Starting phenix.real_space_refine on Mon Jul 22 15:58:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptp_17877/07_2024/8ptp_17877_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptp_17877/07_2024/8ptp_17877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptp_17877/07_2024/8ptp_17877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptp_17877/07_2024/8ptp_17877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptp_17877/07_2024/8ptp_17877_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptp_17877/07_2024/8ptp_17877_neut.cif" } resolution = 3.0 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= 0.004 sd= 0.038 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 97 5.16 5 C 11959 2.51 5 N 3357 2.21 5 O 3626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 13": "OE1" <-> "OE2" Residue "A ASP 33": "OD1" <-> "OD2" Residue "A PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "B GLU 24": "OE1" <-> "OE2" Residue "B ASP 52": "OD1" <-> "OD2" Residue "B ASP 60": "OD1" <-> "OD2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "B PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C ASP 60": "OD1" <-> "OD2" Residue "C ASP 201": "OD1" <-> "OD2" Residue "C GLU 211": "OE1" <-> "OE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 397": "OE1" <-> "OE2" Residue "D ASP 210": "OD1" <-> "OD2" Residue "D GLU 244": "OE1" <-> "OE2" Residue "D GLU 248": "OE1" <-> "OE2" Residue "D ASP 290": "OD1" <-> "OD2" Residue "D ASP 322": "OD1" <-> "OD2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 211": "OE1" <-> "OE2" Residue "E PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 328": "OD1" <-> "OD2" Residue "E TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 3": "OD1" <-> "OD2" Residue "b ASP 42": "OD1" <-> "OD2" Residue "b GLU 83": "OE1" <-> "OE2" Residue "c ASP 42": "OD1" <-> "OD2" Residue "c GLU 59": "OE1" <-> "OE2" Residue "d ASP 11": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 19039 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "B" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "C" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "D" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "E" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "a" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "b" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "c" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "d" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Time building chain proxies: 10.64, per 1000 atoms: 0.56 Number of scatterers: 19039 At special positions: 0 Unit cell: (116.48, 133.12, 164.736, 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 97 16.00 O 3626 8.00 N 3357 7.00 C 11959 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 7.48 Conformation dependent library (CDL) restraints added in 3.5 seconds 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4522 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 22 sheets defined 43.7% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 30 through 46 removed outlier: 3.776A pdb=" N ILE A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 removed outlier: 3.549A pdb=" N ILE A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 132 through 136 removed outlier: 3.503A pdb=" N ASN A 135 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 166 removed outlier: 4.164A pdb=" N THR A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 235 through 255 removed outlier: 3.816A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 325 through 335 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.134A pdb=" N LEU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 388 Processing helix chain 'A' and resid 392 through 403 Processing helix chain 'A' and resid 408 through 417 Processing helix chain 'B' and resid 2 through 9 Processing helix chain 'B' and resid 10 through 22 Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.685A pdb=" N SER B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 125 through 130 removed outlier: 3.733A pdb=" N LYS B 130 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 166 removed outlier: 3.625A pdb=" N LEU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR B 158 " --> pdb=" O THR B 154 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 212 through 223 Processing helix chain 'B' and resid 235 through 256 removed outlier: 3.566A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 285 through 289 removed outlier: 3.690A pdb=" N VAL B 289 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 346 through 352 removed outlier: 3.547A pdb=" N LYS B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 388 Processing helix chain 'B' and resid 391 through 403 Processing helix chain 'B' and resid 408 through 418 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 30 through 46 removed outlier: 3.777A pdb=" N SER C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY C 46 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 123 through 128 removed outlier: 4.114A pdb=" N ARG C 128 " --> pdb=" O PRO C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 166 removed outlier: 4.337A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 212 through 223 Processing helix chain 'C' and resid 235 through 255 Processing helix chain 'C' and resid 266 through 278 Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.557A pdb=" N ALA C 303 " --> pdb=" O ARG C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 removed outlier: 3.844A pdb=" N GLU C 329 " --> pdb=" O SER C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 373 through 388 Processing helix chain 'C' and resid 391 through 405 removed outlier: 3.840A pdb=" N MET C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 418 removed outlier: 3.623A pdb=" N ARG C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 8 Processing helix chain 'D' and resid 10 through 22 Processing helix chain 'D' and resid 30 through 45 removed outlier: 3.777A pdb=" N SER D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 89 removed outlier: 3.504A pdb=" N ILE D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 155 through 166 removed outlier: 4.012A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'D' and resid 212 through 223 Processing helix chain 'D' and resid 235 through 256 removed outlier: 3.506A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 294 through 303 removed outlier: 3.512A pdb=" N ALA D 303 " --> pdb=" O ARG D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 335 Processing helix chain 'D' and resid 346 through 352 removed outlier: 3.611A pdb=" N ALA D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 391 through 406 removed outlier: 4.019A pdb=" N MET D 405 " --> pdb=" O ASN D 401 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR D 406 " --> pdb=" O LYS D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 418 Processing helix chain 'E' and resid 10 through 21 Processing helix chain 'E' and resid 30 through 45 Processing helix chain 'E' and resid 82 through 89 Processing helix chain 'E' and resid 123 through 128 Processing helix chain 'E' and resid 155 through 166 Processing helix chain 'E' and resid 183 through 199 removed outlier: 3.531A pdb=" N HIS E 199 " --> pdb=" O ILE E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 223 Processing helix chain 'E' and resid 235 through 256 Processing helix chain 'E' and resid 266 through 278 Processing helix chain 'E' and resid 290 through 303 removed outlier: 3.701A pdb=" N ARG E 296 " --> pdb=" O ASN E 292 " (cutoff:3.500A) Proline residue: E 297 - end of helix Processing helix chain 'E' and resid 327 through 334 Processing helix chain 'E' and resid 346 through 352 removed outlier: 4.138A pdb=" N ALA E 350 " --> pdb=" O SER E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 372 removed outlier: 3.866A pdb=" N LEU E 371 " --> pdb=" O LYS E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 388 removed outlier: 3.528A pdb=" N LEU E 377 " --> pdb=" O THR E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 399 removed outlier: 3.907A pdb=" N LEU E 399 " --> pdb=" O ALA E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 417 removed outlier: 3.964A pdb=" N PHE E 412 " --> pdb=" O THR E 408 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 23 removed outlier: 3.567A pdb=" N TYR a 13 " --> pdb=" O ASN a 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 23 Processing helix chain 'c' and resid 9 through 22 Processing helix chain 'd' and resid 9 through 22 Processing helix chain 'd' and resid 66 through 68 No H-bonds generated for 'chain 'd' and resid 66 through 68' Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 57 removed outlier: 7.416A pdb=" N TYR A 80 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N LYS A 115 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU A 114 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG A 102 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL A 116 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LYS A 100 " --> pdb=" O VAL A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 231 removed outlier: 6.850A pdb=" N LEU A 204 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL A 228 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL A 206 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N SER A 230 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU A 208 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 203 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU A 263 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET A 205 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ASP A 265 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A 207 " --> pdb=" O ASP A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 226 through 231 removed outlier: 6.850A pdb=" N LEU A 204 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL A 228 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL A 206 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N SER A 230 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU A 208 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 203 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU A 263 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET A 205 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ASP A 265 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A 207 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY A 174 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA A 319 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE A 176 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ARG A 173 " --> pdb=" O MET A 341 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N LEU A 343 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 175 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU A 345 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A 177 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N GLU A 342 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N ASN A 361 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N HIS A 344 " --> pdb=" O ASP A 359 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 285 removed outlier: 3.886A pdb=" N VAL A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 49 through 57 removed outlier: 6.387A pdb=" N LYS B 100 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL B 116 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N SER B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU B 118 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR B 96 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE B 49 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.754A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 144 through 145 removed outlier: 4.517A pdb=" N ILE B 168 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 226 through 231 removed outlier: 6.451A pdb=" N VAL B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE B 316 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE B 262 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR B 318 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU B 264 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N LEU B 320 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ARG B 173 " --> pdb=" O MET B 341 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU B 343 " --> pdb=" O ARG B 173 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU B 175 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEU B 345 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 177 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N GLU B 342 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ASN B 361 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N HIS B 344 " --> pdb=" O ASP B 359 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 49 through 57 removed outlier: 4.014A pdb=" N ILE C 79 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS C 100 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N VAL C 116 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER C 98 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLU C 118 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR C 96 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE C 49 " --> pdb=" O ILE C 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 144 through 145 removed outlier: 4.499A pdb=" N ILE C 168 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 226 through 231 removed outlier: 6.448A pdb=" N LEU C 204 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL C 228 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL C 206 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N SER C 230 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU C 208 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLY C 174 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ALA C 319 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE C 176 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG C 173 " --> pdb=" O MET C 341 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N LEU C 343 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU C 175 " --> pdb=" O LEU C 343 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 49 through 57 removed outlier: 3.930A pdb=" N ILE D 79 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LYS D 100 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL D 116 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N SER D 98 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU D 118 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR D 96 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE D 49 " --> pdb=" O ILE D 101 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 226 through 230 removed outlier: 6.639A pdb=" N LEU D 204 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL D 228 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL D 206 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N SER D 230 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU D 208 " --> pdb=" O SER D 230 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL D 260 " --> pdb=" O THR D 314 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE D 316 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE D 262 " --> pdb=" O ILE D 316 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N THR D 318 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU D 264 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N LEU D 320 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY D 174 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA D 319 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE D 176 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ARG D 173 " --> pdb=" O MET D 341 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU D 343 " --> pdb=" O ARG D 173 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU D 175 " --> pdb=" O LEU D 343 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY D 364 " --> pdb=" O GLU D 342 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 49 through 57 removed outlier: 3.596A pdb=" N ILE E 79 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU E 114 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ARG E 102 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL E 116 " --> pdb=" O LYS E 100 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LYS E 100 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE E 49 " --> pdb=" O ILE E 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 226 through 231 removed outlier: 4.088A pdb=" N GLU E 226 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL E 206 " --> pdb=" O GLU E 226 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL E 260 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ILE E 316 " --> pdb=" O VAL E 260 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE E 262 " --> pdb=" O ILE E 316 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N THR E 318 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU E 264 " --> pdb=" O THR E 318 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N LEU E 320 " --> pdb=" O LEU E 264 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLY E 174 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ALA E 319 " --> pdb=" O GLY E 174 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE E 176 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU E 342 " --> pdb=" O GLY E 364 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY E 364 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'a' and resid 26 through 29 Processing sheet with id=AB8, first strand: chain 'a' and resid 40 through 46 removed outlier: 5.325A pdb=" N ASP a 42 " --> pdb=" O VAL a 53 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL a 53 " --> pdb=" O ASP a 42 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 35 through 37 removed outlier: 3.500A pdb=" N GLU b 29 " --> pdb=" O SER b 70 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER b 70 " --> pdb=" O GLU b 29 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N HIS b 73 " --> pdb=" O GLY b 77 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLY b 77 " --> pdb=" O HIS b 73 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'b' and resid 39 through 42 removed outlier: 7.554A pdb=" N VAL b 53 " --> pdb=" O SER b 41 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'b' and resid 39 through 42 removed outlier: 7.554A pdb=" N VAL b 53 " --> pdb=" O SER b 41 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'c' and resid 61 through 64 removed outlier: 4.097A pdb=" N ASP c 42 " --> pdb=" O VAL c 53 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLU c 55 " --> pdb=" O ALA c 40 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA c 40 " --> pdb=" O GLU c 55 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N THR c 69 " --> pdb=" O VAL c 80 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL c 80 " --> pdb=" O THR c 69 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N PHE c 71 " --> pdb=" O THR c 78 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N THR c 78 " --> pdb=" O PHE c 71 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N HIS c 73 " --> pdb=" O ILE c 76 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'd' and resid 25 through 29 removed outlier: 6.853A pdb=" N VAL d 53 " --> pdb=" O SER d 41 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU d 43 " --> pdb=" O TYR d 51 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR d 51 " --> pdb=" O LEU d 43 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER d 45 " --> pdb=" O VAL d 49 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL d 49 " --> pdb=" O SER d 45 " (cutoff:3.500A) 873 hydrogen bonds defined for protein. 2529 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: 6.51 Time building geometry restraints manager: 8.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6500 1.34 - 1.46: 3654 1.46 - 1.58: 8981 1.58 - 1.70: 0 1.70 - 1.82: 181 Bond restraints: 19316 Sorted by residual: bond pdb=" CB GLN D 59 " pdb=" CG GLN D 59 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.69e+00 bond pdb=" CB LYS c 35 " pdb=" CG LYS c 35 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.69e+00 bond pdb=" CB LYS b 47 " pdb=" CG LYS b 47 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" CG MET E 396 " pdb=" SD MET E 396 " ideal model delta sigma weight residual 1.803 1.774 0.029 2.50e-02 1.60e+03 1.35e+00 bond pdb=" CB PRO A 10 " pdb=" CG PRO A 10 " ideal model delta sigma weight residual 1.492 1.548 -0.056 5.00e-02 4.00e+02 1.28e+00 ... (remaining 19311 not shown) Histogram of bond angle deviations from ideal: 98.22 - 105.39: 355 105.39 - 112.56: 10196 112.56 - 119.73: 6495 119.73 - 126.90: 8827 126.90 - 134.07: 152 Bond angle restraints: 26025 Sorted by residual: angle pdb=" CA MET E 396 " pdb=" CB MET E 396 " pdb=" CG MET E 396 " ideal model delta sigma weight residual 114.10 122.94 -8.84 2.00e+00 2.50e-01 1.95e+01 angle pdb=" CB LYS c 35 " pdb=" CG LYS c 35 " pdb=" CD LYS c 35 " ideal model delta sigma weight residual 111.30 120.28 -8.98 2.30e+00 1.89e-01 1.52e+01 angle pdb=" CB MET A 341 " pdb=" CG MET A 341 " pdb=" SD MET A 341 " ideal model delta sigma weight residual 112.70 123.64 -10.94 3.00e+00 1.11e-01 1.33e+01 angle pdb=" CA GLU C 329 " pdb=" CB GLU C 329 " pdb=" CG GLU C 329 " ideal model delta sigma weight residual 114.10 121.37 -7.27 2.00e+00 2.50e-01 1.32e+01 angle pdb=" CB MET A 415 " pdb=" CG MET A 415 " pdb=" SD MET A 415 " ideal model delta sigma weight residual 112.70 123.07 -10.37 3.00e+00 1.11e-01 1.19e+01 ... (remaining 26020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 10296 17.98 - 35.97: 1304 35.97 - 53.95: 319 53.95 - 71.93: 51 71.93 - 89.92: 21 Dihedral angle restraints: 11991 sinusoidal: 5013 harmonic: 6978 Sorted by residual: dihedral pdb=" CA HIS E 344 " pdb=" C HIS E 344 " pdb=" N LEU E 345 " pdb=" CA LEU E 345 " ideal model delta harmonic sigma weight residual 180.00 157.26 22.74 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA MET c 25 " pdb=" C MET c 25 " pdb=" N LEU c 26 " pdb=" CA LEU c 26 " ideal model delta harmonic sigma weight residual -180.00 -158.22 -21.78 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA PRO A 10 " pdb=" C PRO A 10 " pdb=" N VAL A 11 " pdb=" CA VAL A 11 " ideal model delta harmonic sigma weight residual 180.00 -159.36 -20.64 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 11988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1920 0.033 - 0.066: 689 0.066 - 0.099: 241 0.099 - 0.133: 127 0.133 - 0.166: 3 Chirality restraints: 2980 Sorted by residual: chirality pdb=" CA MET E 396 " pdb=" N MET E 396 " pdb=" C MET E 396 " pdb=" CB MET E 396 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" CG LEU c 28 " pdb=" CB LEU c 28 " pdb=" CD1 LEU c 28 " pdb=" CD2 LEU c 28 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA GLU A 334 " pdb=" N GLU A 334 " pdb=" C GLU A 334 " pdb=" CB GLU A 334 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 2977 not shown) Planarity restraints: 3395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 178 " 0.060 5.00e-02 4.00e+02 9.18e-02 1.35e+01 pdb=" N PRO E 179 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO E 179 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 179 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS b 73 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO b 74 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO b 74 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO b 74 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 210 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C ASP D 210 " 0.037 2.00e-02 2.50e+03 pdb=" O ASP D 210 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU D 211 " -0.012 2.00e-02 2.50e+03 ... (remaining 3392 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 552 2.70 - 3.25: 19215 3.25 - 3.80: 30920 3.80 - 4.35: 39162 4.35 - 4.90: 64663 Nonbonded interactions: 154512 Sorted by model distance: nonbonded pdb=" OG SER C 84 " pdb=" OD1 ASP c 14 " model vdw 2.149 2.440 nonbonded pdb=" OG1 THR E 408 " pdb=" OD1 ASP E 410 " model vdw 2.155 2.440 nonbonded pdb=" O GLU c 29 " pdb=" OG1 THR c 69 " model vdw 2.179 2.440 nonbonded pdb=" ND1 HIS d 73 " pdb=" OE1 GLU d 75 " model vdw 2.180 2.520 nonbonded pdb=" OG1 THR D 158 " pdb=" OD1 ASN D 190 " model vdw 2.184 2.440 ... (remaining 154507 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 51.790 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 0.056 19316 Z= 0.217 Angle : 0.642 10.942 26025 Z= 0.333 Chirality : 0.042 0.166 2980 Planarity : 0.004 0.092 3395 Dihedral : 16.707 89.917 7469 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.14 % Allowed : 25.79 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % 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 (0.17), residues: 2400 helix: 1.41 (0.17), residues: 991 sheet: 0.12 (0.26), residues: 425 loop : 0.23 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 381 HIS 0.014 0.001 HIS c 73 PHE 0.029 0.001 PHE E 301 TYR 0.011 0.001 TYR C 332 ARG 0.007 0.000 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 350 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5664 (ppp) cc_final: 0.4691 (pmm) REVERT: E 193 GLN cc_start: 0.9203 (mt0) cc_final: 0.8997 (mt0) REVERT: E 244 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7138 (mm-30) REVERT: E 416 MET cc_start: 0.8362 (ppp) cc_final: 0.7772 (pmt) REVERT: b 17 GLU cc_start: 0.8954 (tp30) cc_final: 0.8337 (tm-30) REVERT: b 66 ASP cc_start: 0.7697 (t0) cc_final: 0.7449 (t0) REVERT: d 48 ASN cc_start: 0.6448 (t0) cc_final: 0.6125 (t0) outliers start: 3 outliers final: 5 residues processed: 351 average time/residue: 1.3823 time to fit residues: 541.4380 Evaluate side-chains 303 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 298 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain b residue 24 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 0.3980 chunk 179 optimal weight: 20.0000 chunk 99 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 138 optimal weight: 0.5980 chunk 215 optimal weight: 30.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN C 193 GLN ** C 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS E 256 HIS ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19316 Z= 0.192 Angle : 0.608 9.401 26025 Z= 0.301 Chirality : 0.042 0.175 2980 Planarity : 0.004 0.060 3395 Dihedral : 4.455 81.521 2629 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.92 % Allowed : 27.09 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % 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: 1.11 (0.17), residues: 2400 helix: 1.58 (0.17), residues: 991 sheet: 0.12 (0.25), residues: 429 loop : 0.29 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 381 HIS 0.008 0.001 HIS c 73 PHE 0.016 0.001 PHE E 301 TYR 0.024 0.001 TYR c 5 ARG 0.009 0.000 ARG c 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 333 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5575 (ppp) cc_final: 0.4612 (pmm) REVERT: A 274 TYR cc_start: 0.9027 (m-80) cc_final: 0.8796 (m-80) REVERT: C 181 LYS cc_start: 0.8725 (pptt) cc_final: 0.8077 (pptt) REVERT: C 193 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7683 (mp10) REVERT: C 348 LYS cc_start: 0.7999 (mtpt) cc_final: 0.7799 (mtmt) REVERT: D 193 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7136 (mp-120) REVERT: E 175 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8695 (tm) REVERT: E 193 GLN cc_start: 0.9196 (mt0) cc_final: 0.8952 (mt0) REVERT: E 244 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7110 (mm-30) REVERT: b 17 GLU cc_start: 0.9056 (tp30) cc_final: 0.8465 (tm-30) REVERT: b 25 MET cc_start: 0.7732 (tpp) cc_final: 0.7475 (tpp) REVERT: b 50 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8062 (mt-10) REVERT: c 21 GLN cc_start: 0.8260 (pp30) cc_final: 0.7479 (pp30) REVERT: c 22 HIS cc_start: 0.8379 (OUTLIER) cc_final: 0.7894 (m90) outliers start: 61 outliers final: 19 residues processed: 369 average time/residue: 1.3911 time to fit residues: 570.8113 Evaluate side-chains 323 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 300 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 341 MET Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 344 HIS Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain c residue 22 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 119 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 179 optimal weight: 9.9990 chunk 146 optimal weight: 0.2980 chunk 59 optimal weight: 0.8980 chunk 215 optimal weight: 20.0000 chunk 232 optimal weight: 7.9990 chunk 192 optimal weight: 0.0070 chunk 213 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 overall best weight: 0.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN B 120 ASN B 275 ASN C 193 GLN C 344 HIS E 42 HIS E 241 GLN E 256 HIS ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19316 Z= 0.186 Angle : 0.611 12.722 26025 Z= 0.299 Chirality : 0.042 0.153 2980 Planarity : 0.004 0.060 3395 Dihedral : 3.977 23.779 2624 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.88 % Allowed : 28.19 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % 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: 1.12 (0.17), residues: 2400 helix: 1.69 (0.17), residues: 989 sheet: 0.04 (0.27), residues: 397 loop : 0.22 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 381 HIS 0.011 0.001 HIS d 73 PHE 0.014 0.001 PHE A 62 TYR 0.020 0.001 TYR E 197 ARG 0.010 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 317 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5588 (ppp) cc_final: 0.4686 (pmm) REVERT: A 29 MET cc_start: 0.3510 (tpt) cc_final: 0.2759 (tpp) REVERT: A 60 ASP cc_start: 0.6352 (p0) cc_final: 0.5829 (t0) REVERT: A 274 TYR cc_start: 0.9014 (m-80) cc_final: 0.8797 (m-80) REVERT: A 334 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: A 353 ARG cc_start: 0.7082 (tmm160) cc_final: 0.6348 (tmm160) REVERT: D 193 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7143 (mp-120) REVERT: E 175 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8615 (tm) REVERT: E 209 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7790 (tp) REVERT: E 244 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7115 (mm-30) REVERT: E 265 ASP cc_start: 0.7053 (t0) cc_final: 0.6740 (t0) REVERT: b 6 GLN cc_start: 0.8219 (pm20) cc_final: 0.7989 (pm20) REVERT: b 17 GLU cc_start: 0.9066 (tp30) cc_final: 0.8467 (tm-30) REVERT: b 25 MET cc_start: 0.7797 (tpp) cc_final: 0.7546 (tpp) REVERT: b 50 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8044 (mt-10) REVERT: c 21 GLN cc_start: 0.8330 (pp30) cc_final: 0.7639 (pp30) REVERT: c 22 HIS cc_start: 0.8371 (OUTLIER) cc_final: 0.7953 (m90) outliers start: 60 outliers final: 24 residues processed: 351 average time/residue: 1.3631 time to fit residues: 536.3302 Evaluate side-chains 325 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 296 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 341 MET Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 22 HIS Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 60 THR Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 78 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 216 optimal weight: 8.9990 chunk 229 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 HIS E 140 HIS E 241 GLN ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 ASN c 37 GLN ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19316 Z= 0.238 Angle : 0.617 10.463 26025 Z= 0.302 Chirality : 0.042 0.142 2980 Planarity : 0.004 0.060 3395 Dihedral : 3.975 24.118 2620 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.79 % Allowed : 28.19 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % 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: 1.15 (0.17), residues: 2400 helix: 1.73 (0.17), residues: 989 sheet: 0.02 (0.26), residues: 425 loop : 0.24 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 381 HIS 0.012 0.001 HIS d 73 PHE 0.019 0.001 PHE E 121 TYR 0.021 0.001 TYR b 13 ARG 0.011 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 308 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5642 (ppp) cc_final: 0.4682 (pmm) REVERT: A 60 ASP cc_start: 0.6563 (p0) cc_final: 0.6165 (t0) REVERT: D 193 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.7170 (mp-120) REVERT: E 175 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8568 (tm) REVERT: E 193 GLN cc_start: 0.9212 (mt0) cc_final: 0.8983 (mt0) REVERT: E 209 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7848 (tp) REVERT: E 244 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7173 (mm-30) REVERT: E 265 ASP cc_start: 0.7216 (t0) cc_final: 0.6939 (t0) REVERT: b 17 GLU cc_start: 0.9105 (tp30) cc_final: 0.8490 (tm-30) REVERT: b 25 MET cc_start: 0.8001 (tpp) cc_final: 0.7760 (tpp) REVERT: b 50 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8074 (mt-10) REVERT: b 70 SER cc_start: 0.8859 (p) cc_final: 0.8634 (m) REVERT: c 21 GLN cc_start: 0.8328 (pp30) cc_final: 0.7712 (pp30) REVERT: c 22 HIS cc_start: 0.8375 (OUTLIER) cc_final: 0.7955 (m90) outliers start: 79 outliers final: 39 residues processed: 359 average time/residue: 1.3716 time to fit residues: 548.8579 Evaluate side-chains 338 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 295 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 341 MET Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 409 ASN Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 41 SER Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 22 HIS Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 70 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 170 optimal weight: 0.0470 chunk 94 optimal weight: 0.0870 chunk 195 optimal weight: 9.9990 chunk 158 optimal weight: 0.0980 chunk 0 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.4460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 HIS E 140 HIS E 241 GLN ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 ASN ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19316 Z= 0.177 Angle : 0.637 11.647 26025 Z= 0.308 Chirality : 0.042 0.141 2980 Planarity : 0.004 0.064 3395 Dihedral : 3.932 23.525 2620 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.64 % Allowed : 29.43 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.18), residues: 2400 helix: 1.78 (0.17), residues: 989 sheet: -0.02 (0.27), residues: 398 loop : 0.24 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 381 HIS 0.009 0.001 HIS d 73 PHE 0.010 0.001 PHE B 398 TYR 0.023 0.001 TYR b 13 ARG 0.011 0.001 ARG B 299 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 322 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5645 (ppp) cc_final: 0.4786 (pmm) REVERT: A 29 MET cc_start: 0.3674 (tpt) cc_final: 0.2870 (tpp) REVERT: A 58 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7684 (mm) REVERT: A 60 ASP cc_start: 0.6452 (p0) cc_final: 0.6039 (t0) REVERT: A 396 MET cc_start: 0.7674 (mmt) cc_final: 0.7288 (mmm) REVERT: B 244 GLU cc_start: 0.7059 (pp20) cc_final: 0.6762 (pp20) REVERT: D 193 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.7050 (mp-120) REVERT: E 175 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8527 (tm) REVERT: E 244 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7082 (mm-30) REVERT: E 265 ASP cc_start: 0.7209 (t0) cc_final: 0.6958 (t0) REVERT: b 17 GLU cc_start: 0.9091 (tp30) cc_final: 0.8479 (tm-30) REVERT: b 50 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7969 (mt-10) REVERT: b 70 SER cc_start: 0.8903 (p) cc_final: 0.8600 (m) REVERT: b 80 VAL cc_start: 0.9361 (t) cc_final: 0.9025 (t) REVERT: c 21 GLN cc_start: 0.8332 (pp30) cc_final: 0.7979 (pp30) REVERT: c 22 HIS cc_start: 0.8366 (OUTLIER) cc_final: 0.7968 (m-70) outliers start: 76 outliers final: 35 residues processed: 364 average time/residue: 1.3027 time to fit residues: 531.8887 Evaluate side-chains 347 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 308 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 341 MET Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 409 ASN Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 41 SER Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 22 HIS Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 78 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 0.6980 chunk 206 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 229 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 HIS E 140 HIS ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 ASN ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19316 Z= 0.220 Angle : 0.658 11.660 26025 Z= 0.315 Chirality : 0.042 0.166 2980 Planarity : 0.004 0.060 3395 Dihedral : 3.950 24.120 2620 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.55 % Allowed : 29.91 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % 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: 1.14 (0.18), residues: 2400 helix: 1.76 (0.17), residues: 989 sheet: -0.06 (0.26), residues: 398 loop : 0.21 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 381 HIS 0.007 0.001 HIS d 73 PHE 0.028 0.001 PHE A 355 TYR 0.024 0.001 TYR b 13 ARG 0.012 0.001 ARG B 299 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 310 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5875 (ppp) cc_final: 0.5099 (pmm) REVERT: A 29 MET cc_start: 0.3698 (tpt) cc_final: 0.2968 (tpp) REVERT: A 58 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7677 (mm) REVERT: A 60 ASP cc_start: 0.6481 (p0) cc_final: 0.6102 (t0) REVERT: A 334 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: A 396 MET cc_start: 0.7751 (mmt) cc_final: 0.7529 (mmm) REVERT: B 416 MET cc_start: 0.8136 (tpp) cc_final: 0.7634 (mpp) REVERT: D 298 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8396 (mttm) REVERT: E 175 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8484 (tm) REVERT: E 209 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7811 (tp) REVERT: E 244 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7118 (mm-30) REVERT: E 265 ASP cc_start: 0.7284 (t0) cc_final: 0.7019 (t0) REVERT: b 17 GLU cc_start: 0.9098 (tp30) cc_final: 0.8521 (tm-30) REVERT: b 25 MET cc_start: 0.7596 (tpp) cc_final: 0.7243 (tpp) REVERT: b 50 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7949 (mt-10) REVERT: b 70 SER cc_start: 0.8922 (p) cc_final: 0.8521 (m) REVERT: b 80 VAL cc_start: 0.9364 (t) cc_final: 0.9010 (t) REVERT: c 21 GLN cc_start: 0.8304 (pp30) cc_final: 0.8000 (pp30) REVERT: c 22 HIS cc_start: 0.8370 (OUTLIER) cc_final: 0.7973 (m-70) outliers start: 74 outliers final: 41 residues processed: 356 average time/residue: 1.3249 time to fit residues: 528.4334 Evaluate side-chains 345 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 298 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 341 MET Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 298 LYS Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 409 ASN Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 41 SER Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 22 HIS Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 78 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 130 optimal weight: 0.0970 chunk 167 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 193 optimal weight: 0.0670 chunk 128 optimal weight: 3.9990 chunk 228 optimal weight: 30.0000 chunk 142 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN E 42 HIS E 140 HIS ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19316 Z= 0.183 Angle : 0.674 14.981 26025 Z= 0.322 Chirality : 0.042 0.204 2980 Planarity : 0.004 0.060 3395 Dihedral : 3.935 23.343 2620 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.16 % Allowed : 30.97 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % 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: 1.15 (0.17), residues: 2400 helix: 1.77 (0.17), residues: 992 sheet: 0.08 (0.27), residues: 365 loop : 0.13 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 381 HIS 0.009 0.001 HIS d 73 PHE 0.013 0.001 PHE B 412 TYR 0.023 0.001 TYR E 197 ARG 0.015 0.001 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 311 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5913 (ppp) cc_final: 0.5195 (pmm) REVERT: A 29 MET cc_start: 0.3710 (tpt) cc_final: 0.3022 (tpp) REVERT: A 58 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7650 (mm) REVERT: A 60 ASP cc_start: 0.6513 (p0) cc_final: 0.6154 (t0) REVERT: A 334 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: B 93 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8764 (m) REVERT: B 244 GLU cc_start: 0.7031 (pp20) cc_final: 0.6698 (pp20) REVERT: B 245 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7681 (mmm) REVERT: B 416 MET cc_start: 0.8077 (tpp) cc_final: 0.7738 (mpp) REVERT: E 209 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7727 (tp) REVERT: E 244 GLU cc_start: 0.7309 (mm-30) cc_final: 0.7034 (mm-30) REVERT: E 265 ASP cc_start: 0.7287 (t0) cc_final: 0.7018 (t0) REVERT: b 17 GLU cc_start: 0.9092 (tp30) cc_final: 0.8519 (tm-30) REVERT: b 25 MET cc_start: 0.7810 (tpp) cc_final: 0.7483 (tpp) REVERT: b 50 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7920 (mt-10) REVERT: b 70 SER cc_start: 0.8916 (p) cc_final: 0.8489 (m) REVERT: b 80 VAL cc_start: 0.9355 (t) cc_final: 0.8968 (t) REVERT: c 21 GLN cc_start: 0.8304 (pp30) cc_final: 0.8039 (pp30) REVERT: c 22 HIS cc_start: 0.8366 (OUTLIER) cc_final: 0.7973 (m-70) outliers start: 66 outliers final: 36 residues processed: 354 average time/residue: 1.2866 time to fit residues: 510.5864 Evaluate side-chains 339 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 297 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 341 MET Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 409 ASN Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 41 SER Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 22 HIS Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 78 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 112 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 chunk 179 optimal weight: 40.0000 chunk 207 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 HIS E 140 HIS ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19316 Z= 0.211 Angle : 0.694 17.486 26025 Z= 0.332 Chirality : 0.042 0.207 2980 Planarity : 0.004 0.059 3395 Dihedral : 3.953 23.819 2620 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.02 % Allowed : 31.69 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % 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: 1.11 (0.17), residues: 2400 helix: 1.73 (0.17), residues: 992 sheet: 0.05 (0.27), residues: 365 loop : 0.13 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 381 HIS 0.009 0.001 HIS d 73 PHE 0.023 0.001 PHE E 121 TYR 0.028 0.002 TYR b 13 ARG 0.013 0.001 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 300 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5918 (ppp) cc_final: 0.5235 (pmm) REVERT: A 58 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7687 (mm) REVERT: A 60 ASP cc_start: 0.6573 (p0) cc_final: 0.6225 (t0) REVERT: A 334 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: B 341 MET cc_start: 0.7530 (tmm) cc_final: 0.7316 (ttt) REVERT: D 193 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7011 (mp10) REVERT: D 210 ASP cc_start: 0.6631 (t0) cc_final: 0.6414 (OUTLIER) REVERT: D 341 MET cc_start: 0.7810 (pp-130) cc_final: 0.7603 (pp-130) REVERT: E 209 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7736 (tp) REVERT: E 244 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7051 (mm-30) REVERT: E 265 ASP cc_start: 0.7358 (t0) cc_final: 0.7086 (t0) REVERT: b 17 GLU cc_start: 0.9089 (tp30) cc_final: 0.8508 (tm-30) REVERT: b 25 MET cc_start: 0.7924 (tpp) cc_final: 0.7610 (tpp) REVERT: b 50 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7896 (mt-10) REVERT: b 70 SER cc_start: 0.8935 (p) cc_final: 0.8465 (m) REVERT: b 80 VAL cc_start: 0.9344 (t) cc_final: 0.8947 (t) REVERT: c 21 GLN cc_start: 0.8332 (pp30) cc_final: 0.8087 (pp30) REVERT: c 22 HIS cc_start: 0.8392 (OUTLIER) cc_final: 0.8005 (m-70) outliers start: 63 outliers final: 40 residues processed: 342 average time/residue: 1.2912 time to fit residues: 496.1936 Evaluate side-chains 337 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 293 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 341 MET Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 409 ASN Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 41 SER Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 22 HIS Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 73 HIS Chi-restraints excluded: chain d residue 51 TYR Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 78 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 212 optimal weight: 0.0370 chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 0.0470 chunk 167 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 192 optimal weight: 8.9990 chunk 201 optimal weight: 10.0000 chunk 139 optimal weight: 0.9990 chunk 225 optimal weight: 5.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN D 85 GLN E 42 HIS ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN a 15 ASN ** b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19316 Z= 0.200 Angle : 0.730 17.105 26025 Z= 0.344 Chirality : 0.043 0.197 2980 Planarity : 0.005 0.099 3395 Dihedral : 3.973 23.880 2620 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.64 % Allowed : 32.50 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % 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: 1.10 (0.17), residues: 2400 helix: 1.72 (0.17), residues: 992 sheet: 0.05 (0.27), residues: 365 loop : 0.13 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 381 HIS 0.016 0.001 HIS c 73 PHE 0.023 0.001 PHE D 335 TYR 0.024 0.001 TYR E 197 ARG 0.022 0.001 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 305 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6027 (OUTLIER) cc_final: 0.5377 (pmm) REVERT: A 29 MET cc_start: 0.3684 (tpt) cc_final: 0.2902 (tpp) REVERT: A 58 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7666 (mm) REVERT: A 60 ASP cc_start: 0.6526 (p0) cc_final: 0.6184 (t0) REVERT: A 334 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: B 93 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8750 (m) REVERT: B 244 GLU cc_start: 0.7034 (pp20) cc_final: 0.6587 (pp20) REVERT: D 193 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.6982 (mp10) REVERT: E 209 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7683 (tp) REVERT: E 244 GLU cc_start: 0.7317 (mm-30) cc_final: 0.7041 (mm-30) REVERT: E 265 ASP cc_start: 0.7419 (t0) cc_final: 0.7161 (t0) REVERT: E 360 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.6182 (m-10) REVERT: b 17 GLU cc_start: 0.9094 (tp30) cc_final: 0.8518 (tm-30) REVERT: b 25 MET cc_start: 0.8075 (tpp) cc_final: 0.7774 (tpp) REVERT: b 50 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7916 (mt-10) REVERT: b 70 SER cc_start: 0.8954 (p) cc_final: 0.8455 (m) REVERT: b 80 VAL cc_start: 0.9346 (t) cc_final: 0.8947 (t) REVERT: c 21 GLN cc_start: 0.8374 (pp30) cc_final: 0.8140 (pp30) REVERT: c 22 HIS cc_start: 0.8437 (OUTLIER) cc_final: 0.8088 (m-70) outliers start: 55 outliers final: 37 residues processed: 336 average time/residue: 1.2707 time to fit residues: 480.3609 Evaluate side-chains 338 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 293 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 341 MET Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 360 TYR Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 41 SER Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 22 HIS Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 156 optimal weight: 0.6980 chunk 236 optimal weight: 20.0000 chunk 217 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 HIS ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19316 Z= 0.224 Angle : 0.750 16.358 26025 Z= 0.356 Chirality : 0.043 0.217 2980 Planarity : 0.005 0.074 3395 Dihedral : 4.014 23.921 2620 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.44 % Allowed : 32.69 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.17), residues: 2400 helix: 1.65 (0.17), residues: 992 sheet: 0.01 (0.27), residues: 367 loop : 0.13 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 381 HIS 0.008 0.001 HIS d 73 PHE 0.024 0.001 PHE E 121 TYR 0.028 0.001 TYR b 13 ARG 0.017 0.001 ARG A 353 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 292 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6076 (OUTLIER) cc_final: 0.5424 (pmm) REVERT: A 29 MET cc_start: 0.3724 (tpt) cc_final: 0.2936 (tpp) REVERT: A 58 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7675 (mm) REVERT: A 60 ASP cc_start: 0.6592 (p0) cc_final: 0.6265 (t0) REVERT: A 334 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: B 244 GLU cc_start: 0.7071 (pp20) cc_final: 0.6692 (pp20) REVERT: D 193 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.6997 (mp10) REVERT: E 209 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7735 (tp) REVERT: E 244 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7066 (mm-30) REVERT: E 265 ASP cc_start: 0.7442 (t0) cc_final: 0.7209 (t0) REVERT: E 360 TYR cc_start: 0.7452 (OUTLIER) cc_final: 0.6319 (m-80) REVERT: b 17 GLU cc_start: 0.9097 (tp30) cc_final: 0.8522 (tm-30) REVERT: b 25 MET cc_start: 0.8093 (tpp) cc_final: 0.7796 (tpp) REVERT: b 50 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8000 (mt-10) REVERT: b 70 SER cc_start: 0.8931 (p) cc_final: 0.8480 (m) REVERT: c 21 GLN cc_start: 0.8386 (pp30) cc_final: 0.8151 (pp30) REVERT: c 22 HIS cc_start: 0.8387 (OUTLIER) cc_final: 0.8019 (m-70) outliers start: 51 outliers final: 35 residues processed: 325 average time/residue: 1.3121 time to fit residues: 478.1513 Evaluate side-chains 329 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 287 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 341 MET Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 360 TYR Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 41 SER Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 22 HIS Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 27 optimal weight: 0.0870 chunk 52 optimal weight: 2.9990 chunk 188 optimal weight: 0.0970 chunk 78 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN D 85 GLN E 42 HIS ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.106218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.076154 restraints weight = 50260.909| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.40 r_work: 0.3096 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19316 Z= 0.225 Angle : 0.760 15.962 26025 Z= 0.360 Chirality : 0.043 0.220 2980 Planarity : 0.004 0.059 3395 Dihedral : 4.017 23.955 2620 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.54 % Allowed : 32.69 % Favored : 64.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % 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: 1.03 (0.17), residues: 2400 helix: 1.63 (0.17), residues: 992 sheet: 0.01 (0.27), residues: 367 loop : 0.13 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 381 HIS 0.008 0.001 HIS d 73 PHE 0.016 0.001 PHE D 335 TYR 0.024 0.001 TYR E 197 ARG 0.014 0.001 ARG B 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8116.11 seconds wall clock time: 142 minutes 12.23 seconds (8532.23 seconds total)