Starting phenix.real_space_refine on Sat Sep 28 06:00:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hao_34598/09_2024/8hao_34598_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hao_34598/09_2024/8hao_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hao_34598/09_2024/8hao_34598.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hao_34598/09_2024/8hao_34598.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hao_34598/09_2024/8hao_34598_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hao_34598/09_2024/8hao_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 12.23, per 1000 atoms: 0.66 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: 4.59 Conformation dependent library (CDL) restraints added in 2.3 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: 2.11 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: 5.72 Time building geometry restraints manager: 5.36 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: 41.770 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.930 Process input model: 42.210 Find NCS groups from input model: 0.590 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.440 ------------------------------------------------------------------------------- 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 18893 Z= 0.167 Angle : 0.503 10.793 25573 Z= 0.282 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 *********************** 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 fitting. rotamer outliers: 8 poor density : 646 time to evaluate : 2.106 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: 0.3656 time to fit residues: 338.6441 Evaluate side-chains 481 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 479 time to evaluate : 2.328 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5989 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 18893 Z= 0.276 Angle : 0.727 9.871 25573 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 *********************** 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 fitting. rotamer outliers: 100 poor density : 592 time to evaluate : 2.165 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 238 ASN cc_start: 0.8005 (m-40) cc_final: 0.7403 (m-40) REVERT: B 101 MET cc_start: 0.6298 (mmm) cc_final: 0.5969 (mtt) REVERT: B 124 TYR cc_start: 0.5760 (m-10) cc_final: 0.5494 (m-10) REVERT: B 135 VAL cc_start: 0.7580 (t) cc_final: 0.6781 (t) REVERT: B 187 VAL cc_start: 0.8293 (t) cc_final: 0.8045 (p) REVERT: C 13 VAL cc_start: 0.8073 (t) cc_final: 0.7275 (t) REVERT: C 255 ILE cc_start: 0.7158 (OUTLIER) cc_final: 0.6917 (tp) REVERT: C 327 TYR cc_start: 0.6350 (m-80) cc_final: 0.6107 (m-80) REVERT: D 62 HIS cc_start: 0.6648 (t70) cc_final: 0.6342 (t70) REVERT: D 171 ILE cc_start: 0.4490 (OUTLIER) cc_final: 0.4017 (mm) REVERT: D 232 ILE cc_start: 0.7641 (tt) cc_final: 0.7423 (mt) REVERT: D 258 ASP cc_start: 0.6473 (t0) cc_final: 0.6230 (t0) REVERT: E 38 MET cc_start: 0.5139 (mmp) cc_final: 0.4881 (mmp) REVERT: F 29 PHE cc_start: 0.7194 (t80) cc_final: 0.6892 (t80) REVERT: I 425 MET cc_start: 0.3898 (tmm) cc_final: 0.3215 (tmm) REVERT: I 457 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7876 (mm) REVERT: N 84 ASN cc_start: 0.7485 (OUTLIER) cc_final: 0.7079 (p0) REVERT: R 40 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.5904 (tp) REVERT: R 191 TYR cc_start: 0.6086 (OUTLIER) cc_final: 0.5844 (p90) REVERT: R 401 GLN cc_start: 0.7628 (pm20) cc_final: 0.7077 (pm20) REVERT: R 405 LYS cc_start: 0.8473 (tptt) cc_final: 0.8229 (tptt) REVERT: R 441 MET cc_start: 0.6855 (mmp) cc_final: 0.6486 (mmt) outliers start: 100 outliers final: 50 residues processed: 651 average time/residue: 0.3311 time to fit residues: 312.5673 Evaluate side-chains 573 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 517 time to evaluate : 2.021 ------------------------------------------------------------------------------- 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 255 ILE 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 114 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 205 optimal weight: 0.6980 chunk 222 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 203 optimal weight: 0.7980 chunk 70 optimal weight: 0.2980 chunk 164 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18893 Z= 0.232 Angle : 0.664 9.295 25573 Z= 0.355 Chirality : 0.044 0.228 2817 Planarity : 0.005 0.063 3251 Dihedral : 4.396 29.070 2536 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.35 % Favored : 96.48 % Rotamer: Outliers : 4.77 % Allowed : 23.82 % Favored : 71.41 % 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: 1.28 (0.18), residues: 2270 helix: 2.52 (0.16), residues: 905 sheet: 0.57 (0.24), residues: 432 loop : -0.72 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 82 HIS 0.011 0.001 HIS I 216 PHE 0.027 0.002 PHE I 447 TYR 0.021 0.002 TYR I 191 ARG 0.014 0.001 ARG A 247 *********************** 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 665 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 570 time to evaluate : 2.007 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: A 238 ASN cc_start: 0.8317 (m-40) cc_final: 0.7840 (m-40) REVERT: A 357 GLN cc_start: 0.8121 (tp-100) cc_final: 0.7874 (tp-100) REVERT: B 96 ARG cc_start: 0.6778 (mtm-85) cc_final: 0.6395 (ttm110) REVERT: B 101 MET cc_start: 0.6579 (mmm) cc_final: 0.6338 (mtt) REVERT: C 13 VAL cc_start: 0.8037 (t) cc_final: 0.7382 (p) REVERT: D 15 LYS cc_start: 0.8098 (ttpp) cc_final: 0.7738 (ttpp) REVERT: D 55 LEU cc_start: 0.6655 (mp) cc_final: 0.6384 (mp) REVERT: D 99 TRP cc_start: 0.7803 (m100) cc_final: 0.7416 (m100) REVERT: D 188 MET cc_start: 0.7459 (mmt) cc_final: 0.7088 (mmt) REVERT: D 325 MET cc_start: 0.5356 (mmm) cc_final: 0.4900 (mmt) REVERT: F 29 PHE cc_start: 0.7579 (t80) cc_final: 0.7250 (t80) REVERT: I 42 HIS cc_start: 0.7753 (m170) cc_final: 0.7537 (m170) REVERT: I 425 MET cc_start: 0.4248 (tmm) cc_final: 0.3382 (tmm) REVERT: I 437 TRP cc_start: 0.5730 (t60) cc_final: 0.5185 (t60) REVERT: I 457 ILE cc_start: 0.8289 (mm) cc_final: 0.8088 (mm) REVERT: N 84 ASN cc_start: 0.7626 (p0) cc_final: 0.7415 (p0) REVERT: P 24 LEU cc_start: 0.4999 (OUTLIER) cc_final: 0.4631 (tt) REVERT: R 189 MET cc_start: 0.7055 (ttp) cc_final: 0.6843 (tmm) REVERT: R 237 ILE cc_start: 0.8263 (tp) cc_final: 0.7952 (tt) REVERT: R 400 ARG cc_start: 0.7500 (mmm160) cc_final: 0.6479 (mmm160) REVERT: R 401 GLN cc_start: 0.7738 (pm20) cc_final: 0.6878 (pm20) REVERT: R 414 MET cc_start: 0.7308 (tpp) cc_final: 0.6986 (tpp) REVERT: R 425 MET cc_start: 0.4677 (ppp) cc_final: 0.4228 (ppp) REVERT: R 441 MET cc_start: 0.6976 (mmp) cc_final: 0.6659 (mmt) outliers start: 95 outliers final: 53 residues processed: 628 average time/residue: 0.3090 time to fit residues: 282.1642 Evaluate side-chains 588 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 534 time to evaluate : 2.044 ------------------------------------------------------------------------------- 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 233 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 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 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 203 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 chunk 106 optimal weight: 0.0670 chunk 22 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 138 optimal weight: 0.6980 chunk 206 optimal weight: 0.6980 chunk 218 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 195 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 HIS ** 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 C 43 ASN C 354 HIS D 119 ASN ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS H 16 ASN ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 467 GLN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 10 ASN R 220 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.6109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18893 Z= 0.220 Angle : 0.666 10.835 25573 Z= 0.353 Chirality : 0.045 0.319 2817 Planarity : 0.005 0.072 3251 Dihedral : 4.349 22.388 2536 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.48 % Favored : 96.34 % Rotamer: Outliers : 5.33 % Allowed : 25.13 % Favored : 69.55 % 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: 1.17 (0.18), residues: 2270 helix: 2.39 (0.16), residues: 906 sheet: 0.47 (0.24), residues: 438 loop : -0.73 (0.22), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I 352 HIS 0.015 0.001 HIS I 216 PHE 0.023 0.002 PHE I 447 TYR 0.028 0.002 TYR I 403 ARG 0.012 0.001 ARG I 282 *********************** 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 676 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 570 time to evaluate : 2.073 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: A 337 GLU cc_start: 0.6978 (mp0) cc_final: 0.6682 (mp0) REVERT: B 44 GLN cc_start: 0.6964 (pm20) cc_final: 0.6608 (pp30) REVERT: B 96 ARG cc_start: 0.6900 (mtm-85) cc_final: 0.6652 (mtm-85) REVERT: B 97 SER cc_start: 0.7769 (t) cc_final: 0.7493 (p) REVERT: B 101 MET cc_start: 0.6661 (mmm) cc_final: 0.6376 (mtt) REVERT: C 13 VAL cc_start: 0.8089 (t) cc_final: 0.7318 (t) REVERT: C 53 MET cc_start: 0.4095 (mmt) cc_final: 0.2104 (mmt) REVERT: C 233 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7828 (mt) REVERT: C 360 LEU cc_start: 0.7422 (mt) cc_final: 0.7222 (mp) REVERT: D 62 HIS cc_start: 0.6762 (t70) cc_final: 0.5520 (t70) REVERT: D 150 ARG cc_start: 0.7209 (mmt-90) cc_final: 0.6539 (mmt180) REVERT: D 188 MET cc_start: 0.7436 (mmt) cc_final: 0.6890 (mmt) REVERT: F 29 PHE cc_start: 0.7791 (t80) cc_final: 0.7480 (t80) REVERT: I 189 MET cc_start: 0.6439 (ptp) cc_final: 0.6105 (ppp) REVERT: I 425 MET cc_start: 0.4522 (tmm) cc_final: 0.3677 (tmm) REVERT: I 441 MET cc_start: 0.6911 (mmt) cc_final: 0.6057 (mmt) REVERT: I 457 ILE cc_start: 0.8359 (mm) cc_final: 0.8139 (mm) REVERT: I 469 GLU cc_start: 0.6794 (tp30) cc_final: 0.5707 (tp30) REVERT: N 34 MET cc_start: 0.5884 (mmm) cc_final: 0.5636 (mmm) REVERT: P 24 LEU cc_start: 0.4932 (OUTLIER) cc_final: 0.4652 (tt) REVERT: R 189 MET cc_start: 0.7100 (ttp) cc_final: 0.6810 (tmm) REVERT: R 237 ILE cc_start: 0.8276 (tp) cc_final: 0.7986 (tt) REVERT: R 379 ILE cc_start: 0.7231 (mm) cc_final: 0.6688 (tp) REVERT: R 404 ARG cc_start: 0.7745 (ptt-90) cc_final: 0.7280 (ptp90) REVERT: R 425 MET cc_start: 0.4637 (ppp) cc_final: 0.4168 (ppp) REVERT: R 443 TYR cc_start: 0.6848 (t80) cc_final: 0.6646 (t80) REVERT: R 444 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7059 (mm-30) outliers start: 106 outliers final: 73 residues processed: 631 average time/residue: 0.3786 time to fit residues: 350.4358 Evaluate side-chains 621 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 546 time to evaluate : 2.194 ------------------------------------------------------------------------------- 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 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 324 HIS 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 119 ASN 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 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 16 SER Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 233 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 353 MET Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 263 THR 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 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 30 VAL 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 I residue 297 TYR 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 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 171 VAL Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain R residue 238 PHE Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 385 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 181 optimal weight: 0.8980 chunk 124 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 162 optimal weight: 0.0770 chunk 90 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 196 optimal weight: 7.9990 chunk 55 optimal weight: 0.3980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 HIS B 9 GLN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS D 119 ASN ** D 183 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 16 ASN ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 463 ASN I 467 GLN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 220 ASN R 307 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.6577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18893 Z= 0.204 Angle : 0.683 14.312 25573 Z= 0.353 Chirality : 0.045 0.311 2817 Planarity : 0.004 0.045 3251 Dihedral : 4.366 21.900 2536 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.57 % Favored : 96.26 % Rotamer: Outliers : 5.08 % Allowed : 26.68 % Favored : 68.24 % 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: 1.05 (0.18), residues: 2270 helix: 2.28 (0.17), residues: 910 sheet: 0.48 (0.24), residues: 436 loop : -0.82 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP I 352 HIS 0.008 0.001 HIS I 42 PHE 0.034 0.002 PHE N 29 TYR 0.023 0.002 TYR R 305 ARG 0.014 0.001 ARG C 15 *********************** 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 675 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 574 time to evaluate : 2.145 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: A 198 MET cc_start: 0.6886 (tpp) cc_final: 0.6569 (tpp) REVERT: A 224 VAL cc_start: 0.7636 (m) cc_final: 0.7366 (m) REVERT: A 244 TRP cc_start: 0.7228 (t-100) cc_final: 0.6851 (t-100) REVERT: B 96 ARG cc_start: 0.6892 (mtm-85) cc_final: 0.6345 (ttm110) REVERT: B 101 MET cc_start: 0.6680 (mmm) cc_final: 0.6353 (mtt) REVERT: C 13 VAL cc_start: 0.8280 (t) cc_final: 0.7398 (t) REVERT: C 53 MET cc_start: 0.3924 (mmt) cc_final: 0.2152 (mmt) REVERT: C 233 LEU cc_start: 0.8147 (mp) cc_final: 0.7864 (mt) REVERT: C 327 TYR cc_start: 0.6850 (m-80) cc_final: 0.6553 (m-80) REVERT: C 360 LEU cc_start: 0.7525 (mt) cc_final: 0.7311 (mp) REVERT: D 62 HIS cc_start: 0.6806 (t-90) cc_final: 0.5764 (t70) REVERT: D 150 ARG cc_start: 0.7194 (mmt-90) cc_final: 0.6500 (mmt180) REVERT: D 262 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6866 (mpp) REVERT: F 29 PHE cc_start: 0.7815 (t80) cc_final: 0.7432 (t80) REVERT: I 348 ASN cc_start: 0.6812 (t0) cc_final: 0.6545 (t0) REVERT: I 425 MET cc_start: 0.4580 (tmm) cc_final: 0.3725 (tmm) REVERT: I 469 GLU cc_start: 0.6661 (tp30) cc_final: 0.6045 (tp30) REVERT: I 472 LYS cc_start: 0.8527 (tmmt) cc_final: 0.7986 (tmmt) REVERT: P 24 LEU cc_start: 0.5081 (OUTLIER) cc_final: 0.4779 (tt) REVERT: R 189 MET cc_start: 0.7025 (ttp) cc_final: 0.6778 (tmm) REVERT: R 214 ARG cc_start: 0.6818 (tmt170) cc_final: 0.6488 (tmt170) REVERT: R 237 ILE cc_start: 0.8315 (tp) cc_final: 0.8027 (tt) REVERT: R 379 ILE cc_start: 0.7373 (mm) cc_final: 0.7052 (tp) REVERT: R 420 HIS cc_start: 0.7170 (p90) cc_final: 0.6965 (p-80) REVERT: R 425 MET cc_start: 0.4538 (ppp) cc_final: 0.4070 (ppp) REVERT: R 441 MET cc_start: 0.7178 (mmp) cc_final: 0.6546 (mmt) REVERT: R 444 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7079 (mm-30) outliers start: 101 outliers final: 70 residues processed: 634 average time/residue: 0.3584 time to fit residues: 328.1117 Evaluate side-chains 621 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 549 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 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 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 119 ASN 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 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 16 SER Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 56 TYR Chi-restraints excluded: chain C residue 336 THR 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 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 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 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 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 334 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 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 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 225 HIS Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 385 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 73 optimal weight: 4.9990 chunk 196 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 52 GLN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN ** 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 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 220 ASN ** R 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.8035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 18893 Z= 0.367 Angle : 0.814 13.047 25573 Z= 0.433 Chirality : 0.051 0.403 2817 Planarity : 0.005 0.047 3251 Dihedral : 5.097 22.616 2536 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.76 % Favored : 95.11 % Rotamer: Outliers : 6.28 % Allowed : 27.64 % Favored : 66.08 % 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: 0.42 (0.17), residues: 2270 helix: 1.65 (0.16), residues: 916 sheet: -0.01 (0.25), residues: 424 loop : -0.95 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP I 352 HIS 0.015 0.002 HIS B 62 PHE 0.027 0.003 PHE B 222 TYR 0.024 0.003 TYR F 117 ARG 0.014 0.001 ARG I 214 *********************** 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 729 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 604 time to evaluate : 2.263 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 204 GLN cc_start: 0.7681 (tp-100) cc_final: 0.7314 (tp40) REVERT: B 36 ASN cc_start: 0.8112 (p0) cc_final: 0.7899 (p0) REVERT: B 68 ARG cc_start: 0.5442 (mmm160) cc_final: 0.4961 (mmm160) REVERT: B 96 ARG cc_start: 0.6804 (mtm-85) cc_final: 0.6321 (ttm110) REVERT: B 101 MET cc_start: 0.6849 (mmm) cc_final: 0.6581 (mtt) REVERT: B 126 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6706 (mt) REVERT: C 53 MET cc_start: 0.4524 (mmt) cc_final: 0.3356 (mmt) REVERT: C 184 ILE cc_start: 0.7455 (tt) cc_final: 0.7200 (tt) REVERT: D 68 ARG cc_start: 0.6370 (tpt-90) cc_final: 0.6119 (mtp-110) REVERT: D 99 TRP cc_start: 0.8034 (OUTLIER) cc_final: 0.7618 (m100) REVERT: F 11 LEU cc_start: 0.7728 (mt) cc_final: 0.7494 (mt) REVERT: F 29 PHE cc_start: 0.8075 (t80) cc_final: 0.7735 (t80) REVERT: F 63 SER cc_start: 0.7716 (OUTLIER) cc_final: 0.7478 (t) REVERT: I 189 MET cc_start: 0.6531 (ptp) cc_final: 0.6243 (ppp) REVERT: I 425 MET cc_start: 0.4943 (tmm) cc_final: 0.3957 (tmm) REVERT: I 469 GLU cc_start: 0.6838 (tp30) cc_final: 0.5709 (tp30) REVERT: I 472 LYS cc_start: 0.8512 (tmmt) cc_final: 0.8073 (tmmt) REVERT: N 11 LEU cc_start: 0.7723 (tp) cc_final: 0.7487 (tp) REVERT: P 24 LEU cc_start: 0.5131 (OUTLIER) cc_final: 0.4840 (tt) REVERT: R 36 GLU cc_start: 0.8449 (mp0) cc_final: 0.8180 (mp0) REVERT: R 189 MET cc_start: 0.7294 (ttp) cc_final: 0.7087 (tmm) REVERT: R 237 ILE cc_start: 0.8283 (tp) cc_final: 0.8077 (tt) REVERT: R 425 MET cc_start: 0.4624 (OUTLIER) cc_final: 0.4097 (ppp) REVERT: R 429 TYR cc_start: 0.6963 (m-80) cc_final: 0.6555 (m-80) REVERT: R 441 MET cc_start: 0.7496 (mmp) cc_final: 0.7006 (mmt) outliers start: 125 outliers final: 90 residues processed: 675 average time/residue: 0.3468 time to fit residues: 336.4397 Evaluate side-chains 660 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 565 time to evaluate : 2.170 ------------------------------------------------------------------------------- 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 218 VAL Chi-restraints excluded: chain A residue 254 VAL 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 93 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 228 ASP 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 29 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 56 TYR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 99 TRP Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 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 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 18 GLN Chi-restraints excluded: chain G residue 30 VAL 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 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 I residue 283 VAL Chi-restraints excluded: chain I residue 308 SER Chi-restraints excluded: chain I residue 334 VAL Chi-restraints excluded: chain I residue 340 VAL Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 387 THR 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 N residue 122 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 16 ASN 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 33 THR Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 208 ILE 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 374 ASN Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 210 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 217 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN C 24 GLN C 43 ASN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 216 HIS R 448 ASN ** R 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.8391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18893 Z= 0.253 Angle : 0.764 15.433 25573 Z= 0.397 Chirality : 0.048 0.303 2817 Planarity : 0.005 0.069 3251 Dihedral : 4.808 22.297 2536 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 5.23 % Allowed : 30.60 % Favored : 64.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2270 helix: 1.89 (0.16), residues: 903 sheet: 0.09 (0.24), residues: 434 loop : -0.93 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP I 437 HIS 0.008 0.001 HIS B 62 PHE 0.032 0.002 PHE N 29 TYR 0.031 0.002 TYR C 285 ARG 0.010 0.001 ARG I 214 *********************** 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 691 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 587 time to evaluate : 2.053 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 198 MET cc_start: 0.7029 (tpp) cc_final: 0.6672 (tpp) REVERT: A 306 TYR cc_start: 0.7325 (m-80) cc_final: 0.7013 (m-80) REVERT: B 96 ARG cc_start: 0.6687 (mtm-85) cc_final: 0.6306 (ttm110) REVERT: B 101 MET cc_start: 0.6864 (mmm) cc_final: 0.6578 (mtt) REVERT: B 126 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6647 (mt) REVERT: C 13 VAL cc_start: 0.8316 (m) cc_final: 0.7804 (p) REVERT: C 53 MET cc_start: 0.4341 (mmt) cc_final: 0.3283 (mmt) REVERT: C 184 ILE cc_start: 0.7395 (tt) cc_final: 0.7122 (tt) REVERT: C 215 PHE cc_start: 0.7246 (m-10) cc_final: 0.6914 (m-10) REVERT: D 16 ASN cc_start: 0.8113 (m-40) cc_final: 0.7657 (m-40) REVERT: D 57 LYS cc_start: 0.7822 (ptpp) cc_final: 0.7516 (pttm) REVERT: D 99 TRP cc_start: 0.8004 (OUTLIER) cc_final: 0.7241 (m100) REVERT: F 29 PHE cc_start: 0.7976 (t80) cc_final: 0.7614 (t80) REVERT: F 63 SER cc_start: 0.7715 (OUTLIER) cc_final: 0.7448 (t) REVERT: G 52 THR cc_start: 0.7689 (OUTLIER) cc_final: 0.7437 (t) REVERT: I 156 LEU cc_start: 0.0622 (OUTLIER) cc_final: -0.1342 (tt) REVERT: I 189 MET cc_start: 0.6541 (ptp) cc_final: 0.6251 (ppp) REVERT: I 228 LEU cc_start: 0.7749 (tt) cc_final: 0.7460 (tp) REVERT: I 281 CYS cc_start: 0.3578 (OUTLIER) cc_final: 0.3055 (t) REVERT: I 346 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6709 (tt) REVERT: I 425 MET cc_start: 0.4979 (tmm) cc_final: 0.3887 (tmm) REVERT: I 440 GLN cc_start: 0.7987 (pp30) cc_final: 0.6345 (pp30) REVERT: I 441 MET cc_start: 0.7378 (mmt) cc_final: 0.7046 (mmt) REVERT: I 448 ASN cc_start: 0.7676 (m110) cc_final: 0.6972 (t0) REVERT: I 462 CYS cc_start: 0.5143 (m) cc_final: 0.4759 (t) REVERT: P 24 LEU cc_start: 0.5366 (OUTLIER) cc_final: 0.5118 (tt) REVERT: R 43 ARG cc_start: 0.6839 (ptt90) cc_final: 0.6595 (ptt90) REVERT: R 404 ARG cc_start: 0.7783 (ptt-90) cc_final: 0.7428 (ptt-90) REVERT: R 411 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7990 (mp) REVERT: R 425 MET cc_start: 0.4715 (ppp) cc_final: 0.4102 (ppp) REVERT: R 429 TYR cc_start: 0.7027 (m-80) cc_final: 0.6486 (m-80) REVERT: R 441 MET cc_start: 0.7346 (mmp) cc_final: 0.6937 (mmt) REVERT: R 465 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6663 (mt-10) outliers start: 104 outliers final: 75 residues processed: 650 average time/residue: 0.3499 time to fit residues: 327.9559 Evaluate side-chains 641 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 557 time to evaluate : 1.846 ------------------------------------------------------------------------------- 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 48 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 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 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 38 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 56 TYR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 99 TRP 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 190 LEU 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 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 63 SER 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 30 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 9 HIS 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 218 THR Chi-restraints excluded: chain I residue 281 CYS Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 308 SER Chi-restraints excluded: chain I residue 334 VAL Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 53 GLN 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 N residue 122 THR 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 33 THR Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 191 TYR 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 411 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 134 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 130 optimal weight: 0.1980 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 0.0670 chunk 138 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 171 optimal weight: 3.9990 chunk 198 optimal weight: 0.8980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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** A 261 GLN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN D 62 HIS ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.8586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18893 Z= 0.224 Angle : 0.765 14.980 25573 Z= 0.398 Chirality : 0.047 0.324 2817 Planarity : 0.005 0.063 3251 Dihedral : 4.684 21.459 2536 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.49 % Favored : 95.42 % Rotamer: Outliers : 5.23 % Allowed : 31.96 % Favored : 62.81 % 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: 0.63 (0.18), residues: 2270 helix: 1.88 (0.17), residues: 904 sheet: 0.14 (0.24), residues: 430 loop : -0.91 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP R 352 HIS 0.011 0.001 HIS R 420 PHE 0.035 0.002 PHE B 199 TYR 0.028 0.002 TYR I 305 ARG 0.012 0.001 ARG B 19 *********************** 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 687 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 583 time to evaluate : 1.939 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 306 TYR cc_start: 0.7318 (m-80) cc_final: 0.7023 (m-80) REVERT: B 96 ARG cc_start: 0.6681 (mtm-85) cc_final: 0.6301 (ttm110) REVERT: B 101 MET cc_start: 0.6867 (mmm) cc_final: 0.6560 (mtt) REVERT: B 126 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6597 (mt) REVERT: B 263 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7543 (p) REVERT: B 325 MET cc_start: 0.5752 (mmt) cc_final: 0.5463 (mmt) REVERT: C 13 VAL cc_start: 0.8311 (m) cc_final: 0.7490 (p) REVERT: C 17 LYS cc_start: 0.7687 (mmtp) cc_final: 0.7408 (mmtp) REVERT: C 37 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7497 (mt) REVERT: C 53 MET cc_start: 0.4466 (mmt) cc_final: 0.3535 (mmt) REVERT: C 184 ILE cc_start: 0.7318 (tt) cc_final: 0.7046 (tt) REVERT: C 360 LEU cc_start: 0.7397 (mt) cc_final: 0.7171 (mp) REVERT: D 16 ASN cc_start: 0.8138 (m-40) cc_final: 0.7889 (m-40) REVERT: D 57 LYS cc_start: 0.7809 (ptpp) cc_final: 0.7495 (pttm) REVERT: D 99 TRP cc_start: 0.8009 (OUTLIER) cc_final: 0.7229 (m100) REVERT: F 29 PHE cc_start: 0.7839 (t80) cc_final: 0.7590 (t80) REVERT: F 63 SER cc_start: 0.7681 (OUTLIER) cc_final: 0.7450 (t) REVERT: G 52 THR cc_start: 0.7599 (OUTLIER) cc_final: 0.7310 (t) REVERT: I 32 MET cc_start: 0.4977 (tmm) cc_final: 0.4734 (tmm) REVERT: I 42 HIS cc_start: 0.7873 (m-70) cc_final: 0.7588 (m-70) REVERT: I 156 LEU cc_start: 0.0588 (OUTLIER) cc_final: -0.1766 (tt) REVERT: I 189 MET cc_start: 0.6512 (ptp) cc_final: 0.6209 (ppp) REVERT: I 281 CYS cc_start: 0.3509 (OUTLIER) cc_final: 0.2958 (t) REVERT: I 346 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6895 (tt) REVERT: I 425 MET cc_start: 0.4929 (tmm) cc_final: 0.3850 (tmm) REVERT: I 440 GLN cc_start: 0.8041 (pp30) cc_final: 0.6455 (pp30) REVERT: I 441 MET cc_start: 0.7368 (mmt) cc_final: 0.7046 (mmt) REVERT: I 448 ASN cc_start: 0.7779 (m110) cc_final: 0.7176 (t0) REVERT: P 24 LEU cc_start: 0.5510 (OUTLIER) cc_final: 0.5279 (tt) REVERT: R 32 MET cc_start: 0.6826 (tmm) cc_final: 0.6294 (tmm) REVERT: R 400 ARG cc_start: 0.7448 (mmm160) cc_final: 0.6611 (mmm160) REVERT: R 401 GLN cc_start: 0.7739 (pm20) cc_final: 0.7099 (pm20) REVERT: R 403 TYR cc_start: 0.5565 (m-80) cc_final: 0.5192 (m-80) REVERT: R 404 ARG cc_start: 0.7734 (ptt-90) cc_final: 0.7411 (ptt-90) REVERT: R 411 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7943 (mp) REVERT: R 425 MET cc_start: 0.4776 (OUTLIER) cc_final: 0.4101 (ppp) REVERT: R 429 TYR cc_start: 0.7033 (m-80) cc_final: 0.6559 (m-80) REVERT: R 441 MET cc_start: 0.7321 (mmp) cc_final: 0.6907 (mmt) outliers start: 104 outliers final: 73 residues processed: 632 average time/residue: 0.3358 time to fit residues: 306.9057 Evaluate side-chains 644 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 559 time to evaluate : 2.065 ------------------------------------------------------------------------------- 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 48 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 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 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 37 LEU Chi-restraints excluded: chain C residue 56 TYR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 329 HIS Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 82 TRP Chi-restraints excluded: chain D residue 99 TRP 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 228 ASP Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain 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 63 SER 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 30 VAL 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 I residue 33 THR Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 117 CYS Chi-restraints excluded: chain I residue 154 TRP Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 281 CYS 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 N residue 35 ASN Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 53 GLN 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 116 LEU Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 238 PHE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 411 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 208 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 183 optimal weight: 1.9990 chunk 191 optimal weight: 0.5980 chunk 133 optimal weight: 0.0040 chunk 214 optimal weight: 0.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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** A 261 GLN ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS B 259 GLN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 16 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.8835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18893 Z= 0.238 Angle : 0.782 16.183 25573 Z= 0.407 Chirality : 0.047 0.335 2817 Planarity : 0.005 0.068 3251 Dihedral : 4.703 21.355 2536 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.46 % Rotamer: Outliers : 4.67 % Allowed : 32.71 % Favored : 62.61 % 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: 0.52 (0.18), residues: 2270 helix: 1.72 (0.17), residues: 901 sheet: 0.17 (0.25), residues: 430 loop : -0.93 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP R 352 HIS 0.009 0.001 HIS I 42 PHE 0.034 0.002 PHE B 199 TYR 0.029 0.002 TYR I 305 ARG 0.012 0.001 ARG B 19 *********************** 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 667 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 574 time to evaluate : 2.070 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 306 TYR cc_start: 0.7343 (m-80) cc_final: 0.7027 (m-80) REVERT: B 96 ARG cc_start: 0.6633 (mtm-85) cc_final: 0.6298 (ttm110) REVERT: B 101 MET cc_start: 0.6889 (mmm) cc_final: 0.6541 (mtt) REVERT: B 126 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6649 (mt) REVERT: B 325 MET cc_start: 0.5641 (mmt) cc_final: 0.5386 (mmt) REVERT: C 13 VAL cc_start: 0.8373 (m) cc_final: 0.7969 (p) REVERT: C 35 ARG cc_start: 0.7342 (mtt-85) cc_final: 0.7088 (mtt180) REVERT: C 53 MET cc_start: 0.4660 (mmt) cc_final: 0.3999 (mmt) REVERT: C 184 ILE cc_start: 0.7337 (OUTLIER) cc_final: 0.6997 (tt) REVERT: D 57 LYS cc_start: 0.7806 (ptpp) cc_final: 0.7506 (pttm) REVERT: D 99 TRP cc_start: 0.7908 (OUTLIER) cc_final: 0.7610 (m100) REVERT: F 29 PHE cc_start: 0.7879 (t80) cc_final: 0.7603 (t80) REVERT: F 63 SER cc_start: 0.7645 (OUTLIER) cc_final: 0.7412 (t) REVERT: G 52 THR cc_start: 0.7579 (OUTLIER) cc_final: 0.7292 (t) REVERT: I 42 HIS cc_start: 0.7926 (m-70) cc_final: 0.7446 (m90) REVERT: I 156 LEU cc_start: 0.0785 (OUTLIER) cc_final: -0.1139 (tt) REVERT: I 189 MET cc_start: 0.6550 (ptp) cc_final: 0.6238 (ppp) REVERT: I 281 CYS cc_start: 0.3623 (OUTLIER) cc_final: 0.3072 (t) REVERT: I 311 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.7375 (t80) REVERT: I 345 THR cc_start: 0.7637 (t) cc_final: 0.7222 (t) REVERT: I 346 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6939 (tt) REVERT: I 425 MET cc_start: 0.4975 (tmm) cc_final: 0.3866 (tmm) REVERT: I 440 GLN cc_start: 0.8066 (pp30) cc_final: 0.6491 (pp30) REVERT: I 441 MET cc_start: 0.7364 (mmt) cc_final: 0.7056 (mmt) REVERT: I 448 ASN cc_start: 0.7776 (m110) cc_final: 0.7192 (t0) REVERT: P 24 LEU cc_start: 0.5587 (OUTLIER) cc_final: 0.5337 (tt) REVERT: R 32 MET cc_start: 0.6775 (tmm) cc_final: 0.6281 (tmm) REVERT: R 401 GLN cc_start: 0.7790 (pm20) cc_final: 0.7142 (pm20) REVERT: R 404 ARG cc_start: 0.7664 (ptt-90) cc_final: 0.7389 (ptt-90) REVERT: R 405 LYS cc_start: 0.8391 (tptt) cc_final: 0.8147 (tptt) REVERT: R 411 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7935 (mp) REVERT: R 425 MET cc_start: 0.4830 (OUTLIER) cc_final: 0.4238 (ppp) REVERT: R 429 TYR cc_start: 0.7008 (m-80) cc_final: 0.6516 (m-80) REVERT: R 441 MET cc_start: 0.7369 (mmp) cc_final: 0.6892 (mmt) outliers start: 93 outliers final: 76 residues processed: 628 average time/residue: 0.3449 time to fit residues: 311.1647 Evaluate side-chains 641 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 553 time to evaluate : 2.087 ------------------------------------------------------------------------------- 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 48 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 87 THR 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 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 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 56 TYR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 358 TYR Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 82 TRP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 99 TRP 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 228 ASP 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 63 SER 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 30 VAL 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 I residue 112 TRP Chi-restraints excluded: chain I residue 117 CYS Chi-restraints excluded: chain I residue 154 TRP Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 172 LYS Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 224 MET Chi-restraints excluded: chain I residue 281 CYS 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 N residue 35 ASN Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 53 GLN 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 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 336 VAL Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 411 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 131 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 225 optimal weight: 0.6980 chunk 207 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** A 261 GLN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN C 261 GLN ** 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 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.9077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18893 Z= 0.257 Angle : 0.810 15.391 25573 Z= 0.423 Chirality : 0.048 0.340 2817 Planarity : 0.005 0.072 3251 Dihedral : 4.781 21.230 2536 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.46 % Rotamer: Outliers : 4.72 % Allowed : 33.52 % Favored : 61.76 % 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: 0.38 (0.18), residues: 2270 helix: 1.60 (0.17), residues: 903 sheet: 0.05 (0.25), residues: 434 loop : -0.98 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 63 HIS 0.009 0.001 HIS I 42 PHE 0.035 0.002 PHE A 240 TYR 0.035 0.002 TYR R 221 ARG 0.013 0.001 ARG D 19 ********************** 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 663 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 569 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 TYR cc_start: 0.7359 (m-80) cc_final: 0.7079 (m-80) REVERT: B 96 ARG cc_start: 0.6729 (mtm-85) cc_final: 0.6445 (ttm110) REVERT: B 101 MET cc_start: 0.6893 (mmm) cc_final: 0.6521 (mtt) REVERT: B 126 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6834 (mm) REVERT: B 325 MET cc_start: 0.5766 (mmt) cc_final: 0.5502 (mmt) REVERT: C 13 VAL cc_start: 0.8433 (m) cc_final: 0.7572 (p) REVERT: C 17 LYS cc_start: 0.7601 (mmtp) cc_final: 0.7390 (mmtp) REVERT: C 35 ARG cc_start: 0.7311 (mtt-85) cc_final: 0.7035 (mtt180) REVERT: C 184 ILE cc_start: 0.7296 (OUTLIER) cc_final: 0.6977 (tt) REVERT: D 99 TRP cc_start: 0.7951 (OUTLIER) cc_final: 0.7748 (m100) REVERT: F 29 PHE cc_start: 0.7929 (t80) cc_final: 0.7608 (t80) REVERT: F 63 SER cc_start: 0.7689 (OUTLIER) cc_final: 0.7428 (t) REVERT: G 14 LYS cc_start: 0.8410 (pttp) cc_final: 0.7850 (mtmm) REVERT: G 52 THR cc_start: 0.7538 (OUTLIER) cc_final: 0.7243 (t) REVERT: I 42 HIS cc_start: 0.7922 (m-70) cc_final: 0.7400 (m90) REVERT: I 156 LEU cc_start: 0.0846 (OUTLIER) cc_final: -0.1055 (tt) REVERT: I 189 MET cc_start: 0.6613 (ptp) cc_final: 0.6308 (ppp) REVERT: I 281 CYS cc_start: 0.3588 (OUTLIER) cc_final: 0.3095 (t) REVERT: I 311 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.7408 (t80) REVERT: I 346 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7077 (tt) REVERT: I 425 MET cc_start: 0.5012 (tmm) cc_final: 0.3844 (tmm) REVERT: I 440 GLN cc_start: 0.8112 (pp30) cc_final: 0.6417 (pp30) REVERT: I 441 MET cc_start: 0.7426 (mmt) cc_final: 0.7156 (mmt) REVERT: I 448 ASN cc_start: 0.7950 (m110) cc_final: 0.7337 (t0) REVERT: I 469 GLU cc_start: 0.6950 (tp30) cc_final: 0.6075 (tp30) REVERT: I 472 LYS cc_start: 0.8580 (tmmt) cc_final: 0.8222 (tmmt) REVERT: P 24 LEU cc_start: 0.5617 (OUTLIER) cc_final: 0.5348 (tt) REVERT: R 32 MET cc_start: 0.6756 (tmm) cc_final: 0.6530 (tmm) REVERT: R 400 ARG cc_start: 0.7483 (mmm160) cc_final: 0.6451 (mmm160) REVERT: R 401 GLN cc_start: 0.7800 (pm20) cc_final: 0.7137 (pm20) REVERT: R 404 ARG cc_start: 0.7639 (ptt-90) cc_final: 0.7438 (ptt-90) REVERT: R 425 MET cc_start: 0.4820 (OUTLIER) cc_final: 0.4197 (ppp) REVERT: R 429 TYR cc_start: 0.7011 (m-80) cc_final: 0.6530 (m-80) REVERT: R 441 MET cc_start: 0.7404 (mmp) cc_final: 0.6984 (mmt) REVERT: R 465 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6837 (mt-10) outliers start: 94 outliers final: 80 residues processed: 622 average time/residue: 0.3501 time to fit residues: 312.2611 Evaluate side-chains 648 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 557 time to evaluate : 2.139 ------------------------------------------------------------------------------- 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 44 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 254 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 99 TRP 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 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 56 TYR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 358 TYR Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 82 TRP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 99 TRP 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 190 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain 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 63 SER 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 30 VAL 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 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 172 LYS Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 281 CYS 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 338 VAL Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 363 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 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 116 LEU Chi-restraints excluded: chain R residue 191 TYR 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 425 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 54 optimal weight: 0.7980 chunk 165 optimal weight: 0.0470 chunk 26 optimal weight: 0.8980 chunk 49 optimal weight: 0.2980 chunk 179 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 184 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.0270 chunk 157 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 overall best weight: 0.2736 ------------------------------------------------------------------------------- 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** A 259 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN C 261 GLN D 142 HIS ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 HIS G 44 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 HIS I 451 GLN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 16 ASN ** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.151312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.126631 restraints weight = 35840.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.130692 restraints weight = 19088.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.133345 restraints weight = 11951.772| |-----------------------------------------------------------------------------| r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.9171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18893 Z= 0.225 Angle : 0.807 16.286 25573 Z= 0.421 Chirality : 0.047 0.330 2817 Planarity : 0.005 0.053 3251 Dihedral : 4.668 20.393 2536 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.41 % Favored : 95.55 % Rotamer: Outliers : 4.57 % Allowed : 34.27 % Favored : 61.16 % 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: 0.40 (0.18), residues: 2270 helix: 1.58 (0.17), residues: 901 sheet: 0.09 (0.25), residues: 432 loop : -0.94 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 63 HIS 0.009 0.001 HIS I 42 PHE 0.035 0.002 PHE A 240 TYR 0.032 0.002 TYR R 221 ARG 0.023 0.001 ARG E 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5906.53 seconds wall clock time: 107 minutes 32.95 seconds (6452.95 seconds total)