Starting phenix.real_space_refine on Mon Jun 16 07:45:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hao_34598/06_2025/8hao_34598_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hao_34598/06_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_34598/06_2025/8hao_34598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hao_34598/06_2025/8hao_34598.map" model { file = "/net/cci-nas-00/data/ceres_data/8hao_34598/06_2025/8hao_34598_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hao_34598/06_2025/8hao_34598_neut.cif" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.78, per 1000 atoms: 0.69 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: 4.22 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.94 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: 5.94 Time building geometry restraints manager: 5.10 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: 12.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 42.900 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.620 ------------------------------------------------------------------------------- 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 : 5.73 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.011 0.001 TRP I 164 HIS 0.003 0.000 HIS C 324 PHE 0.015 0.001 PHE C 196 TYR 0.021 0.001 TYR R 191 ARG 0.007 0.000 ARG H 20 Details of bonding type rmsd hydrogen bonds : bond 0.16588 ( 987) hydrogen bonds : angle 5.84100 ( 2847) SS BOND : bond 0.00567 ( 12) SS BOND : angle 1.58495 ( 24) covalent geometry : bond 0.00251 (18893) covalent geometry : angle 0.50331 (25573) *********************** 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 : 1.828 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: 0.7131 (t0) REVERT: A 238 ASN cc_start: 0.7077 (m-40) cc_final: 0.6715 (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: 0.7401 (tp) REVERT: C 263 LEU cc_start: 0.7316 (mp) cc_final: 0.6746 (mp) REVERT: D 192 LEU cc_start: 0.5644 (OUTLIER) cc_final: 0.5441 (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: 0.4793 (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: 0.5430 (mt) REVERT: I 457 ILE cc_start: 0.7930 (mm) cc_final: 0.7639 (mm) REVERT: R 403 TYR cc_start: 0.5343 (m-80) cc_final: 0.4916 (m-80) outliers start: 8 outliers final: 0 residues processed: 651 average time/residue: 0.3673 time to fit residues: 340.4743 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 : 2.063 ------------------------------------------------------------------------------- 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 190 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 131 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 234 GLN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN C 28 GLN C 43 ASN ** D 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN D 142 HIS ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 9 HIS H 10 ASN 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 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN N 84 ASN ** R 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 223 HIS R 448 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.162774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.137786 restraints weight = 34724.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.142476 restraints weight = 17693.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.145502 restraints weight = 10670.741| |-----------------------------------------------------------------------------| r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18905 Z= 0.192 Angle : 0.728 9.871 25597 Z= 0.383 Chirality : 0.046 0.283 2817 Planarity : 0.005 0.086 3251 Dihedral : 4.525 44.573 2540 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.30 % Favored : 96.52 % Rotamer: Outliers : 5.03 % Allowed : 21.06 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.18), residues: 2270 helix: 2.53 (0.16), residues: 905 sheet: 0.68 (0.25), residues: 426 loop : -0.72 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 82 HIS 0.013 0.002 HIS D 62 PHE 0.031 0.002 PHE I 291 TYR 0.030 0.002 TYR I 320 ARG 0.016 0.001 ARG R 43 Details of bonding type rmsd hydrogen bonds : bond 0.04799 ( 987) hydrogen bonds : angle 4.63265 ( 2847) SS BOND : bond 0.00856 ( 12) SS BOND : angle 1.24563 ( 24) covalent geometry : bond 0.00421 (18893) covalent geometry : angle 0.72700 (25573) *********************** 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 692 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 592 time to evaluate : 1.983 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 19 ILE cc_start: 0.8435 (mt) cc_final: 0.8214 (mt) REVERT: A 52 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8373 (mm-40) REVERT: A 238 ASN cc_start: 0.7440 (m-40) cc_final: 0.6817 (m-40) REVERT: A 305 LYS cc_start: 0.8485 (pttm) cc_final: 0.8278 (pttm) REVERT: A 310 ASP cc_start: 0.8047 (m-30) cc_final: 0.7712 (m-30) REVERT: B 9 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8662 (mm-40) REVERT: B 17 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7832 (pp30) REVERT: B 124 TYR cc_start: 0.5307 (m-10) cc_final: 0.5059 (m-10) REVERT: B 135 VAL cc_start: 0.7669 (t) cc_final: 0.6708 (t) REVERT: B 187 VAL cc_start: 0.7999 (t) cc_final: 0.7766 (p) REVERT: B 263 THR cc_start: 0.7558 (t) cc_final: 0.7314 (t) REVERT: C 13 VAL cc_start: 0.8620 (t) cc_final: 0.8086 (t) REVERT: C 17 LYS cc_start: 0.8535 (mmtp) cc_final: 0.8285 (mmtp) REVERT: C 190 GLN cc_start: 0.6364 (tt0) cc_final: 0.6093 (mt0) REVERT: C 233 LEU cc_start: 0.7831 (mt) cc_final: 0.7575 (mp) REVERT: C 327 TYR cc_start: 0.6732 (m-80) cc_final: 0.6267 (m-80) REVERT: D 13 GLN cc_start: 0.8296 (tm-30) cc_final: 0.8086 (tm-30) REVERT: D 62 HIS cc_start: 0.6965 (t70) cc_final: 0.6574 (t70) REVERT: D 171 ILE cc_start: 0.4642 (OUTLIER) cc_final: 0.4151 (mm) REVERT: D 183 HIS cc_start: 0.5827 (m-70) cc_final: 0.5584 (m-70) REVERT: D 217 MET cc_start: 0.5775 (ptm) cc_final: 0.5517 (ptm) REVERT: D 232 ILE cc_start: 0.7722 (tt) cc_final: 0.7471 (mt) REVERT: D 258 ASP cc_start: 0.7617 (t0) cc_final: 0.7137 (t0) REVERT: D 279 SER cc_start: 0.8209 (m) cc_final: 0.7935 (p) REVERT: E 17 GLU cc_start: 0.8040 (tp30) cc_final: 0.7624 (tp30) REVERT: E 38 MET cc_start: 0.5945 (mmp) cc_final: 0.5653 (mmp) REVERT: F 29 PHE cc_start: 0.7782 (t80) cc_final: 0.7467 (t80) REVERT: F 90 ASP cc_start: 0.6789 (m-30) cc_final: 0.6452 (m-30) REVERT: G 38 MET cc_start: 0.7926 (mmm) cc_final: 0.7436 (mtt) REVERT: I 32 MET cc_start: 0.5942 (ptt) cc_final: 0.5328 (ptt) REVERT: I 405 LYS cc_start: 0.8192 (mttm) cc_final: 0.7981 (mttm) REVERT: I 425 MET cc_start: 0.4232 (tmm) cc_final: 0.3683 (tmm) REVERT: I 457 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8059 (mm) REVERT: I 473 SER cc_start: 0.8119 (m) cc_final: 0.7818 (p) REVERT: N 83 MET cc_start: 0.7761 (mpp) cc_final: 0.7435 (mpp) REVERT: N 84 ASN cc_start: 0.7759 (OUTLIER) cc_final: 0.7263 (p0) REVERT: R 40 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6192 (tp) REVERT: R 191 TYR cc_start: 0.6386 (OUTLIER) cc_final: 0.6165 (p90) REVERT: R 401 GLN cc_start: 0.8425 (pm20) cc_final: 0.7690 (pm20) REVERT: R 405 LYS cc_start: 0.9164 (tptt) cc_final: 0.8769 (tptt) REVERT: R 441 MET cc_start: 0.7490 (mmp) cc_final: 0.6974 (mmt) outliers start: 100 outliers final: 50 residues processed: 651 average time/residue: 0.3377 time to fit residues: 321.0478 Evaluate side-chains 574 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 519 time to evaluate : 1.907 ------------------------------------------------------------------------------- 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 207 GLU Chi-restraints excluded: chain A residue 326 CYS 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 304 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 336 THR 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 91 THR Chi-restraints excluded: chain F residue 124 VAL 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 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 297 TYR Chi-restraints excluded: chain I residue 387 THR Chi-restraints excluded: chain I residue 446 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 64 VAL Chi-restraints excluded: chain N residue 84 ASN 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 115 ILE Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 238 PHE Chi-restraints excluded: chain R residue 312 MET 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 177 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 161 optimal weight: 0.3980 chunk 185 optimal weight: 0.1980 chunk 149 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 193 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 259 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN D 119 ASN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN G 44 HIS H 6 GLN H 10 ASN H 16 ASN I 139 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** P 9 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.160669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.135140 restraints weight = 35445.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.139577 restraints weight = 18452.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.142465 restraints weight = 11355.735| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18905 Z= 0.154 Angle : 0.650 9.501 25597 Z= 0.347 Chirality : 0.044 0.237 2817 Planarity : 0.005 0.071 3251 Dihedral : 4.357 29.206 2536 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.44 % Favored : 96.39 % Rotamer: Outliers : 4.67 % Allowed : 23.37 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.18), residues: 2270 helix: 2.54 (0.16), residues: 906 sheet: 0.61 (0.24), residues: 432 loop : -0.72 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 82 HIS 0.007 0.001 HIS I 216 PHE 0.028 0.002 PHE I 447 TYR 0.021 0.002 TYR R 305 ARG 0.017 0.001 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.04471 ( 987) hydrogen bonds : angle 4.44662 ( 2847) SS BOND : bond 0.01027 ( 12) SS BOND : angle 1.03385 ( 24) covalent geometry : bond 0.00329 (18893) covalent geometry : angle 0.64995 (25573) *********************** 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 655 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 562 time to evaluate : 2.262 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: 0.8659 (mttt) cc_final: 0.8241 (mtmt) REVERT: A 51 LYS cc_start: 0.7533 (tptt) cc_final: 0.7210 (tptt) REVERT: A 52 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8439 (mm-40) REVERT: A 238 ASN cc_start: 0.7791 (m-40) cc_final: 0.7271 (m-40) REVERT: A 244 TRP cc_start: 0.7065 (t-100) cc_final: 0.6539 (t-100) REVERT: A 261 GLN cc_start: 0.7921 (mp10) cc_final: 0.7621 (mp10) REVERT: A 310 ASP cc_start: 0.8034 (m-30) cc_final: 0.7656 (m-30) REVERT: A 357 GLN cc_start: 0.8467 (tp-100) cc_final: 0.8102 (tp-100) REVERT: B 9 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8669 (mm-40) REVERT: B 96 ARG cc_start: 0.7447 (mtm-85) cc_final: 0.7002 (ttm110) REVERT: C 17 LYS cc_start: 0.8660 (mmtp) cc_final: 0.8351 (mmtp) REVERT: C 190 GLN cc_start: 0.6624 (tt0) cc_final: 0.6173 (mt0) REVERT: D 13 GLN cc_start: 0.8292 (tm-30) cc_final: 0.8084 (tm-30) REVERT: D 15 LYS cc_start: 0.8937 (ttpp) cc_final: 0.8449 (ttpp) REVERT: D 99 TRP cc_start: 0.8136 (m100) cc_final: 0.7627 (m100) REVERT: D 188 MET cc_start: 0.7513 (mmt) cc_final: 0.7215 (mmt) REVERT: D 215 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7511 (pt0) REVERT: E 17 GLU cc_start: 0.8223 (tp30) cc_final: 0.7894 (tp30) REVERT: F 29 PHE cc_start: 0.8055 (t80) cc_final: 0.7735 (t80) REVERT: F 33 LYS cc_start: 0.7749 (tttt) cc_final: 0.7520 (tmtt) REVERT: G 38 MET cc_start: 0.8183 (mmm) cc_final: 0.7705 (mmm) REVERT: H 20 ARG cc_start: 0.7280 (ttm110) cc_final: 0.6211 (mtt180) REVERT: I 42 HIS cc_start: 0.8500 (m170) cc_final: 0.8215 (m170) REVERT: I 180 GLU cc_start: 0.8427 (mp0) cc_final: 0.8226 (mp0) REVERT: I 352 TRP cc_start: 0.6855 (m-10) cc_final: 0.6590 (m-90) REVERT: I 425 MET cc_start: 0.4641 (tmm) cc_final: 0.3789 (tmm) REVERT: I 437 TRP cc_start: 0.6005 (t60) cc_final: 0.5314 (t60) REVERT: I 441 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7212 (mmt) REVERT: I 469 GLU cc_start: 0.7561 (tp30) cc_final: 0.6765 (tp30) REVERT: I 473 SER cc_start: 0.8012 (m) cc_final: 0.7275 (p) REVERT: N 84 ASN cc_start: 0.7909 (p0) cc_final: 0.7375 (p0) REVERT: P 24 LEU cc_start: 0.4958 (OUTLIER) cc_final: 0.4609 (tt) REVERT: R 189 MET cc_start: 0.7510 (ttp) cc_final: 0.7233 (tmm) REVERT: R 237 ILE cc_start: 0.8041 (tp) cc_final: 0.7746 (tt) REVERT: R 400 ARG cc_start: 0.8489 (mmm160) cc_final: 0.7448 (mmm160) REVERT: R 401 GLN cc_start: 0.8419 (pm20) cc_final: 0.7558 (pm20) REVERT: R 405 LYS cc_start: 0.9216 (tptt) cc_final: 0.8814 (tptt) REVERT: R 414 MET cc_start: 0.7959 (tpp) cc_final: 0.7636 (tpp) REVERT: R 425 MET cc_start: 0.5168 (ppp) cc_final: 0.4553 (ppp) REVERT: R 441 MET cc_start: 0.7547 (mmp) cc_final: 0.7043 (mmt) outliers start: 93 outliers final: 53 residues processed: 620 average time/residue: 0.4015 time to fit residues: 363.1447 Evaluate side-chains 586 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 531 time to evaluate : 3.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 201 VAL 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 87 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 287 THR 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 98 SER 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 263 THR Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 107 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 16 ASN 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 172 LYS Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 237 ILE Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 334 VAL Chi-restraints excluded: chain I residue 441 MET Chi-restraints excluded: chain N residue 1 GLN 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 P residue 2 VAL Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain P residue 21 VAL 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 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 101 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 214 optimal weight: 0.0010 chunk 164 optimal weight: 0.0570 chunk 159 optimal weight: 0.7980 chunk 225 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 191 optimal weight: 0.5980 chunk 73 optimal weight: 0.0040 overall best weight: 0.2516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN D 119 ASN D 183 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 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 10 ASN R 220 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.162051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.136315 restraints weight = 35304.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.140796 restraints weight = 18392.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.143675 restraints weight = 11349.578| |-----------------------------------------------------------------------------| r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18905 Z= 0.130 Angle : 0.647 13.616 25597 Z= 0.337 Chirality : 0.044 0.285 2817 Planarity : 0.004 0.067 3251 Dihedral : 4.229 23.116 2536 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.44 % Favored : 96.39 % Rotamer: Outliers : 4.32 % Allowed : 25.23 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.18), residues: 2270 helix: 2.49 (0.16), residues: 906 sheet: 0.57 (0.24), residues: 440 loop : -0.78 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 63 HIS 0.012 0.001 HIS I 216 PHE 0.026 0.001 PHE I 447 TYR 0.028 0.002 TYR I 403 ARG 0.009 0.001 ARG C 303 Details of bonding type rmsd hydrogen bonds : bond 0.04062 ( 987) hydrogen bonds : angle 4.25930 ( 2847) SS BOND : bond 0.00285 ( 12) SS BOND : angle 0.84684 ( 24) covalent geometry : bond 0.00280 (18893) covalent geometry : angle 0.64713 (25573) *********************** 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 639 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 553 time to evaluate : 1.863 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 25 LYS cc_start: 0.8686 (mttt) cc_final: 0.8470 (mttt) REVERT: A 51 LYS cc_start: 0.7584 (tptt) cc_final: 0.7248 (tptt) REVERT: A 52 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8458 (mt0) REVERT: A 244 TRP cc_start: 0.7066 (t-100) cc_final: 0.6539 (t-100) REVERT: A 310 ASP cc_start: 0.7945 (m-30) cc_final: 0.7556 (m-30) REVERT: B 9 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8722 (mm-40) REVERT: B 97 SER cc_start: 0.8221 (t) cc_final: 0.7921 (p) REVERT: C 13 VAL cc_start: 0.8453 (t) cc_final: 0.8220 (t) REVERT: C 17 LYS cc_start: 0.8531 (mmtp) cc_final: 0.8277 (mmtp) REVERT: C 18 MET cc_start: 0.7405 (ptp) cc_final: 0.5787 (ptp) REVERT: C 53 MET cc_start: 0.3780 (mmt) cc_final: 0.1830 (mmt) REVERT: C 190 GLN cc_start: 0.6705 (tt0) cc_final: 0.6387 (mt0) REVERT: C 212 ILE cc_start: 0.8414 (tp) cc_final: 0.8201 (tt) REVERT: C 215 PHE cc_start: 0.7805 (m-80) cc_final: 0.7258 (m-10) REVERT: C 275 ILE cc_start: 0.7537 (tt) cc_final: 0.7285 (tt) REVERT: C 360 LEU cc_start: 0.7891 (mt) cc_final: 0.7666 (mp) REVERT: D 12 GLU cc_start: 0.7926 (pp20) cc_final: 0.7601 (pp20) REVERT: D 15 LYS cc_start: 0.8772 (ttpp) cc_final: 0.7788 (ttpp) REVERT: D 19 ARG cc_start: 0.8166 (ptp90) cc_final: 0.7725 (ptp-170) REVERT: D 62 HIS cc_start: 0.6971 (t70) cc_final: 0.5833 (t70) REVERT: D 99 TRP cc_start: 0.8043 (m100) cc_final: 0.7090 (m100) REVERT: D 150 ARG cc_start: 0.7215 (mmt-90) cc_final: 0.6424 (mmt180) REVERT: D 171 ILE cc_start: 0.4735 (OUTLIER) cc_final: 0.4250 (mm) REVERT: D 188 MET cc_start: 0.7500 (mmt) cc_final: 0.7232 (mmt) REVERT: F 29 PHE cc_start: 0.8072 (t80) cc_final: 0.7847 (t80) REVERT: F 59 SER cc_start: 0.5771 (OUTLIER) cc_final: 0.5439 (p) REVERT: F 77 ASN cc_start: 0.6896 (t0) cc_final: 0.6589 (t0) REVERT: G 38 MET cc_start: 0.8248 (mmm) cc_final: 0.7628 (mmm) REVERT: I 42 HIS cc_start: 0.8428 (m170) cc_final: 0.8133 (m170) REVERT: I 425 MET cc_start: 0.4947 (tmm) cc_final: 0.4083 (tmm) REVERT: I 440 GLN cc_start: 0.8266 (tt0) cc_final: 0.7706 (tt0) REVERT: I 441 MET cc_start: 0.7804 (mmt) cc_final: 0.7196 (mmt) REVERT: I 469 GLU cc_start: 0.7773 (tp30) cc_final: 0.6992 (tp30) REVERT: I 472 LYS cc_start: 0.8643 (tmmt) cc_final: 0.8189 (tmmt) REVERT: R 36 GLU cc_start: 0.8587 (mm-30) cc_final: 0.7977 (mp0) REVERT: R 189 MET cc_start: 0.7495 (ttp) cc_final: 0.7156 (tmm) REVERT: R 237 ILE cc_start: 0.8107 (tp) cc_final: 0.7800 (tt) REVERT: R 400 ARG cc_start: 0.8382 (mmm160) cc_final: 0.8056 (mmm160) REVERT: R 404 ARG cc_start: 0.8475 (ptt-90) cc_final: 0.8271 (ptp90) REVERT: R 405 LYS cc_start: 0.9273 (tptt) cc_final: 0.8939 (tptt) REVERT: R 414 MET cc_start: 0.7921 (tpp) cc_final: 0.7640 (tpp) REVERT: R 425 MET cc_start: 0.5145 (ppp) cc_final: 0.4512 (ppp) outliers start: 86 outliers final: 58 residues processed: 598 average time/residue: 0.3590 time to fit residues: 308.6373 Evaluate side-chains 589 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 529 time to evaluate : 2.095 ------------------------------------------------------------------------------- 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 260 LYS Chi-restraints excluded: chain A residue 324 HIS 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 87 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 329 HIS Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 91 THR 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 H residue 16 ASN 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 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 86 LEU 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 R residue 112 TRP Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain R residue 225 HIS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 59 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 191 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 199 optimal weight: 0.0980 chunk 5 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 48 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 C 43 ASN D 119 ASN ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN G 44 HIS H 16 ASN ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 220 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.157765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.132846 restraints weight = 35559.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.137053 restraints weight = 18942.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.139780 restraints weight = 11843.586| |-----------------------------------------------------------------------------| r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.6322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18905 Z= 0.141 Angle : 0.672 14.248 25597 Z= 0.348 Chirality : 0.044 0.288 2817 Planarity : 0.004 0.044 3251 Dihedral : 4.289 21.781 2536 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.66 % Favored : 96.21 % Rotamer: Outliers : 5.23 % Allowed : 25.73 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.18), residues: 2270 helix: 2.31 (0.17), residues: 910 sheet: 0.46 (0.24), residues: 440 loop : -0.81 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP I 437 HIS 0.008 0.001 HIS B 62 PHE 0.026 0.002 PHE I 447 TYR 0.023 0.002 TYR R 305 ARG 0.008 0.001 ARG C 323 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 987) hydrogen bonds : angle 4.30399 ( 2847) SS BOND : bond 0.00262 ( 12) SS BOND : angle 1.03377 ( 24) covalent geometry : bond 0.00311 (18893) covalent geometry : angle 0.67165 (25573) *********************** 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 667 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 563 time to evaluate : 2.091 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: 0.8743 (mttt) cc_final: 0.8512 (mttt) REVERT: A 51 LYS cc_start: 0.7645 (tptt) cc_final: 0.7317 (tptt) REVERT: A 52 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8446 (mt0) REVERT: A 198 MET cc_start: 0.7504 (tpp) cc_final: 0.7113 (tpp) REVERT: A 244 TRP cc_start: 0.7160 (t-100) cc_final: 0.6776 (t-100) REVERT: A 310 ASP cc_start: 0.7942 (m-30) cc_final: 0.7493 (m-30) REVERT: A 357 GLN cc_start: 0.8451 (tp-100) cc_final: 0.7997 (tp-100) REVERT: B 8 ARG cc_start: 0.8516 (ptt-90) cc_final: 0.8278 (ptt-90) REVERT: B 9 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8806 (mm-40) REVERT: B 96 ARG cc_start: 0.7509 (mtm-85) cc_final: 0.6987 (ttm110) REVERT: C 20 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7602 (mm-30) REVERT: C 53 MET cc_start: 0.4084 (mmt) cc_final: 0.2240 (mmt) REVERT: C 186 GLU cc_start: 0.7624 (pm20) cc_final: 0.7234 (pm20) REVERT: C 215 PHE cc_start: 0.8030 (m-80) cc_final: 0.7355 (m-10) REVERT: C 327 TYR cc_start: 0.7062 (m-80) cc_final: 0.6783 (m-80) REVERT: C 360 LEU cc_start: 0.7931 (mt) cc_final: 0.7714 (mp) REVERT: D 19 ARG cc_start: 0.8153 (ptp90) cc_final: 0.7924 (ptp90) REVERT: D 62 HIS cc_start: 0.7097 (t70) cc_final: 0.5489 (t70) REVERT: D 99 TRP cc_start: 0.8131 (m100) cc_final: 0.7251 (m100) REVERT: D 150 ARG cc_start: 0.7243 (mmt-90) cc_final: 0.6466 (mmt180) REVERT: D 171 ILE cc_start: 0.4719 (OUTLIER) cc_final: 0.4262 (mm) REVERT: D 188 MET cc_start: 0.7499 (mmt) cc_final: 0.6982 (mmt) REVERT: F 29 PHE cc_start: 0.8272 (t80) cc_final: 0.8015 (t80) REVERT: F 77 ASN cc_start: 0.6936 (t0) cc_final: 0.6646 (t0) REVERT: G 38 MET cc_start: 0.8356 (mmm) cc_final: 0.7995 (mmm) REVERT: I 42 HIS cc_start: 0.8456 (m170) cc_final: 0.8162 (m170) REVERT: I 352 TRP cc_start: 0.6793 (m-10) cc_final: 0.6201 (m-10) REVERT: I 425 MET cc_start: 0.5048 (tmm) cc_final: 0.4148 (tmm) REVERT: I 437 TRP cc_start: 0.5646 (t60) cc_final: 0.5349 (t60) REVERT: I 469 GLU cc_start: 0.7801 (tp30) cc_final: 0.6395 (tp30) REVERT: I 472 LYS cc_start: 0.8744 (tmmt) cc_final: 0.8307 (tmmt) REVERT: I 476 ARG cc_start: 0.8466 (tmm160) cc_final: 0.8227 (tmm160) REVERT: P 24 LEU cc_start: 0.4869 (OUTLIER) cc_final: 0.4623 (tt) REVERT: R 36 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8327 (mp0) REVERT: R 189 MET cc_start: 0.7422 (ttp) cc_final: 0.7115 (tmm) REVERT: R 214 ARG cc_start: 0.7564 (tmt170) cc_final: 0.6870 (tmt170) REVERT: R 237 ILE cc_start: 0.8113 (tp) cc_final: 0.7836 (tt) REVERT: R 379 ILE cc_start: 0.7508 (mm) cc_final: 0.7036 (tp) REVERT: R 401 GLN cc_start: 0.8174 (pm20) cc_final: 0.7378 (pm20) REVERT: R 404 ARG cc_start: 0.8373 (ptt-90) cc_final: 0.7889 (ptt-90) REVERT: R 405 LYS cc_start: 0.9251 (tptt) cc_final: 0.8907 (tptt) REVERT: R 411 LEU cc_start: 0.8416 (mp) cc_final: 0.8131 (mp) REVERT: R 425 MET cc_start: 0.5125 (ppp) cc_final: 0.4514 (ppp) REVERT: R 441 MET cc_start: 0.7742 (mmp) cc_final: 0.6946 (mmt) REVERT: R 444 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7474 (mm-30) REVERT: R 469 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6387 (mm-30) outliers start: 104 outliers final: 71 residues processed: 630 average time/residue: 0.3396 time to fit residues: 310.8723 Evaluate side-chains 607 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 534 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 37 LEU 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 263 LEU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 335 ASP 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 122 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 315 VAL 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 361 LEU Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 98 SER 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 45 LEU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 91 THR 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 16 ASN 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 239 VAL 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 99 CYS Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 3 SER 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 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 122 optimal weight: 1.9990 chunk 131 optimal weight: 0.0980 chunk 80 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 178 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 HIS ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS D 119 ASN ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 220 ASN R 307 HIS R 380 ASN ** 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 = 0.4525 r_free = 0.4525 target = 0.154111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.129388 restraints weight = 35668.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.133503 restraints weight = 19001.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.136200 restraints weight = 11879.796| |-----------------------------------------------------------------------------| r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.6961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18905 Z= 0.163 Angle : 0.698 13.543 25597 Z= 0.362 Chirality : 0.046 0.299 2817 Planarity : 0.004 0.042 3251 Dihedral : 4.477 20.864 2536 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.88 % Favored : 95.99 % Rotamer: Outliers : 4.87 % Allowed : 27.14 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.18), residues: 2270 helix: 2.19 (0.17), residues: 908 sheet: 0.48 (0.24), residues: 438 loop : -0.78 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 437 HIS 0.015 0.001 HIS B 62 PHE 0.041 0.002 PHE N 29 TYR 0.022 0.002 TYR R 305 ARG 0.006 0.001 ARG R 233 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 987) hydrogen bonds : angle 4.40110 ( 2847) SS BOND : bond 0.00291 ( 12) SS BOND : angle 1.22598 ( 24) covalent geometry : bond 0.00366 (18893) covalent geometry : angle 0.69751 (25573) *********************** 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 685 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 588 time to evaluate : 2.051 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: A 51 LYS cc_start: 0.7594 (tptt) cc_final: 0.7271 (tptt) REVERT: A 57 HIS cc_start: 0.6479 (t-90) cc_final: 0.6271 (t70) REVERT: A 198 MET cc_start: 0.7467 (tpp) cc_final: 0.7140 (tpp) REVERT: A 310 ASP cc_start: 0.7929 (m-30) cc_final: 0.7510 (m-30) REVERT: A 347 ARG cc_start: 0.7639 (tpp-160) cc_final: 0.7387 (mmp-170) REVERT: B 8 ARG cc_start: 0.8421 (ptt-90) cc_final: 0.8186 (ptt-90) REVERT: B 9 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8786 (mm-40) REVERT: B 27 ASP cc_start: 0.5579 (m-30) cc_final: 0.4961 (p0) REVERT: B 62 HIS cc_start: 0.7134 (t-90) cc_final: 0.6819 (t70) REVERT: B 96 ARG cc_start: 0.7506 (mtm-85) cc_final: 0.6935 (ttm110) REVERT: B 150 ARG cc_start: 0.7051 (mmt180) cc_final: 0.6703 (tpp-160) REVERT: C 20 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7657 (mm-30) REVERT: C 53 MET cc_start: 0.4227 (mmt) cc_final: 0.2538 (mmt) REVERT: C 215 PHE cc_start: 0.7840 (m-80) cc_final: 0.6832 (m-80) REVERT: C 327 TYR cc_start: 0.7189 (m-80) cc_final: 0.6837 (m-80) REVERT: D 12 GLU cc_start: 0.7961 (pp20) cc_final: 0.7639 (pp20) REVERT: D 15 LYS cc_start: 0.8756 (ttpp) cc_final: 0.7657 (ttpp) REVERT: D 16 ASN cc_start: 0.8435 (m-40) cc_final: 0.7779 (m-40) REVERT: D 19 ARG cc_start: 0.8060 (ptp90) cc_final: 0.7787 (ptp-170) REVERT: D 59 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.7234 (m-80) REVERT: D 62 HIS cc_start: 0.7111 (t-90) cc_final: 0.5826 (t70) REVERT: D 99 TRP cc_start: 0.8127 (m100) cc_final: 0.7368 (m100) REVERT: D 150 ARG cc_start: 0.7222 (mmt-90) cc_final: 0.6457 (mmt180) REVERT: D 188 MET cc_start: 0.7544 (mmt) cc_final: 0.7148 (mmt) REVERT: F 29 PHE cc_start: 0.8309 (t80) cc_final: 0.8052 (t80) REVERT: F 77 ASN cc_start: 0.6939 (t0) cc_final: 0.6632 (t0) REVERT: G 38 MET cc_start: 0.8365 (mmm) cc_final: 0.7905 (mmm) REVERT: I 32 MET cc_start: 0.5918 (tmm) cc_final: 0.5394 (tmm) REVERT: I 42 HIS cc_start: 0.8463 (m170) cc_final: 0.8147 (m170) REVERT: I 352 TRP cc_start: 0.6763 (m-10) cc_final: 0.6360 (m-90) REVERT: I 425 MET cc_start: 0.5097 (tmm) cc_final: 0.4166 (tmm) REVERT: I 437 TRP cc_start: 0.6078 (t60) cc_final: 0.5585 (t60) REVERT: I 469 GLU cc_start: 0.7796 (tp30) cc_final: 0.6439 (tp30) REVERT: I 472 LYS cc_start: 0.8798 (tmmt) cc_final: 0.8354 (tmmt) REVERT: P 24 LEU cc_start: 0.5090 (OUTLIER) cc_final: 0.4827 (tt) REVERT: R 36 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8246 (mp0) REVERT: R 189 MET cc_start: 0.7440 (ttp) cc_final: 0.7165 (tmm) REVERT: R 214 ARG cc_start: 0.7542 (tmt170) cc_final: 0.6921 (tmt170) REVERT: R 379 ILE cc_start: 0.7733 (mm) cc_final: 0.7448 (tp) REVERT: R 405 LYS cc_start: 0.9252 (tptt) cc_final: 0.8920 (tptt) REVERT: R 425 MET cc_start: 0.4992 (ppp) cc_final: 0.4365 (ppp) REVERT: R 429 TYR cc_start: 0.7072 (m-80) cc_final: 0.6572 (m-80) REVERT: R 441 MET cc_start: 0.7802 (mmp) cc_final: 0.7073 (mmt) REVERT: R 465 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7532 (mt-10) REVERT: R 469 GLU cc_start: 0.6749 (mm-30) cc_final: 0.6495 (mm-30) outliers start: 97 outliers final: 80 residues processed: 645 average time/residue: 0.3258 time to fit residues: 303.5396 Evaluate side-chains 645 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 563 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU 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 263 LEU 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 122 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS 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 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 256 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 98 SER Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 121 CYS 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 262 MET Chi-restraints excluded: chain D residue 263 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 63 SER Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 91 THR 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 6 GLN Chi-restraints excluded: chain H residue 9 HIS Chi-restraints excluded: chain H residue 16 ASN Chi-restraints excluded: chain H residue 17 SER 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 239 VAL Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 334 VAL 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 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 208 ILE Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 385 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 139 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 184 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN ** D 142 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 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 307 HIS ** R 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.153082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.128332 restraints weight = 35497.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.132388 restraints weight = 18939.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.135124 restraints weight = 11888.594| |-----------------------------------------------------------------------------| r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.7518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18905 Z= 0.163 Angle : 0.729 12.196 25597 Z= 0.379 Chirality : 0.046 0.313 2817 Planarity : 0.004 0.056 3251 Dihedral : 4.538 21.621 2536 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.27 % Favored : 95.59 % Rotamer: Outliers : 5.58 % Allowed : 28.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.18), residues: 2270 helix: 2.12 (0.17), residues: 909 sheet: 0.35 (0.24), residues: 438 loop : -0.90 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 63 HIS 0.009 0.001 HIS B 62 PHE 0.048 0.002 PHE B 199 TYR 0.029 0.002 TYR D 145 ARG 0.007 0.001 ARG A 15 Details of bonding type rmsd hydrogen bonds : bond 0.04335 ( 987) hydrogen bonds : angle 4.40489 ( 2847) SS BOND : bond 0.00436 ( 12) SS BOND : angle 1.29666 ( 24) covalent geometry : bond 0.00360 (18893) covalent geometry : angle 0.72850 (25573) *********************** 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: 111 poor density : 583 time to evaluate : 1.868 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: A 25 LYS cc_start: 0.8531 (mttt) cc_final: 0.8220 (mtmm) REVERT: A 31 ARG cc_start: 0.7715 (mmm-85) cc_final: 0.7467 (mmm-85) REVERT: A 51 LYS cc_start: 0.7810 (tptt) cc_final: 0.7541 (tptt) REVERT: A 186 GLU cc_start: 0.7573 (pm20) cc_final: 0.7287 (pm20) REVERT: A 204 GLN cc_start: 0.8187 (tp-100) cc_final: 0.7785 (tp-100) REVERT: A 310 ASP cc_start: 0.7940 (m-30) cc_final: 0.7524 (m-30) REVERT: A 325 TYR cc_start: 0.6692 (t80) cc_final: 0.6454 (t80) REVERT: A 347 ARG cc_start: 0.7688 (tpp-160) cc_final: 0.7415 (mmp-170) REVERT: B 8 ARG cc_start: 0.8432 (ptt-90) cc_final: 0.8167 (ptt-90) REVERT: B 9 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8793 (mm-40) REVERT: B 62 HIS cc_start: 0.7100 (t-90) cc_final: 0.6896 (t-90) REVERT: B 96 ARG cc_start: 0.7537 (mtm-85) cc_final: 0.7019 (ttm110) REVERT: B 150 ARG cc_start: 0.7107 (mmt180) cc_final: 0.6840 (tpp-160) REVERT: B 166 CYS cc_start: 0.7328 (m) cc_final: 0.7022 (m) REVERT: C 17 LYS cc_start: 0.8481 (mmtp) cc_final: 0.8208 (mmtp) REVERT: C 20 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7803 (mm-30) REVERT: C 53 MET cc_start: 0.4264 (mmt) cc_final: 0.2726 (mmt) REVERT: D 12 GLU cc_start: 0.8005 (pp20) cc_final: 0.7684 (pp20) REVERT: D 15 LYS cc_start: 0.8785 (ttpp) cc_final: 0.7879 (ttpp) REVERT: D 16 ASN cc_start: 0.8456 (m-40) cc_final: 0.7935 (m-40) REVERT: D 19 ARG cc_start: 0.8101 (ptp90) cc_final: 0.7799 (ptp-170) REVERT: D 59 TYR cc_start: 0.7529 (OUTLIER) cc_final: 0.7234 (m-80) REVERT: D 62 HIS cc_start: 0.7129 (t-90) cc_final: 0.5848 (t70) REVERT: D 143 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8439 (t) REVERT: D 150 ARG cc_start: 0.7191 (mmt-90) cc_final: 0.6368 (mmt180) REVERT: D 188 MET cc_start: 0.7504 (mmt) cc_final: 0.7122 (mmt) REVERT: F 29 PHE cc_start: 0.8321 (t80) cc_final: 0.8116 (t80) REVERT: G 38 MET cc_start: 0.8366 (mmm) cc_final: 0.7901 (mmm) REVERT: I 42 HIS cc_start: 0.8460 (m170) cc_final: 0.8148 (m170) REVERT: I 156 LEU cc_start: 0.2778 (OUTLIER) cc_final: 0.0045 (tt) REVERT: I 189 MET cc_start: 0.6900 (ptp) cc_final: 0.6506 (ppp) REVERT: I 346 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6722 (tt) REVERT: I 352 TRP cc_start: 0.6866 (m-10) cc_final: 0.6337 (m-90) REVERT: I 380 ASN cc_start: 0.6972 (t0) cc_final: 0.6689 (t0) REVERT: I 425 MET cc_start: 0.5246 (tmm) cc_final: 0.4247 (tmm) REVERT: I 469 GLU cc_start: 0.7843 (tp30) cc_final: 0.6474 (tp30) REVERT: I 472 LYS cc_start: 0.8835 (tmmt) cc_final: 0.8443 (tmmt) REVERT: I 476 ARG cc_start: 0.8529 (tmm160) cc_final: 0.8114 (tmm160) REVERT: N 11 LEU cc_start: 0.7806 (tp) cc_final: 0.7576 (tp) REVERT: N 29 PHE cc_start: 0.7983 (t80) cc_final: 0.7652 (t80) REVERT: P 24 LEU cc_start: 0.5123 (OUTLIER) cc_final: 0.4846 (tt) REVERT: R 32 MET cc_start: 0.7218 (tmm) cc_final: 0.6752 (tmm) REVERT: R 36 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8395 (mp0) REVERT: R 172 LYS cc_start: 0.7696 (tmtt) cc_final: 0.7338 (mttt) REVERT: R 189 MET cc_start: 0.7493 (ttp) cc_final: 0.7218 (tmm) REVERT: R 213 ARG cc_start: 0.8558 (tpp80) cc_final: 0.8268 (ttm170) REVERT: R 214 ARG cc_start: 0.7529 (tmt170) cc_final: 0.7023 (tmt170) REVERT: R 401 GLN cc_start: 0.8275 (pm20) cc_final: 0.7750 (pm20) REVERT: R 404 ARG cc_start: 0.8366 (ptt-90) cc_final: 0.7942 (ptt-90) REVERT: R 405 LYS cc_start: 0.9270 (tptt) cc_final: 0.8755 (tptt) REVERT: R 425 MET cc_start: 0.4998 (OUTLIER) cc_final: 0.4325 (ppp) REVERT: R 429 TYR cc_start: 0.7106 (m-80) cc_final: 0.6583 (m-80) REVERT: R 441 MET cc_start: 0.7792 (mmp) cc_final: 0.7199 (mmt) REVERT: R 444 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7754 (mm-30) REVERT: R 469 GLU cc_start: 0.6759 (mm-30) cc_final: 0.6476 (mm-30) outliers start: 111 outliers final: 81 residues processed: 647 average time/residue: 0.3425 time to fit residues: 318.1496 Evaluate side-chains 646 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 559 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 263 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 361 LEU 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 122 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 228 ASP 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 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 256 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 98 SER Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 121 CYS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 143 THR 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 190 LEU Chi-restraints excluded: chain D residue 262 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 12 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 91 THR 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 6 GLN Chi-restraints excluded: chain H residue 9 HIS Chi-restraints excluded: chain H residue 16 ASN Chi-restraints excluded: chain H residue 18 MET Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 117 CYS 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 308 SER 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 84 ASN 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 232 LEU Chi-restraints excluded: chain R residue 238 PHE Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 334 VAL 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 425 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 115 optimal weight: 0.9990 chunk 120 optimal weight: 0.0770 chunk 207 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 204 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 147 optimal weight: 0.0670 chunk 72 optimal weight: 1.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- 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** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 139 ASN I 451 GLN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 307 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.153374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.128595 restraints weight = 35696.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.132707 restraints weight = 19002.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.135454 restraints weight = 11920.525| |-----------------------------------------------------------------------------| r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.7796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 18905 Z= 0.153 Angle : 0.747 11.581 25597 Z= 0.387 Chirality : 0.046 0.330 2817 Planarity : 0.004 0.043 3251 Dihedral : 4.546 21.463 2536 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.73 % Rotamer: Outliers : 4.82 % Allowed : 30.15 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.18), residues: 2270 helix: 2.12 (0.17), residues: 903 sheet: 0.38 (0.24), residues: 438 loop : -0.90 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP I 437 HIS 0.006 0.001 HIS B 62 PHE 0.038 0.002 PHE B 199 TYR 0.033 0.002 TYR R 221 ARG 0.009 0.001 ARG I 214 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 987) hydrogen bonds : angle 4.38404 ( 2847) SS BOND : bond 0.00322 ( 12) SS BOND : angle 0.94165 ( 24) covalent geometry : bond 0.00350 (18893) covalent geometry : angle 0.74651 (25573) *********************** 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 661 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 565 time to evaluate : 1.897 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: 0.8573 (mttt) cc_final: 0.8156 (mtmt) REVERT: A 31 ARG cc_start: 0.7709 (mmm-85) cc_final: 0.7478 (mmm-85) REVERT: A 51 LYS cc_start: 0.7909 (tptt) cc_final: 0.7679 (tptt) REVERT: A 186 GLU cc_start: 0.7634 (pm20) cc_final: 0.7183 (pm20) REVERT: A 204 GLN cc_start: 0.8177 (tp-100) cc_final: 0.7852 (tp-100) REVERT: A 306 TYR cc_start: 0.7917 (m-80) cc_final: 0.7507 (m-80) REVERT: A 310 ASP cc_start: 0.7902 (m-30) cc_final: 0.7485 (m-30) REVERT: A 325 TYR cc_start: 0.6736 (t80) cc_final: 0.6509 (t80) REVERT: A 347 ARG cc_start: 0.7719 (tpp-160) cc_final: 0.7493 (mmp-170) REVERT: B 8 ARG cc_start: 0.8445 (ptt-90) cc_final: 0.8205 (ptt-90) REVERT: B 9 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8780 (mm-40) REVERT: B 52 ARG cc_start: 0.5499 (mtt90) cc_final: 0.4375 (mtt90) REVERT: B 62 HIS cc_start: 0.7095 (t-170) cc_final: 0.6796 (t-170) REVERT: B 96 ARG cc_start: 0.7474 (mtm-85) cc_final: 0.6895 (ttm110) REVERT: B 150 ARG cc_start: 0.7192 (mmt180) cc_final: 0.6732 (tpp-160) REVERT: B 166 CYS cc_start: 0.7333 (m) cc_final: 0.7049 (m) REVERT: B 335 PHE cc_start: 0.7321 (m-80) cc_final: 0.6966 (m-80) REVERT: C 20 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7719 (mm-30) REVERT: C 27 LYS cc_start: 0.8138 (ttmm) cc_final: 0.7891 (ttmm) REVERT: C 53 MET cc_start: 0.4059 (mmt) cc_final: 0.2600 (mmt) REVERT: C 198 MET cc_start: 0.7144 (ttm) cc_final: 0.6914 (ttm) REVERT: D 12 GLU cc_start: 0.7957 (pp20) cc_final: 0.7635 (pp20) REVERT: D 15 LYS cc_start: 0.8765 (ttpp) cc_final: 0.7814 (ttpp) REVERT: D 16 ASN cc_start: 0.8450 (m-40) cc_final: 0.7931 (m-40) REVERT: D 19 ARG cc_start: 0.8100 (ptp90) cc_final: 0.7774 (ptp-170) REVERT: D 59 TYR cc_start: 0.7515 (OUTLIER) cc_final: 0.7224 (m-80) REVERT: D 62 HIS cc_start: 0.7046 (t-90) cc_final: 0.5784 (t70) REVERT: D 143 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8392 (t) REVERT: D 150 ARG cc_start: 0.7155 (mmt-90) cc_final: 0.6340 (mmt180) REVERT: D 176 GLN cc_start: 0.8227 (mp10) cc_final: 0.7659 (mt0) REVERT: D 188 MET cc_start: 0.7496 (mmt) cc_final: 0.7112 (mmt) REVERT: E 17 GLU cc_start: 0.8270 (tp30) cc_final: 0.7764 (tp30) REVERT: F 29 PHE cc_start: 0.8309 (t80) cc_final: 0.8088 (t80) REVERT: F 63 SER cc_start: 0.7902 (m) cc_final: 0.7611 (t) REVERT: G 38 MET cc_start: 0.8363 (mmm) cc_final: 0.8011 (mmm) REVERT: G 52 THR cc_start: 0.7600 (OUTLIER) cc_final: 0.7345 (t) REVERT: I 42 HIS cc_start: 0.8459 (m170) cc_final: 0.8165 (m170) REVERT: I 156 LEU cc_start: 0.2606 (OUTLIER) cc_final: 0.0505 (tt) REVERT: I 228 LEU cc_start: 0.7666 (tt) cc_final: 0.7262 (tp) REVERT: I 346 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6733 (tt) REVERT: I 352 TRP cc_start: 0.6808 (m-10) cc_final: 0.6253 (m-90) REVERT: I 425 MET cc_start: 0.5310 (tmm) cc_final: 0.4276 (tmm) REVERT: I 469 GLU cc_start: 0.7868 (tp30) cc_final: 0.6533 (tp30) REVERT: I 472 LYS cc_start: 0.8864 (tmmt) cc_final: 0.8490 (tmmt) REVERT: P 24 LEU cc_start: 0.5093 (OUTLIER) cc_final: 0.4840 (tt) REVERT: R 32 MET cc_start: 0.7336 (tmm) cc_final: 0.6786 (tmm) REVERT: R 36 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8405 (mp0) REVERT: R 115 ILE cc_start: 0.4900 (OUTLIER) cc_final: 0.4680 (pt) REVERT: R 189 MET cc_start: 0.7483 (ttp) cc_final: 0.7232 (tmm) REVERT: R 208 ILE cc_start: 0.8244 (mt) cc_final: 0.8032 (tp) REVERT: R 214 ARG cc_start: 0.7508 (tmt170) cc_final: 0.7091 (tmt170) REVERT: R 309 LEU cc_start: 0.7045 (mt) cc_final: 0.6841 (mt) REVERT: R 400 ARG cc_start: 0.8229 (mmm160) cc_final: 0.7587 (mmm160) REVERT: R 401 GLN cc_start: 0.8304 (pm20) cc_final: 0.7707 (pm20) REVERT: R 403 TYR cc_start: 0.6463 (m-80) cc_final: 0.6216 (m-80) REVERT: R 404 ARG cc_start: 0.8345 (ptt-90) cc_final: 0.7963 (ptt-90) REVERT: R 405 LYS cc_start: 0.9268 (tptt) cc_final: 0.8777 (tptt) REVERT: R 425 MET cc_start: 0.5098 (OUTLIER) cc_final: 0.4393 (ppp) REVERT: R 429 TYR cc_start: 0.7147 (m-80) cc_final: 0.6607 (m-80) REVERT: R 441 MET cc_start: 0.7797 (mmp) cc_final: 0.7238 (mmt) REVERT: R 469 GLU cc_start: 0.6756 (mm-30) cc_final: 0.6477 (mm-30) outliers start: 96 outliers final: 76 residues processed: 623 average time/residue: 0.3561 time to fit residues: 321.2580 Evaluate side-chains 633 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 549 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU 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 263 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 361 LEU 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 157 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET 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 315 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 329 HIS Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 143 THR 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 190 LEU Chi-restraints excluded: chain D residue 262 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 91 THR 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 6 GLN Chi-restraints excluded: chain H residue 9 HIS 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 117 CYS 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 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 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 232 LEU Chi-restraints excluded: chain R residue 238 PHE Chi-restraints excluded: chain R residue 334 VAL 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 425 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 164 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 165 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 190 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 142 optimal weight: 0.3980 chunk 168 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS C 24 GLN D 119 ASN ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN R 307 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.150969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.126177 restraints weight = 35926.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.130225 restraints weight = 19295.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.132912 restraints weight = 12088.648| |-----------------------------------------------------------------------------| r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.8163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 18905 Z= 0.170 Angle : 0.774 12.305 25597 Z= 0.401 Chirality : 0.047 0.351 2817 Planarity : 0.004 0.047 3251 Dihedral : 4.619 21.316 2536 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.41 % Favored : 95.51 % Rotamer: Outliers : 4.67 % Allowed : 30.50 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2270 helix: 2.03 (0.17), residues: 903 sheet: 0.15 (0.24), residues: 446 loop : -0.89 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP I 437 HIS 0.006 0.001 HIS B 311 PHE 0.047 0.002 PHE B 199 TYR 0.026 0.002 TYR I 443 ARG 0.009 0.001 ARG D 214 Details of bonding type rmsd hydrogen bonds : bond 0.04425 ( 987) hydrogen bonds : angle 4.48854 ( 2847) SS BOND : bond 0.00381 ( 12) SS BOND : angle 1.19534 ( 24) covalent geometry : bond 0.00387 (18893) covalent geometry : angle 0.77328 (25573) *********************** 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 664 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 571 time to evaluate : 2.018 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: A 25 LYS cc_start: 0.8629 (mttt) cc_final: 0.8244 (mtmt) REVERT: A 31 ARG cc_start: 0.7757 (mmm-85) cc_final: 0.7529 (mmm-85) REVERT: A 51 LYS cc_start: 0.7953 (tptt) cc_final: 0.7689 (tptt) REVERT: A 186 GLU cc_start: 0.7665 (pm20) cc_final: 0.7279 (pm20) REVERT: A 204 GLN cc_start: 0.8159 (tp-100) cc_final: 0.7806 (tp-100) REVERT: A 274 LYS cc_start: 0.8258 (tppt) cc_final: 0.7839 (ptmm) REVERT: A 306 TYR cc_start: 0.7946 (m-80) cc_final: 0.7555 (m-80) REVERT: A 310 ASP cc_start: 0.7885 (m-30) cc_final: 0.7478 (m-30) REVERT: A 347 ARG cc_start: 0.7711 (tpp-160) cc_final: 0.7493 (mmp-170) REVERT: A 360 LEU cc_start: 0.8089 (mt) cc_final: 0.7883 (mt) REVERT: B 9 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8808 (mm-40) REVERT: B 52 ARG cc_start: 0.5613 (mtt90) cc_final: 0.4654 (mtt90) REVERT: B 63 TRP cc_start: 0.6794 (m-10) cc_final: 0.6569 (m-10) REVERT: B 96 ARG cc_start: 0.7312 (mtm-85) cc_final: 0.6837 (ttm110) REVERT: B 150 ARG cc_start: 0.7195 (mmt180) cc_final: 0.6809 (tpp-160) REVERT: B 166 CYS cc_start: 0.7265 (m) cc_final: 0.6852 (m) REVERT: B 325 MET cc_start: 0.5887 (mmt) cc_final: 0.5624 (mmt) REVERT: B 335 PHE cc_start: 0.7318 (m-80) cc_final: 0.6903 (m-80) REVERT: C 15 ARG cc_start: 0.8123 (mmm-85) cc_final: 0.7694 (mmm-85) REVERT: C 17 LYS cc_start: 0.8537 (mmtp) cc_final: 0.8247 (mmtp) REVERT: C 20 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7621 (mm-30) REVERT: C 23 LEU cc_start: 0.8939 (mt) cc_final: 0.8689 (mt) REVERT: C 27 LYS cc_start: 0.8217 (ttmm) cc_final: 0.7918 (ttmm) REVERT: C 35 ARG cc_start: 0.7174 (mtt-85) cc_final: 0.6808 (mtt180) REVERT: C 52 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7930 (mp10) REVERT: C 53 MET cc_start: 0.4171 (mmt) cc_final: 0.3086 (mmt) REVERT: C 198 MET cc_start: 0.7263 (ttm) cc_final: 0.7021 (ttm) REVERT: C 281 GLU cc_start: 0.7618 (tp30) cc_final: 0.7268 (tp30) REVERT: D 12 GLU cc_start: 0.7966 (pp20) cc_final: 0.7720 (pp20) REVERT: D 59 TYR cc_start: 0.7575 (OUTLIER) cc_final: 0.7258 (m-80) REVERT: D 62 HIS cc_start: 0.7024 (t-90) cc_final: 0.5941 (t70) REVERT: D 82 TRP cc_start: 0.7618 (m100) cc_final: 0.7156 (m100) REVERT: D 143 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8431 (t) REVERT: D 150 ARG cc_start: 0.7162 (mmt-90) cc_final: 0.6472 (mmt180) REVERT: D 176 GLN cc_start: 0.8187 (mp10) cc_final: 0.7636 (mt0) REVERT: F 29 PHE cc_start: 0.8372 (t80) cc_final: 0.8072 (t80) REVERT: F 63 SER cc_start: 0.7986 (m) cc_final: 0.7701 (t) REVERT: G 38 MET cc_start: 0.8397 (mmm) cc_final: 0.7978 (mmm) REVERT: I 156 LEU cc_start: 0.2699 (OUTLIER) cc_final: 0.0619 (tt) REVERT: I 228 LEU cc_start: 0.7685 (tt) cc_final: 0.7330 (tp) REVERT: I 346 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6863 (tt) REVERT: I 352 TRP cc_start: 0.6950 (m-10) cc_final: 0.6250 (m-90) REVERT: I 425 MET cc_start: 0.5330 (tmm) cc_final: 0.4216 (tmm) REVERT: I 440 GLN cc_start: 0.8262 (pp30) cc_final: 0.6959 (pp30) REVERT: I 441 MET cc_start: 0.7949 (mmt) cc_final: 0.7649 (mmt) REVERT: I 469 GLU cc_start: 0.7900 (tp30) cc_final: 0.6599 (tp30) REVERT: I 472 LYS cc_start: 0.8898 (tmmt) cc_final: 0.8522 (tmmt) REVERT: N 118 ARG cc_start: 0.8431 (mtm180) cc_final: 0.8054 (mtm180) REVERT: P 24 LEU cc_start: 0.5168 (OUTLIER) cc_final: 0.4886 (tt) REVERT: R 32 MET cc_start: 0.7321 (tmm) cc_final: 0.6761 (tmm) REVERT: R 36 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8348 (mp0) REVERT: R 43 ARG cc_start: 0.7101 (ptt90) cc_final: 0.6894 (ptt90) REVERT: R 189 MET cc_start: 0.7499 (ttp) cc_final: 0.7265 (tmm) REVERT: R 208 ILE cc_start: 0.8291 (mt) cc_final: 0.8077 (tt) REVERT: R 214 ARG cc_start: 0.7606 (tmt170) cc_final: 0.7201 (tmt170) REVERT: R 400 ARG cc_start: 0.8203 (mmm160) cc_final: 0.7470 (mmm160) REVERT: R 401 GLN cc_start: 0.8316 (pm20) cc_final: 0.7708 (pm20) REVERT: R 403 TYR cc_start: 0.6629 (m-80) cc_final: 0.5898 (m-80) REVERT: R 404 ARG cc_start: 0.8354 (ptt-90) cc_final: 0.7972 (ptt-90) REVERT: R 405 LYS cc_start: 0.9263 (tptt) cc_final: 0.8798 (tptt) REVERT: R 425 MET cc_start: 0.5137 (OUTLIER) cc_final: 0.4389 (ppp) REVERT: R 429 TYR cc_start: 0.7151 (m-80) cc_final: 0.6638 (m-80) REVERT: R 441 MET cc_start: 0.7814 (mmp) cc_final: 0.7296 (mmt) REVERT: R 469 GLU cc_start: 0.6868 (mm-30) cc_final: 0.6543 (mm-30) outliers start: 93 outliers final: 78 residues processed: 624 average time/residue: 0.3569 time to fit residues: 322.0123 Evaluate side-chains 639 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 554 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 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 A residue 263 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 361 LEU 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 157 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET 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 315 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 256 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 98 SER Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 143 THR 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 190 LEU Chi-restraints excluded: chain D residue 262 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 34 MET Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 115 TYR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 9 HIS 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 117 CYS 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 283 VAL Chi-restraints excluded: chain I residue 311 PHE Chi-restraints excluded: chain I residue 334 VAL Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 436 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 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 191 TYR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 238 PHE Chi-restraints excluded: chain R residue 334 VAL 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 425 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 199 optimal weight: 0.5980 chunk 142 optimal weight: 6.9990 chunk 225 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 62 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 167 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 380 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 HIS ** 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 = 0.151238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.126450 restraints weight = 35980.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.130537 restraints weight = 19182.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.133204 restraints weight = 12019.675| |-----------------------------------------------------------------------------| r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.8456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18905 Z= 0.161 Angle : 0.793 15.644 25597 Z= 0.408 Chirality : 0.047 0.344 2817 Planarity : 0.005 0.053 3251 Dihedral : 4.665 20.888 2536 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.46 % Rotamer: Outliers : 4.32 % Allowed : 31.26 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.18), residues: 2270 helix: 1.98 (0.17), residues: 903 sheet: 0.12 (0.24), residues: 436 loop : -0.90 (0.21), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP I 437 HIS 0.006 0.001 HIS B 62 PHE 0.044 0.002 PHE B 199 TYR 0.027 0.002 TYR C 285 ARG 0.016 0.001 ARG C 314 Details of bonding type rmsd hydrogen bonds : bond 0.04421 ( 987) hydrogen bonds : angle 4.52096 ( 2847) SS BOND : bond 0.00309 ( 12) SS BOND : angle 1.04730 ( 24) covalent geometry : bond 0.00366 (18893) covalent geometry : angle 0.79273 (25573) ********************** 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 653 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 567 time to evaluate : 2.001 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: 0.8656 (mttt) cc_final: 0.8285 (mtmt) REVERT: A 31 ARG cc_start: 0.7758 (mmm-85) cc_final: 0.7535 (mmm-85) REVERT: A 51 LYS cc_start: 0.7932 (tptt) cc_final: 0.7708 (tptt) REVERT: A 186 GLU cc_start: 0.7697 (pm20) cc_final: 0.7283 (pm20) REVERT: A 274 LYS cc_start: 0.8186 (tppt) cc_final: 0.7701 (ptmm) REVERT: A 306 TYR cc_start: 0.7950 (m-80) cc_final: 0.7533 (m-80) REVERT: A 310 ASP cc_start: 0.7867 (m-30) cc_final: 0.7438 (m-30) REVERT: A 347 ARG cc_start: 0.7703 (tpp-160) cc_final: 0.7501 (mmp-170) REVERT: A 360 LEU cc_start: 0.8091 (mt) cc_final: 0.7863 (mt) REVERT: B 9 GLN cc_start: 0.9103 (mm-40) cc_final: 0.8835 (mm-40) REVERT: B 52 ARG cc_start: 0.5684 (mtt90) cc_final: 0.4644 (mtt90) REVERT: B 62 HIS cc_start: 0.6882 (t70) cc_final: 0.6670 (t70) REVERT: B 96 ARG cc_start: 0.7260 (mtm-85) cc_final: 0.6835 (ttm110) REVERT: B 126 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6639 (mt) REVERT: B 166 CYS cc_start: 0.7222 (m) cc_final: 0.6814 (m) REVERT: B 325 MET cc_start: 0.5905 (mmt) cc_final: 0.5649 (mmt) REVERT: B 335 PHE cc_start: 0.7182 (m-80) cc_final: 0.6862 (m-80) REVERT: C 15 ARG cc_start: 0.8002 (mmm-85) cc_final: 0.7510 (mmm-85) REVERT: C 20 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7659 (mm-30) REVERT: C 23 LEU cc_start: 0.8940 (mt) cc_final: 0.8695 (mt) REVERT: C 27 LYS cc_start: 0.8214 (ttmm) cc_final: 0.7957 (ttmm) REVERT: C 35 ARG cc_start: 0.7161 (mtt-85) cc_final: 0.6807 (mtt180) REVERT: C 52 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7936 (mp10) REVERT: C 53 MET cc_start: 0.4325 (mmt) cc_final: 0.3098 (mmt) REVERT: C 198 MET cc_start: 0.7272 (ttm) cc_final: 0.7026 (ttm) REVERT: C 209 ARG cc_start: 0.8001 (ptp90) cc_final: 0.7724 (ptt90) REVERT: C 281 GLU cc_start: 0.7440 (tp30) cc_final: 0.7141 (tp30) REVERT: C 316 SER cc_start: 0.8285 (t) cc_final: 0.7920 (p) REVERT: D 12 GLU cc_start: 0.7984 (pp20) cc_final: 0.7581 (pp20) REVERT: D 59 TYR cc_start: 0.7538 (OUTLIER) cc_final: 0.7170 (m-80) REVERT: D 62 HIS cc_start: 0.6974 (t-90) cc_final: 0.6146 (t-90) REVERT: D 143 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8426 (t) REVERT: D 150 ARG cc_start: 0.7170 (mmt-90) cc_final: 0.6679 (mmt180) REVERT: D 176 GLN cc_start: 0.8214 (mp10) cc_final: 0.7641 (mt0) REVERT: G 38 MET cc_start: 0.8378 (mmm) cc_final: 0.7958 (mmm) REVERT: G 52 THR cc_start: 0.7505 (OUTLIER) cc_final: 0.7241 (t) REVERT: I 156 LEU cc_start: 0.2964 (OUTLIER) cc_final: 0.0953 (tt) REVERT: I 228 LEU cc_start: 0.7698 (tt) cc_final: 0.7379 (tp) REVERT: I 346 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6874 (tt) REVERT: I 352 TRP cc_start: 0.6950 (m-10) cc_final: 0.6183 (m-90) REVERT: I 425 MET cc_start: 0.5385 (tmm) cc_final: 0.4273 (tmm) REVERT: I 469 GLU cc_start: 0.7895 (tp30) cc_final: 0.6524 (tp30) REVERT: I 472 LYS cc_start: 0.8892 (tmmt) cc_final: 0.8509 (tmmt) REVERT: P 24 LEU cc_start: 0.5085 (OUTLIER) cc_final: 0.4873 (tt) REVERT: R 32 MET cc_start: 0.7334 (tmm) cc_final: 0.6998 (tmm) REVERT: R 36 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8349 (mp0) REVERT: R 189 MET cc_start: 0.7466 (ttp) cc_final: 0.7216 (tmm) REVERT: R 214 ARG cc_start: 0.7625 (tmt170) cc_final: 0.7217 (tmt170) REVERT: R 400 ARG cc_start: 0.8177 (mmm160) cc_final: 0.7398 (mmm160) REVERT: R 401 GLN cc_start: 0.8331 (pm20) cc_final: 0.7719 (pm20) REVERT: R 403 TYR cc_start: 0.6703 (m-80) cc_final: 0.5943 (m-80) REVERT: R 404 ARG cc_start: 0.8327 (ptt-90) cc_final: 0.7939 (ptt-90) REVERT: R 405 LYS cc_start: 0.9257 (tptt) cc_final: 0.8800 (tptt) REVERT: R 425 MET cc_start: 0.5200 (OUTLIER) cc_final: 0.4421 (ppp) REVERT: R 429 TYR cc_start: 0.7198 (m-80) cc_final: 0.6683 (m-80) REVERT: R 441 MET cc_start: 0.7831 (mmp) cc_final: 0.7355 (mmt) REVERT: R 469 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6574 (mm-30) outliers start: 86 outliers final: 72 residues processed: 618 average time/residue: 0.3800 time to fit residues: 338.4913 Evaluate side-chains 632 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 551 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 361 LEU 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 121 CYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET 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 315 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 52 GLN 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 98 SER Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 143 THR 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 190 LEU Chi-restraints excluded: chain D residue 262 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 91 THR 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 6 GLN Chi-restraints excluded: chain H residue 9 HIS 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 117 CYS 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 283 VAL Chi-restraints excluded: chain I residue 311 PHE Chi-restraints excluded: chain I residue 334 VAL Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 380 ASN 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 116 LEU Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 238 PHE Chi-restraints excluded: chain R residue 334 VAL 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 425 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 51 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 123 optimal weight: 0.0980 chunk 15 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 153 optimal weight: 0.5980 chunk 218 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN D 119 ASN ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 380 ASN ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.150787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.126143 restraints weight = 35687.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.130120 restraints weight = 19219.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.132763 restraints weight = 12141.819| |-----------------------------------------------------------------------------| r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.8635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18905 Z= 0.164 Angle : 0.796 15.548 25597 Z= 0.414 Chirality : 0.047 0.344 2817 Planarity : 0.005 0.055 3251 Dihedral : 4.697 21.241 2536 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.20 % Rotamer: Outliers : 4.22 % Allowed : 31.91 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.18), residues: 2270 helix: 1.87 (0.17), residues: 903 sheet: 0.06 (0.24), residues: 434 loop : -0.93 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP R 154 HIS 0.007 0.001 HIS B 62 PHE 0.043 0.002 PHE B 199 TYR 0.028 0.002 TYR F 80 ARG 0.010 0.001 ARG R 43 Details of bonding type rmsd hydrogen bonds : bond 0.04451 ( 987) hydrogen bonds : angle 4.57370 ( 2847) SS BOND : bond 0.00293 ( 12) SS BOND : angle 1.21237 ( 24) covalent geometry : bond 0.00372 (18893) covalent geometry : angle 0.79584 (25573) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10711.69 seconds wall clock time: 190 minutes 6.61 seconds (11406.61 seconds total)