8491.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.135989 restraints weight = 6483.480| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.8183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18905 Z= 0.162 Angle : 0.783 14.131 25597 Z= 0.407 Chirality : 0.047 0.283 2817 Planarity : 0.004 0.047 3251 Dihedral : 4.609 22.071 2536 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.81 % Rotamer: Outliers : 4.17 % Allowed : 30.90 % Favored : 64.92 % 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: 0.66 (0.18), residues: 2270 helix: 2.00 (0.17), residues: 899 sheet: 0.14 (0.25), residues: 430 loop : -0.97 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 15 TYR 0.024 0.002 TYR I 443 PHE 0.037 0.002 PHE B 199 TRP 0.052 0.002 TRP I 437 HIS 0.005 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00367 (18893) covalent geometry : angle 0.78213 (25573) SS BOND : bond 0.00314 ( 12) SS BOND : angle 1.28688 ( 24) hydrogen bonds : bond 0.04408 ( 987) hydrogen bonds : angle 4.48694 ( 2847) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 565 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8619 (mttt) cc_final: 0.8280 (mtmt) REVERT: A 51 LYS cc_start: 0.7971 (tptt) cc_final: 0.7744 (tptt) REVERT: A 186 GLU cc_start: 0.7658 (pm20) cc_final: 0.7321 (pm20) REVERT: A 204 GLN cc_start: 0.8127 (tp-100) cc_final: 0.7677 (tp-100) REVERT: A 247 ARG cc_start: 0.7218 (tpp-160) cc_final: 0.6781 (tpp-160) REVERT: A 255 ILE cc_start: 0.8941 (mp) cc_final: 0.8729 (mt) REVERT: A 306 TYR cc_start: 0.7944 (m-80) cc_final: 0.7475 (m-80) REVERT: A 325 TYR cc_start: 0.6734 (t80) cc_final: 0.6502 (t80) REVERT: B 96 ARG cc_start: 0.7316 (mtm-85) cc_final: 0.6898 (ttm110) REVERT: B 143 THR cc_start: 0.8257 (p) cc_final: 0.8028 (t) REVERT: C 17 LYS cc_start: 0.8379 (mmtp) cc_final: 0.8106 (mmtp) REVERT: C 20 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7569 (mm-30) REVERT: C 23 LEU cc_start: 0.8900 (mt) cc_final: 0.8673 (mt) REVERT: C 53 MET cc_start: 0.4629 (mmt) cc_final: 0.3826 (mmt) REVERT: C 214 CYS cc_start: 0.6901 (p) cc_final: 0.6188 (t) REVERT: C 241 LYS cc_start: 0.7484 (tttp) cc_final: 0.7233 (tttp) REVERT: C 316 SER cc_start: 0.8229 (t) cc_final: 0.7936 (p) REVERT: D 59 TYR cc_start: 0.7615 (OUTLIER) cc_final: 0.7318 (m-80) REVERT: D 62 HIS cc_start: 0.7121 (t70) cc_final: 0.5731 (t70) REVERT: D 82 TRP cc_start: 0.7695 (m100) cc_final: 0.7289 (m100) REVERT: D 150 ARG cc_start: 0.7164 (mmt-90) cc_final: 0.6313 (mmt180) REVERT: D 151 PHE cc_start: 0.6960 (m-80) cc_final: 0.6690 (m-80) REVERT: D 176 GLN cc_start: 0.8172 (mp10) cc_final: 0.7651 (mt0) REVERT: D 293 ASN cc_start: 0.7973 (p0) cc_final: 0.7628 (p0) REVERT: F 29 PHE cc_start: 0.8304 (t80) cc_final: 0.8045 (t80) REVERT: F 63 SER cc_start: 0.7916 (m) cc_final: 0.7638 (t) REVERT: G 14 LYS cc_start: 0.9014 (pttp) cc_final: 0.8653 (pttm) REVERT: G 38 MET cc_start: 0.8363 (mmm) cc_final: 0.7890 (mmm) REVERT: G 52 THR cc_start: 0.7459 (OUTLIER) cc_final: 0.7207 (t) REVERT: H 20 ARG cc_start: 0.6330 (ttm170) cc_final: 0.5639 (ttm170) REVERT: I 32 MET cc_start: 0.5161 (tmm) cc_final: 0.4710 (tmm) REVERT: I 42 HIS cc_start: 0.8517 (m170) cc_final: 0.8196 (m170) REVERT: I 156 LEU cc_start: 0.2391 (OUTLIER) cc_final: -0.0194 (tt) REVERT: I 164 TRP cc_start: 0.4292 (t60) cc_final: 0.3982 (t60) REVERT: I 228 LEU cc_start: 0.7666 (tt) cc_final: 0.7328 (tp) REVERT: I 345 THR cc_start: 0.7469 (t) cc_final: 0.7035 (t) REVERT: I 346 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6814 (tt) REVERT: I 352 TRP cc_start: 0.6912 (m-10) cc_final: 0.6618 (m-90) REVERT: I 425 MET cc_start: 0.5361 (tmm) cc_final: 0.4310 (tmm) REVERT: I 440 GLN cc_start: 0.8287 (pp30) cc_final: 0.6802 (pp30) REVERT: I 441 MET cc_start: 0.7766 (mmt) cc_final: 0.7208 (mmt) REVERT: I 469 GLU cc_start: 0.7875 (tp30) cc_final: 0.7214 (tp30) REVERT: I 472 LYS cc_start: 0.8742 (tmmt) cc_final: 0.8378 (tmmt) REVERT: R 32 MET cc_start: 0.6992 (tmm) cc_final: 0.6468 (tmm) REVERT: R 189 MET cc_start: 0.7514 (ttp) cc_final: 0.7236 (tmm) REVERT: R 214 ARG cc_start: 0.7614 (tmt170) cc_final: 0.7169 (tmt170) REVERT: R 405 LYS cc_start: 0.9238 (tptt) cc_final: 0.8801 (tptt) REVERT: R 425 MET cc_start: 0.5064 (OUTLIER) cc_final: 0.4287 (ppp) REVERT: R 429 TYR cc_start: 0.7076 (m-80) cc_final: 0.6563 (m-80) REVERT: R 441 MET cc_start: 0.7833 (mmp) cc_final: 0.7320 (mmt) REVERT: R 469 GLU cc_start: 0.6857 (mm-30) cc_final: 0.6511 (mm-30) outliers start: 83 outliers final: 68 residues processed: 615 average time/residue: 0.1566 time to fit residues: 139.0755 Evaluate side-chains 616 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 543 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 56 TYR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 358 TYR Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 107 CYS Chi-restraints excluded: chain F residue 115 TYR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 117 CYS Chi-restraints excluded: chain I residue 154 TRP Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 202 LEU Chi-restraints excluded: chain I residue 224 MET Chi-restraints excluded: chain I residue 311 PHE Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 436 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 238 PHE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 15 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 139 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 189 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 42 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 HIS D 183 HIS ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS H 16 ASN ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 139 ASN ** R 307 HIS ** 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 = 0.4493 r_free = 0.4493 target = 0.151365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.126435 restraints weight = 35687.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.130469 restraints weight = 19118.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.133159 restraints weight = 12030.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.134944 restraints weight = 8451.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.136131 restraints weight = 6457.622| |-----------------------------------------------------------------------------| r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.8435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18905 Z= 0.159 Angle : 0.809 16.186 25597 Z= 0.419 Chirality : 0.047 0.259 2817 Planarity : 0.005 0.056 3251 Dihedral : 4.642 21.194 2536 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.81 % Rotamer: Outliers : 3.77 % Allowed : 31.86 % Favored : 64.37 % 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: 0.54 (0.18), residues: 2270 helix: 1.85 (0.17), residues: 903 sheet: 0.14 (0.25), residues: 442 loop : -1.04 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 15 TYR 0.034 0.002 TYR R 221 PHE 0.035 0.002 PHE B 199 TRP 0.054 0.003 TRP I 437 HIS 0.008 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00363 (18893) covalent geometry : angle 0.80818 (25573) SS BOND : bond 0.00261 ( 12) SS BOND : angle 1.35209 ( 24) hydrogen bonds : bond 0.04428 ( 987) hydrogen bonds : angle 4.50610 ( 2847) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 562 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8596 (mptt) cc_final: 0.8351 (mptt) REVERT: A 25 LYS cc_start: 0.8586 (mttt) cc_final: 0.8244 (mtmt) REVERT: A 51 LYS cc_start: 0.7891 (tptt) cc_final: 0.7682 (tptt) REVERT: A 186 GLU cc_start: 0.7631 (pm20) cc_final: 0.7270 (pm20) REVERT: A 204 GLN cc_start: 0.8035 (tp-100) cc_final: 0.7683 (tp-100) REVERT: A 247 ARG cc_start: 0.7182 (tpp-160) cc_final: 0.6765 (tpp-160) REVERT: A 300 ARG cc_start: 0.7708 (mtm180) cc_final: 0.7459 (mtm180) REVERT: A 305 LYS cc_start: 0.8584 (pttt) cc_final: 0.8323 (pttm) REVERT: A 306 TYR cc_start: 0.7982 (m-80) cc_final: 0.7516 (m-80) REVERT: B 9 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8744 (mm-40) REVERT: B 96 ARG cc_start: 0.7171 (mtm-85) cc_final: 0.6799 (ttm110) REVERT: B 325 MET cc_start: 0.5495 (mmt) cc_final: 0.5230 (mmt) REVERT: C 15 ARG cc_start: 0.8237 (mmm-85) cc_final: 0.7957 (mmm-85) REVERT: C 17 LYS cc_start: 0.8351 (mmtp) cc_final: 0.8076 (mmtp) REVERT: C 20 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7536 (mm-30) REVERT: C 23 LEU cc_start: 0.8856 (mt) cc_final: 0.8611 (mt) REVERT: C 281 GLU cc_start: 0.7424 (tp30) cc_final: 0.7090 (tp30) REVERT: C 316 SER cc_start: 0.8300 (t) cc_final: 0.8042 (p) REVERT: D 59 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.7202 (m-80) REVERT: D 62 HIS cc_start: 0.7011 (t70) cc_final: 0.6278 (t70) REVERT: D 82 TRP cc_start: 0.7692 (m100) cc_final: 0.7230 (m100) REVERT: D 150 ARG cc_start: 0.7227 (mmt-90) cc_final: 0.6695 (mmp80) REVERT: D 151 PHE cc_start: 0.6916 (m-80) cc_final: 0.6635 (m-80) REVERT: D 176 GLN cc_start: 0.8171 (mp10) cc_final: 0.7638 (mt0) REVERT: D 293 ASN cc_start: 0.7946 (p0) cc_final: 0.7590 (p0) REVERT: F 29 PHE cc_start: 0.8245 (t80) cc_final: 0.8037 (t80) REVERT: F 63 SER cc_start: 0.7889 (m) cc_final: 0.7612 (t) REVERT: G 14 LYS cc_start: 0.8934 (pttp) cc_final: 0.8605 (pttm) REVERT: G 38 MET cc_start: 0.8314 (mmm) cc_final: 0.7855 (mmm) REVERT: G 52 THR cc_start: 0.7452 (OUTLIER) cc_final: 0.7179 (t) REVERT: H 20 ARG cc_start: 0.6310 (ttm170) cc_final: 0.5594 (ttm170) REVERT: I 32 MET cc_start: 0.5122 (tmm) cc_final: 0.4680 (tmm) REVERT: I 156 LEU cc_start: 0.2363 (OUTLIER) cc_final: 0.0333 (tt) REVERT: I 164 TRP cc_start: 0.4472 (t60) cc_final: 0.4201 (t60) REVERT: I 345 THR cc_start: 0.7580 (t) cc_final: 0.7206 (t) REVERT: I 346 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6882 (tt) REVERT: I 380 ASN cc_start: 0.7227 (t0) cc_final: 0.6914 (t0) REVERT: I 425 MET cc_start: 0.5371 (tmm) cc_final: 0.4251 (tmm) REVERT: I 440 GLN cc_start: 0.8271 (pp30) cc_final: 0.6781 (pp30) REVERT: I 441 MET cc_start: 0.7688 (mmt) cc_final: 0.7275 (mmt) REVERT: I 469 GLU cc_start: 0.7829 (tp30) cc_final: 0.7079 (tp30) REVERT: I 472 LYS cc_start: 0.8762 (tmmt) cc_final: 0.8349 (tmmt) REVERT: R 32 MET cc_start: 0.7020 (tmm) cc_final: 0.6701 (tmm) REVERT: R 189 MET cc_start: 0.7402 (ttp) cc_final: 0.7185 (tmm) REVERT: R 208 ILE cc_start: 0.8388 (tt) cc_final: 0.7910 (pt) REVERT: R 214 ARG cc_start: 0.7514 (tmt170) cc_final: 0.7123 (tmt170) REVERT: R 405 LYS cc_start: 0.9185 (tptt) cc_final: 0.8745 (tptt) REVERT: R 425 MET cc_start: 0.5128 (ppp) cc_final: 0.4327 (ppp) REVERT: R 429 TYR cc_start: 0.7084 (m-80) cc_final: 0.6479 (m-80) REVERT: R 441 MET cc_start: 0.7733 (mmp) cc_final: 0.7227 (mmt) REVERT: R 469 GLU cc_start: 0.6805 (mm-30) cc_final: 0.6505 (mm-30) outliers start: 75 outliers final: 62 residues processed: 609 average time/residue: 0.1616 time to fit residues: 141.9960 Evaluate side-chains 616 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 550 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 56 TYR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 329 HIS Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 358 TYR Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 107 CYS Chi-restraints excluded: chain F residue 115 TYR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 117 CYS Chi-restraints excluded: chain I residue 154 TRP Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 311 PHE Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 436 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 238 PHE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 127 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 160 optimal weight: 0.0370 chunk 128 optimal weight: 0.8980 chunk 204 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 201 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 HIS ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 HIS ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS H 9 HIS H 16 ASN ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 HIS ** 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 = 0.4445 r_free = 0.4445 target = 0.147462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.122675 restraints weight = 36125.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.126600 restraints weight = 19466.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.129175 restraints weight = 12278.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.130921 restraints weight = 8656.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.132122 restraints weight = 6660.460| |-----------------------------------------------------------------------------| r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.8805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18905 Z= 0.194 Angle : 0.843 16.200 25597 Z= 0.439 Chirality : 0.049 0.277 2817 Planarity : 0.005 0.052 3251 Dihedral : 4.856 21.672 2536 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.71 % Favored : 95.24 % Rotamer: Outliers : 4.02 % Allowed : 31.91 % Favored : 64.07 % 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: 0.38 (0.18), residues: 2270 helix: 1.67 (0.17), residues: 903 sheet: 0.12 (0.25), residues: 434 loop : -1.10 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 15 TYR 0.032 0.002 TYR R 221 PHE 0.037 0.002 PHE B 199 TRP 0.060 0.003 TRP R 352 HIS 0.011 0.002 HIS I 42 Details of bonding type rmsd covalent geometry : bond 0.00441 (18893) covalent geometry : angle 0.84153 (25573) SS BOND : bond 0.00378 ( 12) SS BOND : angle 1.64614 ( 24) hydrogen bonds : bond 0.04711 ( 987) hydrogen bonds : angle 4.65541 ( 2847) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4733.52 seconds wall clock time: 82 minutes 12.69 seconds (4932.69 seconds total)