Starting phenix.real_space_refine on Sun Mar 17 17:46:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hao_34598/03_2024/8hao_34598_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hao_34598/03_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_34598/03_2024/8hao_34598.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hao_34598/03_2024/8hao_34598.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hao_34598/03_2024/8hao_34598_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hao_34598/03_2024/8hao_34598_neut.pdb" } 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 Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "D GLU 3": "OE1" <-> "OE2" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "E GLU 17": "OE1" <-> "OE2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "F GLU 6": "OE1" <-> "OE2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "H GLU 4": "OE1" <-> "OE2" Residue "H GLU 19": "OE1" <-> "OE2" Residue "I GLU 35": "OE1" <-> "OE2" Residue "I GLU 36": "OE1" <-> "OE2" Residue "I GLU 177": "OE1" <-> "OE2" Residue "I GLU 302": "OE1" <-> "OE2" Residue "I GLU 444": "OE1" <-> "OE2" Residue "I GLU 465": "OE1" <-> "OE2" Residue "I GLU 469": "OE1" <-> "OE2" Residue "R PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 391": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9.31, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 6.28 Conformation dependent library (CDL) restraints added in 3.3 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: 1.85 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: 5.56 Time building geometry restraints manager: 6.93 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: 98.48 - 105.65: 245 105.65 - 112.82: 10031 112.82 - 119.99: 6528 119.99 - 127.16: 8538 127.16 - 134.33: 231 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 2.440 nonbonded pdb=" OE2 GLU A 266 " pdb=" OG1 THR C 48 " model vdw 1.899 2.440 nonbonded pdb=" O ALA I 242 " pdb=" OG SER I 246 " model vdw 1.974 2.440 nonbonded pdb=" OD2 ASP D 163 " pdb=" OG1 THR D 165 " model vdw 2.081 2.440 nonbonded pdb=" NE2 GLN D 75 " pdb=" O VAL D 100 " model vdw 2.188 2.520 ... (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 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: 7.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 27.180 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 46.290 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.200 ------------------------------------------------------------------------------- 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 : 2.720 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: 0.3732 time to fit residues: 349.0641 Evaluate side-chains 481 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 479 time to evaluate : 2.047 ------------------------------------------------------------------------------- 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: 1.9990 chunk 95 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 43 ASN ** D 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 82 GLN N 84 ASN ** R 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 448 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18893 Z= 0.255 Angle : 0.711 10.210 25573 Z= 0.373 Chirality : 0.045 0.240 2817 Planarity : 0.005 0.075 3251 Dihedral : 4.540 45.327 2540 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.52 % Favored : 96.30 % Rotamer: Outliers : 5.53 % Allowed : 21.16 % Favored : 73.32 % 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: 1.21 (0.18), residues: 2270 helix: 2.37 (0.16), residues: 923 sheet: 0.60 (0.25), residues: 426 loop : -0.76 (0.21), residues: 921 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 0.035 0.003 PHE I 291 TYR 0.038 0.003 TYR I 320 ARG 0.010 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 705 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 595 time to evaluate : 1.942 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 337 GLU cc_start: 0.6868 (mp0) cc_final: 0.6551 (mp0) REVERT: B 17 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7638 (pp30) REVERT: B 101 MET cc_start: 0.6382 (mmm) cc_final: 0.5993 (mtt) REVERT: B 187 VAL cc_start: 0.8290 (t) cc_final: 0.8042 (p) REVERT: B 263 THR cc_start: 0.7742 (t) cc_final: 0.7540 (t) REVERT: C 13 VAL cc_start: 0.8055 (t) cc_final: 0.7481 (t) REVERT: C 53 MET cc_start: 0.1770 (tpt) cc_final: -0.0237 (mmt) REVERT: C 327 TYR cc_start: 0.6375 (m-80) cc_final: 0.6162 (m-80) REVERT: D 62 HIS cc_start: 0.6676 (t70) cc_final: 0.6334 (t70) REVERT: D 188 MET cc_start: 0.7224 (mmm) cc_final: 0.6992 (mmt) REVERT: D 325 MET cc_start: 0.5114 (mmm) cc_final: 0.4575 (mmt) REVERT: E 38 MET cc_start: 0.5144 (mmp) cc_final: 0.4838 (mmp) REVERT: F 29 PHE cc_start: 0.7341 (t80) cc_final: 0.6986 (t80) REVERT: I 300 LEU cc_start: 0.6812 (tp) cc_final: 0.6264 (tt) REVERT: I 425 MET cc_start: 0.3926 (tmm) cc_final: 0.3135 (tmm) REVERT: I 457 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7786 (mm) REVERT: N 84 ASN cc_start: 0.7463 (OUTLIER) cc_final: 0.7235 (p0) REVERT: P 33 ASN cc_start: 0.7611 (p0) cc_final: 0.7409 (p0) REVERT: R 40 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.5905 (tp) REVERT: R 401 GLN cc_start: 0.7654 (pm20) cc_final: 0.7074 (pm20) REVERT: R 405 LYS cc_start: 0.8490 (tptt) cc_final: 0.8228 (tptt) REVERT: R 425 MET cc_start: 0.4697 (ppp) cc_final: 0.4273 (ppp) REVERT: R 441 MET cc_start: 0.6801 (mmp) cc_final: 0.6444 (mmt) outliers start: 110 outliers final: 57 residues processed: 655 average time/residue: 0.3277 time to fit residues: 310.5938 Evaluate side-chains 575 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 515 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 292 THR 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 122 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 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 186 ASP 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 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 112 TRP Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 192 THR 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 196 SER Chi-restraints excluded: chain R residue 218 THR 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: 1.9990 chunk 170 optimal weight: 0.0050 chunk 139 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 205 optimal weight: 0.7980 chunk 222 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 203 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 164 optimal weight: 0.5980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 238 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN C 24 GLN C 28 GLN D 259 GLN ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN G 44 HIS H 10 ASN H 16 ASN I 139 ASN ** I 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 223 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18893 Z= 0.216 Angle : 0.642 8.959 25573 Z= 0.339 Chirality : 0.043 0.232 2817 Planarity : 0.004 0.045 3251 Dihedral : 4.268 24.964 2536 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.22 % Favored : 96.61 % Rotamer: Outliers : 5.48 % Allowed : 23.27 % Favored : 71.26 % 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: 2.54 (0.16), residues: 906 sheet: 0.53 (0.24), residues: 432 loop : -0.73 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP I 154 HIS 0.007 0.001 HIS I 216 PHE 0.031 0.002 PHE N 29 TYR 0.020 0.002 TYR R 191 ARG 0.011 0.001 ARG C 15 *********************** 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 678 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 569 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ARG cc_start: 0.4941 (tpt-90) cc_final: 0.4665 (mmm160) REVERT: B 101 MET cc_start: 0.6584 (mmm) cc_final: 0.6285 (mtt) REVERT: C 13 VAL cc_start: 0.8186 (t) cc_final: 0.7202 (p) REVERT: C 17 LYS cc_start: 0.7753 (mmtp) cc_final: 0.7514 (mmtp) REVERT: C 53 MET cc_start: 0.2684 (tpt) cc_final: 0.0701 (mmt) REVERT: D 99 TRP cc_start: 0.7643 (m100) cc_final: 0.7237 (m100) REVERT: D 171 ILE cc_start: 0.4826 (OUTLIER) cc_final: 0.4320 (mm) REVERT: D 201 SER cc_start: 0.8406 (OUTLIER) cc_final: 0.8121 (p) REVERT: F 29 PHE cc_start: 0.7582 (t80) cc_final: 0.7234 (t80) REVERT: G 38 MET cc_start: 0.7095 (mmm) cc_final: 0.6893 (mmm) REVERT: I 156 LEU cc_start: -0.0226 (OUTLIER) cc_final: -0.3334 (tp) REVERT: I 216 HIS cc_start: 0.6374 (m-70) cc_final: 0.6154 (m-70) REVERT: I 231 MET cc_start: 0.6289 (mtp) cc_final: 0.6021 (mtp) REVERT: I 299 ILE cc_start: 0.7203 (mt) cc_final: 0.6769 (mt) REVERT: I 425 MET cc_start: 0.4148 (tmm) cc_final: 0.3332 (tmm) REVERT: I 437 TRP cc_start: 0.5786 (t60) cc_final: 0.5527 (t60) REVERT: I 441 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.6574 (mmt) REVERT: I 457 ILE cc_start: 0.8280 (mm) cc_final: 0.8036 (mm) REVERT: P 24 LEU cc_start: 0.4925 (OUTLIER) cc_final: 0.4542 (tt) REVERT: P 33 ASN cc_start: 0.7489 (p0) cc_final: 0.7221 (p0) REVERT: R 36 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8095 (mp0) REVERT: R 186 ARG cc_start: 0.7577 (mtp180) cc_final: 0.6998 (ptt180) REVERT: R 189 MET cc_start: 0.7101 (ttp) cc_final: 0.6870 (tmm) REVERT: R 237 ILE cc_start: 0.8246 (tp) cc_final: 0.7937 (tt) REVERT: R 400 ARG cc_start: 0.7543 (mmm160) cc_final: 0.6524 (mmm160) REVERT: R 414 MET cc_start: 0.7303 (tpp) cc_final: 0.6954 (tpp) REVERT: R 425 MET cc_start: 0.4600 (ppp) cc_final: 0.4156 (ppp) outliers start: 109 outliers final: 64 residues processed: 628 average time/residue: 0.3329 time to fit residues: 302.0447 Evaluate side-chains 599 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 530 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 201 SER 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 D residue 312 ASP Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 16 ASN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 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 310 ILE Chi-restraints excluded: chain I residue 334 VAL Chi-restraints excluded: chain I residue 441 MET Chi-restraints excluded: chain I residue 443 TYR Chi-restraints excluded: chain I residue 473 SER Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 192 THR 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 203 optimal weight: 0.7980 chunk 154 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 206 optimal weight: 0.9980 chunk 218 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN C 28 GLN C 354 HIS ** 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 I 216 HIS ** I 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 223 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 moved from start: 0.6452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18893 Z= 0.228 Angle : 0.673 11.150 25573 Z= 0.352 Chirality : 0.044 0.255 2817 Planarity : 0.004 0.069 3251 Dihedral : 4.398 28.612 2536 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.96 % Favored : 95.81 % Rotamer: Outliers : 5.78 % Allowed : 25.43 % Favored : 68.79 % 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: 1.04 (0.18), residues: 2270 helix: 2.37 (0.16), residues: 906 sheet: 0.35 (0.24), residues: 442 loop : -0.86 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 248 HIS 0.006 0.001 HIS I 42 PHE 0.031 0.002 PHE I 447 TYR 0.025 0.002 TYR I 403 ARG 0.011 0.001 ARG R 404 *********************** 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 694 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 579 time to evaluate : 2.004 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: B 101 MET cc_start: 0.6779 (mmm) cc_final: 0.6389 (mtt) REVERT: C 13 VAL cc_start: 0.8121 (t) cc_final: 0.7387 (p) REVERT: C 53 MET cc_start: 0.3101 (tpt) cc_final: 0.1558 (mmt) REVERT: C 233 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7957 (mt) REVERT: D 19 ARG cc_start: 0.7278 (ptp90) cc_final: 0.7057 (ptp-170) REVERT: D 62 HIS cc_start: 0.6788 (t70) cc_final: 0.5747 (t70) REVERT: D 150 ARG cc_start: 0.7203 (mmt-90) cc_final: 0.6594 (mmt180) REVERT: D 171 ILE cc_start: 0.4574 (OUTLIER) cc_final: 0.4101 (mm) REVERT: D 201 SER cc_start: 0.8326 (OUTLIER) cc_final: 0.8064 (p) REVERT: F 29 PHE cc_start: 0.7968 (t80) cc_final: 0.7520 (t80) REVERT: I 156 LEU cc_start: 0.0349 (OUTLIER) cc_final: -0.2621 (tt) REVERT: I 189 MET cc_start: 0.6402 (ptp) cc_final: 0.6038 (ppp) REVERT: I 228 LEU cc_start: 0.7562 (tt) cc_final: 0.7144 (tp) REVERT: I 425 MET cc_start: 0.4431 (tmm) cc_final: 0.3552 (tmm) REVERT: I 437 TRP cc_start: 0.5759 (t60) cc_final: 0.5391 (t60) REVERT: I 441 MET cc_start: 0.6903 (OUTLIER) cc_final: 0.6335 (mmt) REVERT: P 24 LEU cc_start: 0.5045 (OUTLIER) cc_final: 0.4746 (tt) REVERT: R 36 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8171 (mm-30) REVERT: R 43 ARG cc_start: 0.6964 (ptt90) cc_final: 0.6733 (ptt90) REVERT: R 186 ARG cc_start: 0.7473 (mtp180) cc_final: 0.7170 (ptt180) REVERT: R 189 MET cc_start: 0.7236 (ttp) cc_final: 0.7023 (tmm) REVERT: R 379 ILE cc_start: 0.7382 (mm) cc_final: 0.6938 (tp) REVERT: R 404 ARG cc_start: 0.7602 (ptt-90) cc_final: 0.7286 (ptt-90) REVERT: R 425 MET cc_start: 0.4509 (ppp) cc_final: 0.4102 (ppp) REVERT: R 441 MET cc_start: 0.7179 (mmm) cc_final: 0.6815 (mmm) outliers start: 115 outliers final: 79 residues processed: 638 average time/residue: 0.3377 time to fit residues: 312.9158 Evaluate side-chains 639 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 554 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 292 THR 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 102 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 184 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 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 361 LEU Chi-restraints excluded: chain D residue 5 ASP 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 171 ILE Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 201 SER 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 279 SER Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 54 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 109 ASP Chi-restraints excluded: chain F residue 118 ARG 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 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 156 LEU Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 237 ILE Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 334 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 441 MET Chi-restraints excluded: chain I residue 473 SER 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 85 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 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 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 314 PHE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 449 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 181 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 162 optimal weight: 0.1980 chunk 90 optimal weight: 0.8980 chunk 186 optimal weight: 0.3980 chunk 151 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 196 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 HIS D 62 HIS ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 10 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.7017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18893 Z= 0.214 Angle : 0.675 13.658 25573 Z= 0.349 Chirality : 0.045 0.282 2817 Planarity : 0.004 0.049 3251 Dihedral : 4.408 24.511 2536 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.57 % Favored : 96.30 % Rotamer: Outliers : 5.78 % Allowed : 27.89 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.18), residues: 2270 helix: 2.28 (0.17), residues: 916 sheet: 0.33 (0.24), residues: 432 loop : -0.92 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 437 HIS 0.008 0.001 HIS I 216 PHE 0.046 0.002 PHE B 199 TYR 0.024 0.002 TYR R 305 ARG 0.008 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 701 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 586 time to evaluate : 2.112 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: A 198 MET cc_start: 0.6825 (tpp) cc_final: 0.6491 (tpp) REVERT: B 101 MET cc_start: 0.6871 (mmm) cc_final: 0.6471 (mtt) REVERT: B 226 GLU cc_start: 0.3450 (mt-10) cc_final: 0.3203 (mt-10) REVERT: C 53 MET cc_start: 0.3100 (tpt) cc_final: 0.2027 (mmt) REVERT: C 227 SER cc_start: 0.8383 (p) cc_final: 0.8102 (t) REVERT: C 233 LEU cc_start: 0.8202 (mp) cc_final: 0.7981 (mt) REVERT: C 327 TYR cc_start: 0.6934 (m-80) cc_final: 0.6516 (m-80) REVERT: C 360 LEU cc_start: 0.7360 (mt) cc_final: 0.7142 (mp) REVERT: D 62 HIS cc_start: 0.6824 (t-90) cc_final: 0.5741 (t70) REVERT: D 150 ARG cc_start: 0.7193 (mmt-90) cc_final: 0.6573 (mmt180) REVERT: D 171 ILE cc_start: 0.4707 (OUTLIER) cc_final: 0.4237 (mm) REVERT: F 29 PHE cc_start: 0.7965 (t80) cc_final: 0.7522 (t80) REVERT: I 42 HIS cc_start: 0.7769 (m170) cc_final: 0.7531 (m170) REVERT: I 156 LEU cc_start: 0.0312 (OUTLIER) cc_final: -0.2737 (tp) REVERT: I 189 MET cc_start: 0.6426 (ptp) cc_final: 0.6080 (ppp) REVERT: I 228 LEU cc_start: 0.7675 (tt) cc_final: 0.7353 (tp) REVERT: I 231 MET cc_start: 0.6528 (mtp) cc_final: 0.6276 (mtp) REVERT: I 343 ARG cc_start: 0.6046 (tpt90) cc_final: 0.5734 (tpp-160) REVERT: I 352 TRP cc_start: 0.6626 (m-10) cc_final: 0.6045 (m-90) REVERT: I 425 MET cc_start: 0.4482 (tmm) cc_final: 0.3627 (tmm) REVERT: I 437 TRP cc_start: 0.5855 (t60) cc_final: 0.5465 (t60) REVERT: I 441 MET cc_start: 0.6962 (OUTLIER) cc_final: 0.6192 (mmt) REVERT: P 24 LEU cc_start: 0.5207 (OUTLIER) cc_final: 0.4880 (tt) REVERT: R 36 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8143 (mp0) REVERT: R 171 VAL cc_start: 0.7569 (OUTLIER) cc_final: 0.7366 (p) REVERT: R 379 ILE cc_start: 0.7485 (mm) cc_final: 0.7203 (tp) REVERT: R 385 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8322 (tt) REVERT: R 400 ARG cc_start: 0.7503 (mmm160) cc_final: 0.6945 (mmm160) REVERT: R 404 ARG cc_start: 0.7702 (ptt-90) cc_final: 0.7477 (ptt-90) REVERT: R 425 MET cc_start: 0.4468 (ppp) cc_final: 0.4017 (ppp) outliers start: 115 outliers final: 87 residues processed: 643 average time/residue: 0.3443 time to fit residues: 317.4570 Evaluate side-chains 649 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 556 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER 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 237 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR 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 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 229 ASP Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 184 THR 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 279 SER 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 E residue 52 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 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 F residue 118 ARG 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 129 VAL Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 334 VAL Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 387 THR Chi-restraints excluded: chain I residue 441 MET Chi-restraints excluded: chain I residue 457 ILE Chi-restraints excluded: chain I residue 473 SER 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 109 ASP 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 115 ILE Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 191 TYR 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 Chi-restraints excluded: chain R residue 449 SER 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: 0.9990 chunk 43 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 218 optimal weight: 0.8980 chunk 181 optimal weight: 0.0040 chunk 101 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 114 optimal weight: 0.0060 overall best weight: 0.4408 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 295 ASN R 307 HIS ** R 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.7403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18893 Z= 0.203 Angle : 0.685 14.715 25573 Z= 0.353 Chirality : 0.044 0.294 2817 Planarity : 0.004 0.056 3251 Dihedral : 4.361 23.292 2536 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.52 % Favored : 96.34 % Rotamer: Outliers : 5.48 % Allowed : 29.95 % Favored : 64.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.94 (0.18), residues: 2270 helix: 2.23 (0.17), residues: 916 sheet: 0.35 (0.24), residues: 428 loop : -0.91 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 99 HIS 0.015 0.001 HIS B 62 PHE 0.032 0.002 PHE B 199 TYR 0.027 0.002 TYR R 221 ARG 0.007 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 682 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 573 time to evaluate : 2.223 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 17 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7493 (mptt) REVERT: A 198 MET cc_start: 0.6746 (tpp) cc_final: 0.6120 (ttt) REVERT: A 340 ARG cc_start: 0.8307 (tpp-160) cc_final: 0.8061 (tpp-160) REVERT: B 85 TYR cc_start: 0.4940 (m-10) cc_final: 0.4614 (m-80) REVERT: B 101 MET cc_start: 0.6875 (mmm) cc_final: 0.6464 (mtt) REVERT: B 226 GLU cc_start: 0.3427 (mt-10) cc_final: 0.3194 (mt-10) REVERT: C 13 VAL cc_start: 0.8024 (t) cc_final: 0.7697 (p) REVERT: C 53 MET cc_start: 0.3194 (tpt) cc_final: 0.2184 (mmt) REVERT: C 227 SER cc_start: 0.8426 (p) cc_final: 0.8130 (t) REVERT: C 233 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7894 (mt) REVERT: C 267 LYS cc_start: 0.8515 (mtmm) cc_final: 0.8311 (mttp) REVERT: C 327 TYR cc_start: 0.6935 (m-80) cc_final: 0.6595 (m-80) REVERT: D 62 HIS cc_start: 0.6795 (t-90) cc_final: 0.5776 (t70) REVERT: D 99 TRP cc_start: 0.7663 (m100) cc_final: 0.7399 (m100) REVERT: D 150 ARG cc_start: 0.7147 (mmt-90) cc_final: 0.6542 (mmt180) REVERT: D 171 ILE cc_start: 0.4744 (OUTLIER) cc_final: 0.4277 (mm) REVERT: F 29 PHE cc_start: 0.7952 (t80) cc_final: 0.7549 (t80) REVERT: F 63 SER cc_start: 0.7667 (m) cc_final: 0.7409 (t) REVERT: G 52 THR cc_start: 0.7585 (OUTLIER) cc_final: 0.7349 (t) REVERT: I 156 LEU cc_start: 0.0184 (OUTLIER) cc_final: -0.2600 (tt) REVERT: I 189 MET cc_start: 0.6371 (ptp) cc_final: 0.6034 (ppp) REVERT: I 228 LEU cc_start: 0.7623 (tt) cc_final: 0.7207 (tp) REVERT: I 425 MET cc_start: 0.4606 (tmm) cc_final: 0.3703 (tmm) REVERT: P 8 MET cc_start: 0.7080 (OUTLIER) cc_final: 0.6777 (ttm) REVERT: P 24 LEU cc_start: 0.5229 (OUTLIER) cc_final: 0.4930 (tt) REVERT: R 36 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8175 (mp0) REVERT: R 385 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8359 (tt) REVERT: R 405 LYS cc_start: 0.8504 (tptt) cc_final: 0.8286 (tptt) REVERT: R 425 MET cc_start: 0.4530 (ppp) cc_final: 0.4074 (ppp) REVERT: R 429 TYR cc_start: 0.6269 (OUTLIER) cc_final: 0.5863 (m-80) REVERT: R 441 MET cc_start: 0.7183 (mmp) cc_final: 0.6744 (mmt) outliers start: 109 outliers final: 76 residues processed: 629 average time/residue: 0.3488 time to fit residues: 312.9493 Evaluate side-chains 627 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 542 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 45 MET 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 102 THR 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 184 THR 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 39 LEU Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 184 THR 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 279 SER Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 107 CYS Chi-restraints excluded: chain F residue 115 TYR Chi-restraints excluded: chain F residue 118 ARG 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 154 TRP Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 473 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 54 SER 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 114 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 8 MET 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 232 LEU Chi-restraints excluded: chain R residue 238 PHE Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 429 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 210 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 124 optimal weight: 0.0980 chunk 159 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 184 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 217 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS H 10 ASN ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 295 ASN R 307 HIS ** R 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.7836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18893 Z= 0.222 Angle : 0.695 13.906 25573 Z= 0.361 Chirality : 0.045 0.290 2817 Planarity : 0.004 0.051 3251 Dihedral : 4.443 23.457 2536 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.27 % Favored : 95.59 % Rotamer: Outliers : 6.13 % Allowed : 30.70 % Favored : 63.17 % 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: 0.79 (0.18), residues: 2270 helix: 2.05 (0.17), residues: 922 sheet: 0.17 (0.25), residues: 422 loop : -0.89 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 99 HIS 0.007 0.001 HIS B 62 PHE 0.038 0.002 PHE B 199 TYR 0.031 0.002 TYR F 80 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 687 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 565 time to evaluate : 1.791 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 17 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7570 (mptt) REVERT: A 198 MET cc_start: 0.7008 (tpp) cc_final: 0.6718 (tpp) REVERT: B 8 ARG cc_start: 0.7696 (ptt-90) cc_final: 0.7455 (ptt-90) REVERT: B 101 MET cc_start: 0.7027 (mmm) cc_final: 0.6579 (mtt) REVERT: B 126 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6591 (mt) REVERT: B 226 GLU cc_start: 0.3512 (mt-10) cc_final: 0.3298 (mt-10) REVERT: C 13 VAL cc_start: 0.8083 (t) cc_final: 0.7678 (p) REVERT: C 53 MET cc_start: 0.3309 (tpt) cc_final: 0.2499 (mmt) REVERT: C 184 ILE cc_start: 0.7286 (tt) cc_final: 0.7004 (tt) REVERT: C 233 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7950 (mt) REVERT: D 62 HIS cc_start: 0.6906 (t-90) cc_final: 0.5814 (t70) REVERT: D 82 TRP cc_start: 0.7890 (m100) cc_final: 0.7509 (m100) REVERT: D 99 TRP cc_start: 0.7822 (m100) cc_final: 0.7476 (m100) REVERT: D 150 ARG cc_start: 0.7168 (mmt-90) cc_final: 0.6600 (mmt180) REVERT: F 29 PHE cc_start: 0.7980 (t80) cc_final: 0.7581 (t80) REVERT: F 63 SER cc_start: 0.7694 (m) cc_final: 0.7421 (t) REVERT: I 156 LEU cc_start: 0.0594 (OUTLIER) cc_final: -0.2117 (tt) REVERT: I 189 MET cc_start: 0.6411 (ptp) cc_final: 0.6046 (ppp) REVERT: I 228 LEU cc_start: 0.7683 (tt) cc_final: 0.7394 (tp) REVERT: I 346 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6519 (tt) REVERT: I 425 MET cc_start: 0.4777 (tmm) cc_final: 0.3830 (tmm) REVERT: P 24 LEU cc_start: 0.5128 (OUTLIER) cc_final: 0.4829 (tt) REVERT: R 36 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7934 (mt-10) REVERT: R 115 ILE cc_start: 0.4892 (OUTLIER) cc_final: 0.4659 (pt) REVERT: R 385 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8408 (tt) REVERT: R 400 ARG cc_start: 0.7428 (mmm160) cc_final: 0.6770 (mmm160) REVERT: R 404 ARG cc_start: 0.7704 (ptt-90) cc_final: 0.7436 (ptt-90) REVERT: R 425 MET cc_start: 0.4563 (OUTLIER) cc_final: 0.4038 (ppp) REVERT: R 429 TYR cc_start: 0.6218 (OUTLIER) cc_final: 0.6003 (m-80) REVERT: R 441 MET cc_start: 0.7322 (mmp) cc_final: 0.6855 (mmt) outliers start: 122 outliers final: 90 residues processed: 629 average time/residue: 0.3685 time to fit residues: 334.8786 Evaluate side-chains 643 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 543 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR 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 16 SER Chi-restraints excluded: chain C residue 21 LYS 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 194 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 121 CYS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 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 279 SER Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 33 LYS 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 115 TYR Chi-restraints excluded: chain F residue 118 ARG 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 187 LEU Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 237 ILE Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 334 VAL Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 457 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 238 PHE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 425 MET Chi-restraints excluded: chain R residue 429 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 134 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 138 optimal weight: 0.6980 chunk 148 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 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** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS B 259 GLN ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 295 ASN ** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 463 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.8288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18893 Z= 0.233 Angle : 0.728 14.625 25573 Z= 0.379 Chirality : 0.045 0.308 2817 Planarity : 0.004 0.043 3251 Dihedral : 4.525 22.633 2536 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 5.78 % Allowed : 31.31 % Favored : 62.91 % 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: 0.68 (0.18), residues: 2270 helix: 1.91 (0.17), residues: 930 sheet: 0.11 (0.25), residues: 436 loop : -0.92 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 99 HIS 0.006 0.001 HIS B 62 PHE 0.034 0.002 PHE B 199 TYR 0.024 0.002 TYR F 80 ARG 0.008 0.001 ARG I 214 *********************** 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 684 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 569 time to evaluate : 1.941 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 198 MET cc_start: 0.6878 (tpp) cc_final: 0.6599 (tpp) REVERT: A 204 GLN cc_start: 0.7497 (tp-100) cc_final: 0.6980 (tp40) REVERT: B 8 ARG cc_start: 0.7739 (ptt-90) cc_final: 0.7494 (ptt-90) REVERT: B 101 MET cc_start: 0.7018 (mmm) cc_final: 0.6612 (mtt) REVERT: B 126 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6603 (mt) REVERT: C 35 ARG cc_start: 0.7196 (mtt-85) cc_final: 0.6977 (mtt180) REVERT: C 53 MET cc_start: 0.3847 (OUTLIER) cc_final: 0.3323 (mmt) REVERT: C 184 ILE cc_start: 0.7320 (tt) cc_final: 0.7017 (tt) REVERT: C 316 SER cc_start: 0.8315 (t) cc_final: 0.7961 (p) REVERT: D 62 HIS cc_start: 0.6879 (t-90) cc_final: 0.5665 (t70) REVERT: D 82 TRP cc_start: 0.7926 (m100) cc_final: 0.7558 (m100) REVERT: D 99 TRP cc_start: 0.8030 (OUTLIER) cc_final: 0.7524 (m100) REVERT: D 150 ARG cc_start: 0.7162 (mmt-90) cc_final: 0.6525 (mmt180) REVERT: F 29 PHE cc_start: 0.7993 (t80) cc_final: 0.7589 (t80) REVERT: F 63 SER cc_start: 0.7682 (m) cc_final: 0.7426 (t) REVERT: G 52 THR cc_start: 0.7583 (OUTLIER) cc_final: 0.7300 (t) REVERT: I 42 HIS cc_start: 0.7823 (m170) cc_final: 0.7577 (m170) REVERT: I 156 LEU cc_start: 0.0821 (OUTLIER) cc_final: -0.2136 (tt) REVERT: I 189 MET cc_start: 0.6406 (ptp) cc_final: 0.6049 (ppp) REVERT: I 228 LEU cc_start: 0.7733 (tt) cc_final: 0.7388 (tp) REVERT: I 346 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6587 (tt) REVERT: I 425 MET cc_start: 0.4926 (tmm) cc_final: 0.4133 (tmm) REVERT: N 11 LEU cc_start: 0.7633 (tp) cc_final: 0.7413 (tp) REVERT: P 24 LEU cc_start: 0.5104 (OUTLIER) cc_final: 0.4817 (tt) REVERT: R 32 MET cc_start: 0.6872 (tmm) cc_final: 0.6319 (tmm) REVERT: R 400 ARG cc_start: 0.7400 (mmm160) cc_final: 0.6730 (mmm160) REVERT: R 401 GLN cc_start: 0.7678 (pm20) cc_final: 0.6798 (pm20) REVERT: R 404 ARG cc_start: 0.7729 (ptt-90) cc_final: 0.7449 (ptt-90) REVERT: R 425 MET cc_start: 0.4598 (ppp) cc_final: 0.4055 (ppp) REVERT: R 441 MET cc_start: 0.7341 (mmp) cc_final: 0.6877 (mmt) outliers start: 115 outliers final: 91 residues processed: 633 average time/residue: 0.3486 time to fit residues: 315.7920 Evaluate side-chains 654 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 556 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 45 MET 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 102 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR 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 21 LYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 56 TYR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 99 TRP Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 121 CYS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 184 THR 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 279 SER 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 E residue 52 THR Chi-restraints excluded: chain F residue 33 LYS 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 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 187 LEU Chi-restraints excluded: chain I residue 191 TYR Chi-restraints excluded: chain I residue 224 MET Chi-restraints excluded: chain I residue 237 ILE Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 308 SER Chi-restraints excluded: chain I residue 310 ILE 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 457 ILE Chi-restraints excluded: chain I residue 473 SER 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 109 ASP 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 208 optimal weight: 0.5980 chunk 190 optimal weight: 0.8980 chunk 202 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 88 optimal weight: 0.4980 chunk 159 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 214 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 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 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN ** R 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 420 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.8640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18893 Z= 0.243 Angle : 0.743 13.817 25573 Z= 0.388 Chirality : 0.047 0.298 2817 Planarity : 0.004 0.045 3251 Dihedral : 4.590 22.808 2536 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.58 % Favored : 95.33 % Rotamer: Outliers : 5.68 % Allowed : 31.81 % Favored : 62.51 % 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: 0.56 (0.18), residues: 2270 helix: 1.82 (0.17), residues: 929 sheet: 0.01 (0.25), residues: 436 loop : -0.96 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP I 437 HIS 0.010 0.001 HIS R 420 PHE 0.036 0.002 PHE B 199 TYR 0.026 0.002 TYR C 285 ARG 0.009 0.001 ARG D 214 *********************** 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 687 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 574 time to evaluate : 2.831 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 17 LYS cc_start: 0.7919 (mptt) cc_final: 0.7640 (mptt) REVERT: A 198 MET cc_start: 0.6881 (tpp) cc_final: 0.6607 (tpp) REVERT: B 8 ARG cc_start: 0.7740 (ptt-90) cc_final: 0.7499 (ptt-90) REVERT: B 101 MET cc_start: 0.7051 (mmm) cc_final: 0.6579 (mtt) REVERT: B 126 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6688 (mt) REVERT: C 35 ARG cc_start: 0.7284 (mtt-85) cc_final: 0.7026 (mtt180) REVERT: C 184 ILE cc_start: 0.7354 (tt) cc_final: 0.7030 (tt) REVERT: C 316 SER cc_start: 0.8286 (t) cc_final: 0.7945 (p) REVERT: D 62 HIS cc_start: 0.6903 (t-90) cc_final: 0.5784 (t70) REVERT: D 68 ARG cc_start: 0.6214 (tpt-90) cc_final: 0.5908 (mmm160) REVERT: D 82 TRP cc_start: 0.7937 (m100) cc_final: 0.7629 (m100) REVERT: D 99 TRP cc_start: 0.8124 (OUTLIER) cc_final: 0.7583 (m100) REVERT: D 150 ARG cc_start: 0.7108 (mmt-90) cc_final: 0.6561 (mmt180) REVERT: D 151 PHE cc_start: 0.6351 (m-80) cc_final: 0.6041 (m-80) REVERT: F 29 PHE cc_start: 0.8028 (t80) cc_final: 0.7590 (t80) REVERT: G 52 THR cc_start: 0.7584 (OUTLIER) cc_final: 0.7274 (t) REVERT: I 156 LEU cc_start: 0.0931 (OUTLIER) cc_final: -0.1965 (tt) REVERT: I 189 MET cc_start: 0.6423 (ptp) cc_final: 0.6092 (ppp) REVERT: I 425 MET cc_start: 0.5040 (tmm) cc_final: 0.4153 (tmm) REVERT: I 441 MET cc_start: 0.7286 (mmt) cc_final: 0.6625 (mmt) REVERT: R 425 MET cc_start: 0.4640 (OUTLIER) cc_final: 0.4089 (ppp) REVERT: R 441 MET cc_start: 0.7355 (mmp) cc_final: 0.6927 (mmt) outliers start: 113 outliers final: 92 residues processed: 638 average time/residue: 0.3440 time to fit residues: 315.4297 Evaluate side-chains 645 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 548 time to evaluate : 2.010 ------------------------------------------------------------------------------- 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 263 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 45 MET 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 121 CYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR 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 21 LYS Chi-restraints excluded: chain C residue 56 TYR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 210 LYS 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 5 ASP Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 99 TRP Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 121 CYS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 184 THR 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 279 SER 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 E residue 52 THR 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 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 224 MET Chi-restraints excluded: chain I residue 237 ILE Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 308 SER Chi-restraints excluded: chain I residue 310 ILE 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 457 ILE Chi-restraints excluded: chain I residue 473 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 51 ILE 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 109 ASP 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 21 VAL Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 420 HIS 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: 3.9990 chunk 101 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 chunk 225 optimal weight: 0.7980 chunk 207 optimal weight: 0.2980 chunk 179 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 295 ASN ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.8880 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= 0.254 Angle : 0.802 15.386 25573 Z= 0.412 Chirality : 0.048 0.290 2817 Planarity : 0.004 0.062 3251 Dihedral : 4.713 22.525 2536 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.29 % Rotamer: Outliers : 5.63 % Allowed : 33.27 % Favored : 61.11 % 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: 0.47 (0.18), residues: 2270 helix: 1.68 (0.17), residues: 929 sheet: -0.06 (0.25), residues: 426 loop : -0.91 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.003 TRP R 352 HIS 0.015 0.001 HIS R 420 PHE 0.046 0.002 PHE B 199 TYR 0.033 0.002 TYR I 443 ARG 0.014 0.001 ARG I 214 ********************** 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 664 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 552 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.6875 (tpp) cc_final: 0.6596 (tpp) REVERT: B 8 ARG cc_start: 0.7740 (ptt-90) cc_final: 0.7488 (ptt-90) REVERT: B 54 HIS cc_start: 0.7817 (m90) cc_final: 0.7588 (m-70) REVERT: B 101 MET cc_start: 0.7065 (mmm) cc_final: 0.6560 (mtt) REVERT: B 126 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6805 (mm) REVERT: C 35 ARG cc_start: 0.7295 (mtt-85) cc_final: 0.6943 (mtt180) REVERT: C 53 MET cc_start: 0.3614 (tpt) cc_final: 0.2978 (mmt) REVERT: C 184 ILE cc_start: 0.7469 (tt) cc_final: 0.7170 (tt) REVERT: C 274 LYS cc_start: 0.7878 (mmmm) cc_final: 0.7460 (mmmm) REVERT: C 316 SER cc_start: 0.8278 (t) cc_final: 0.7917 (p) REVERT: D 62 HIS cc_start: 0.6842 (t-90) cc_final: 0.5754 (t70) REVERT: D 68 ARG cc_start: 0.6158 (tpt-90) cc_final: 0.5896 (mmm160) REVERT: D 82 TRP cc_start: 0.7936 (m100) cc_final: 0.7592 (m100) REVERT: D 99 TRP cc_start: 0.8164 (OUTLIER) cc_final: 0.7640 (m100) REVERT: D 150 ARG cc_start: 0.7092 (mmt-90) cc_final: 0.6575 (mmt180) REVERT: F 29 PHE cc_start: 0.8012 (t80) cc_final: 0.7605 (t80) REVERT: F 63 SER cc_start: 0.7686 (m) cc_final: 0.7481 (t) REVERT: G 52 THR cc_start: 0.7557 (OUTLIER) cc_final: 0.7241 (t) REVERT: I 42 HIS cc_start: 0.7833 (m-70) cc_final: 0.7401 (m90) REVERT: I 156 LEU cc_start: 0.0844 (OUTLIER) cc_final: -0.1716 (tt) REVERT: I 189 MET cc_start: 0.6465 (ptp) cc_final: 0.6155 (ppp) REVERT: I 346 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6746 (tt) REVERT: I 425 MET cc_start: 0.5083 (tmm) cc_final: 0.4135 (tmm) REVERT: I 441 MET cc_start: 0.7286 (mmt) cc_final: 0.6696 (mmt) REVERT: R 400 ARG cc_start: 0.7538 (mmm160) cc_final: 0.6516 (mmm160) REVERT: R 404 ARG cc_start: 0.7711 (ptt-90) cc_final: 0.7359 (ptt-90) REVERT: R 405 LYS cc_start: 0.8413 (tptt) cc_final: 0.8124 (tptt) REVERT: R 425 MET cc_start: 0.4664 (ppp) cc_final: 0.4141 (ppp) REVERT: R 441 MET cc_start: 0.7362 (mmp) cc_final: 0.6967 (tpt) outliers start: 112 outliers final: 94 residues processed: 619 average time/residue: 0.3485 time to fit residues: 310.4293 Evaluate side-chains 652 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 553 time to evaluate : 2.031 ------------------------------------------------------------------------------- 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 243 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR 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 21 LYS Chi-restraints excluded: chain C residue 56 TYR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 99 TRP Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 121 CYS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 184 THR 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 279 SER 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 E residue 52 THR 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 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 224 MET Chi-restraints excluded: chain I residue 237 ILE Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 308 SER Chi-restraints excluded: chain I residue 310 ILE 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 408 LYS Chi-restraints excluded: chain I residue 457 ILE Chi-restraints excluded: chain I residue 473 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 51 ILE 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 109 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 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 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 365 VAL Chi-restraints excluded: chain R residue 373 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 54 optimal weight: 0.9990 chunk 165 optimal weight: 0.4980 chunk 26 optimal weight: 0.0470 chunk 49 optimal weight: 0.0050 chunk 179 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 184 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 157 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 overall best weight: 0.3692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 HIS ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.149895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.125278 restraints weight = 36063.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.129276 restraints weight = 19167.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.131881 restraints weight = 11998.962| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.9036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18893 Z= 0.218 Angle : 0.781 15.334 25573 Z= 0.402 Chirality : 0.047 0.295 2817 Planarity : 0.004 0.046 3251 Dihedral : 4.622 21.895 2536 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.36 % Favored : 95.55 % Rotamer: Outliers : 4.67 % Allowed : 34.12 % Favored : 61.21 % 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: 0.49 (0.18), residues: 2270 helix: 1.79 (0.17), residues: 911 sheet: -0.03 (0.26), residues: 420 loop : -0.98 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP R 352 HIS 0.010 0.001 HIS I 42 PHE 0.042 0.002 PHE B 199 TYR 0.032 0.002 TYR I 305 ARG 0.013 0.001 ARG I 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5795.93 seconds wall clock time: 104 minutes 38.02 seconds (6278.02 seconds total)