Starting phenix.real_space_refine on Tue Aug 6 07:23:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v46_42966/08_2024/8v46_42966.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v46_42966/08_2024/8v46_42966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v46_42966/08_2024/8v46_42966.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v46_42966/08_2024/8v46_42966.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v46_42966/08_2024/8v46_42966.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v46_42966/08_2024/8v46_42966.cif" } resolution = 3.09 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= -0.000 sd= 0.015 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 1 5.21 5 S 57 5.16 5 C 9956 2.51 5 N 2627 2.21 5 O 2985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 15632 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3320 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 10, 'TRANS': 401} Chain breaks: 4 Chain: "B" Number of atoms: 3225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3225 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 10, 'TRANS': 389} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2422 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 6, 'TRANS': 298} Chain: "C" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3301 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 10, 'TRANS': 399} Chain breaks: 4 Chain: "F" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3301 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 10, 'TRANS': 399} Chain breaks: 4 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.73, per 1000 atoms: 0.56 Number of scatterers: 15632 At special positions: 0 Unit cell: (95.37, 163.625, 154.275, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 57 16.00 P 6 15.00 Mg 1 11.99 O 2985 8.00 N 2627 7.00 C 9956 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: 5.83 Conformation dependent library (CDL) restraints added in 2.7 seconds 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3702 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 15 sheets defined 55.0% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 38 through 51 Processing helix chain 'A' and resid 53 through 60 removed outlier: 3.679A pdb=" N ALA A 58 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 60 " --> pdb=" O PHE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 114 Processing helix chain 'A' and resid 125 through 138 removed outlier: 3.522A pdb=" N ASN A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 161 removed outlier: 3.574A pdb=" N ALA A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 189 Processing helix chain 'A' and resid 199 through 238 removed outlier: 4.313A pdb=" N PHE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 264 removed outlier: 3.707A pdb=" N LYS A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 269 removed outlier: 3.565A pdb=" N ASN A 268 " --> pdb=" O SER A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 removed outlier: 3.550A pdb=" N VAL A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 319 removed outlier: 3.874A pdb=" N ALA A 300 " --> pdb=" O SER A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 331 Processing helix chain 'A' and resid 367 through 379 Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.694A pdb=" N GLU A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU A 407 " --> pdb=" O GLN A 403 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LYS A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 52 Processing helix chain 'B' and resid 53 through 60 removed outlier: 3.579A pdb=" N ALA B 58 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 60 " --> pdb=" O PHE B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 127 through 139 Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 199 through 237 removed outlier: 4.013A pdb=" N SER B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 264 Processing helix chain 'B' and resid 273 through 288 removed outlier: 4.055A pdb=" N VAL B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 319 removed outlier: 3.759A pdb=" N SER B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 319 " --> pdb=" O GLN B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 331 Processing helix chain 'B' and resid 362 through 366 removed outlier: 3.527A pdb=" N VAL B 365 " --> pdb=" O PRO B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 380 removed outlier: 3.656A pdb=" N ALA B 380 " --> pdb=" O MET B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 412 removed outlier: 4.070A pdb=" N ASP B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU B 407 " --> pdb=" O GLN B 403 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LYS B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'D' and resid 7 through 18 Processing helix chain 'D' and resid 27 through 42 removed outlier: 3.759A pdb=" N PHE D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 59 through 64 removed outlier: 4.399A pdb=" N LYS D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 77 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 127 through 138 Processing helix chain 'D' and resid 143 through 172 removed outlier: 3.590A pdb=" N GLU D 153 " --> pdb=" O GLU D 149 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER D 156 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N SER D 157 " --> pdb=" O GLU D 153 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE D 159 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ALA D 160 " --> pdb=" O SER D 156 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL D 161 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE D 172 " --> pdb=" O ALA D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 182 removed outlier: 3.988A pdb=" N ALA D 180 " --> pdb=" O GLY D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'D' and resid 205 through 225 Proline residue: D 221 - end of helix Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 236 through 257 removed outlier: 3.571A pdb=" N ILE D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU D 242 " --> pdb=" O HIS D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 275 through 291 Processing helix chain 'D' and resid 300 through 307 Processing helix chain 'C' and resid 38 through 51 Processing helix chain 'C' and resid 53 through 60 removed outlier: 3.585A pdb=" N ARG C 56 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA C 58 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU C 60 " --> pdb=" O PHE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 114 Processing helix chain 'C' and resid 125 through 138 Processing helix chain 'C' and resid 151 through 161 Processing helix chain 'C' and resid 177 through 189 Processing helix chain 'C' and resid 199 through 234 removed outlier: 3.768A pdb=" N PHE C 234 " --> pdb=" O PHE C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 264 Processing helix chain 'C' and resid 265 through 269 removed outlier: 3.639A pdb=" N ASN C 268 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY C 269 " --> pdb=" O ILE C 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 265 through 269' Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.803A pdb=" N VAL C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 319 removed outlier: 3.518A pdb=" N ALA C 300 " --> pdb=" O SER C 296 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU C 316 " --> pdb=" O GLN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 331 Processing helix chain 'C' and resid 362 through 366 removed outlier: 3.661A pdb=" N VAL C 365 " --> pdb=" O PRO C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 380 Processing helix chain 'C' and resid 399 through 413 removed outlier: 3.845A pdb=" N GLU C 404 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP C 405 " --> pdb=" O ASP C 401 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU C 407 " --> pdb=" O GLN C 403 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LYS C 408 " --> pdb=" O GLU C 404 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'F' and resid 13 through 16 Processing helix chain 'F' and resid 38 through 51 Processing helix chain 'F' and resid 53 through 60 removed outlier: 3.578A pdb=" N ALA F 58 " --> pdb=" O ILE F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 114 Processing helix chain 'F' and resid 125 through 138 Processing helix chain 'F' and resid 151 through 161 Processing helix chain 'F' and resid 177 through 188 Processing helix chain 'F' and resid 199 through 234 removed outlier: 4.492A pdb=" N PHE F 230 " --> pdb=" O PHE F 226 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL F 231 " --> pdb=" O SER F 227 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 264 removed outlier: 3.945A pdb=" N LYS F 253 " --> pdb=" O GLY F 249 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU F 254 " --> pdb=" O GLU F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 288 removed outlier: 3.881A pdb=" N VAL F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN F 288 " --> pdb=" O LEU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 319 Processing helix chain 'F' and resid 319 through 331 removed outlier: 3.509A pdb=" N SER F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 366 removed outlier: 3.651A pdb=" N VAL F 365 " --> pdb=" O PRO F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 380 Processing helix chain 'F' and resid 399 through 413 removed outlier: 3.675A pdb=" N GLU F 404 " --> pdb=" O ILE F 400 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP F 405 " --> pdb=" O ASP F 401 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU F 407 " --> pdb=" O GLN F 403 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS F 408 " --> pdb=" O GLU F 404 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN F 413 " --> pdb=" O ARG F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 434 No H-bonds generated for 'chain 'F' and resid 432 through 434' Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 101 removed outlier: 6.744A pdb=" N GLU A 64 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU A 11 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS A 66 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE A 9 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR A 68 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N TYR A 18 " --> pdb=" O LYS A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 148 removed outlier: 7.472A pdb=" N ALA A 387 " --> pdb=" O GLN A 418 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N ILE A 420 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL A 389 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N CYS A 422 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ILE A 391 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE A 437 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL A 30 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE A 439 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N HIS A 32 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 337 through 341 Processing sheet with id=AA4, first strand: chain 'B' and resid 97 through 101 removed outlier: 6.881A pdb=" N GLU B 64 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU B 11 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LYS B 66 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE B 9 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR B 68 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N TYR B 18 " --> pdb=" O LYS B 13 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 144 through 148 removed outlier: 7.150A pdb=" N ALA B 387 " --> pdb=" O GLN B 418 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N ILE B 420 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 389 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N CYS B 422 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE B 391 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE B 437 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL B 30 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 337 through 341 Processing sheet with id=AA7, first strand: chain 'D' and resid 48 through 51 removed outlier: 6.198A pdb=" N LEU D 23 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG D 22 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU D 86 " --> pdb=" O ARG D 22 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU D 24 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 94 through 96 Processing sheet with id=AA9, first strand: chain 'C' and resid 97 through 101 removed outlier: 3.669A pdb=" N GLU C 64 " --> pdb=" O SER C 12 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 8 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N TYR C 18 " --> pdb=" O LYS C 13 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 144 through 148 removed outlier: 7.054A pdb=" N ALA C 387 " --> pdb=" O GLN C 418 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ILE C 420 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL C 389 " --> pdb=" O ILE C 420 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N CYS C 422 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE C 391 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE C 437 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL C 30 " --> pdb=" O ILE C 437 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 337 through 341 Processing sheet with id=AB3, first strand: chain 'F' and resid 21 through 23 removed outlier: 3.719A pdb=" N GLU F 64 " --> pdb=" O SER F 12 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 18 through 19 Processing sheet with id=AB5, first strand: chain 'F' and resid 146 through 148 removed outlier: 7.567A pdb=" N ILE F 437 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL F 30 " --> pdb=" O ILE F 437 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 337 through 341 875 hydrogen bonds defined for protein. 2505 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: 4.81 Time building geometry restraints manager: 6.41 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: 5018 1.34 - 1.46: 2968 1.46 - 1.58: 7819 1.58 - 1.69: 6 1.69 - 1.81: 103 Bond restraints: 15914 Sorted by residual: bond pdb=" C LEU D 220 " pdb=" N PRO D 221 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.28e-02 6.10e+03 3.01e+00 bond pdb=" C LYS B 354 " pdb=" N PHE B 355 " ideal model delta sigma weight residual 1.327 1.297 0.030 1.71e-02 3.42e+03 3.00e+00 bond pdb=" C LEU D 177 " pdb=" N PRO D 178 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.19e-02 7.06e+03 2.54e+00 bond pdb=" CA LEU D 220 " pdb=" C LEU D 220 " ideal model delta sigma weight residual 1.520 1.535 -0.015 1.23e-02 6.61e+03 1.39e+00 bond pdb=" CA LEU D 177 " pdb=" C LEU D 177 " ideal model delta sigma weight residual 1.520 1.534 -0.014 1.23e-02 6.61e+03 1.31e+00 ... (remaining 15909 not shown) Histogram of bond angle deviations from ideal: 99.86 - 107.84: 433 107.84 - 115.83: 9635 115.83 - 123.81: 11020 123.81 - 131.79: 326 131.79 - 139.78: 21 Bond angle restraints: 21435 Sorted by residual: angle pdb=" C ASP C 83 " pdb=" N GLU C 84 " pdb=" CA GLU C 84 " ideal model delta sigma weight residual 121.54 130.80 -9.26 1.91e+00 2.74e-01 2.35e+01 angle pdb=" C4' ATP A 501 " pdb=" C5' ATP A 501 " pdb=" O5' ATP A 501 " ideal model delta sigma weight residual 108.83 119.19 -10.36 2.33e+00 1.85e-01 1.98e+01 angle pdb=" N VAL A 365 " pdb=" CA VAL A 365 " pdb=" C VAL A 365 " ideal model delta sigma weight residual 112.29 108.30 3.99 9.40e-01 1.13e+00 1.80e+01 angle pdb=" C ASP F 83 " pdb=" N GLU F 84 " pdb=" CA GLU F 84 " ideal model delta sigma weight residual 125.02 130.62 -5.60 1.76e+00 3.23e-01 1.01e+01 angle pdb=" C HIS C 15 " pdb=" N ASN C 16 " pdb=" CA ASN C 16 " ideal model delta sigma weight residual 122.08 126.45 -4.37 1.47e+00 4.63e-01 8.84e+00 ... (remaining 21430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 9106 17.38 - 34.75: 446 34.75 - 52.13: 92 52.13 - 69.50: 28 69.50 - 86.88: 8 Dihedral angle restraints: 9680 sinusoidal: 3977 harmonic: 5703 Sorted by residual: dihedral pdb=" CA LEU A 192 " pdb=" CB LEU A 192 " pdb=" CG LEU A 192 " pdb=" CD1 LEU A 192 " ideal model delta sinusoidal sigma weight residual 60.00 119.27 -59.27 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB ARG B 56 " pdb=" CG ARG B 56 " pdb=" CD ARG B 56 " pdb=" NE ARG B 56 " ideal model delta sinusoidal sigma weight residual 60.00 118.75 -58.75 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N LEU A 308 " pdb=" CA LEU A 308 " pdb=" CB LEU A 308 " pdb=" CG LEU A 308 " ideal model delta sinusoidal sigma weight residual -60.00 -117.90 57.90 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 9677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1512 0.036 - 0.072: 600 0.072 - 0.107: 170 0.107 - 0.143: 77 0.143 - 0.179: 11 Chirality restraints: 2370 Sorted by residual: chirality pdb=" CA ILE D 204 " pdb=" N ILE D 204 " pdb=" C ILE D 204 " pdb=" CB ILE D 204 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" CB ILE D 204 " pdb=" CA ILE D 204 " pdb=" CG1 ILE D 204 " pdb=" CG2 ILE D 204 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CA LEU D 220 " pdb=" N LEU D 220 " pdb=" C LEU D 220 " pdb=" CB LEU D 220 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 2367 not shown) Planarity restraints: 2727 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 123 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C ASN D 123 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN D 123 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR D 124 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 132 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" C ILE D 132 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE D 132 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP D 133 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 196 " 0.011 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" C LEU D 196 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU D 196 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE D 197 " 0.014 2.00e-02 2.50e+03 ... (remaining 2724 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 151 2.64 - 3.21: 13372 3.21 - 3.77: 23687 3.77 - 4.34: 33433 4.34 - 4.90: 55027 Nonbonded interactions: 125670 Sorted by model distance: nonbonded pdb="MG MG B 501 " pdb=" O2B ATP B 502 " model vdw 2.079 2.170 nonbonded pdb="MG MG B 501 " pdb=" O1G ATP B 502 " model vdw 2.187 2.170 nonbonded pdb=" O ALA F 380 " pdb=" OG SER F 415 " model vdw 2.329 3.040 nonbonded pdb=" O ASN B 177 " pdb=" OG SER B 181 " model vdw 2.337 3.040 nonbonded pdb=" O ALA A 380 " pdb=" OG SER A 415 " model vdw 2.337 3.040 ... (remaining 125665 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 112 or resid 126 through 162 or resid 175 throug \ h 236 or resid 249 through 310 or (resid 311 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name NE or name NH1 or name NH2)) or \ resid 312 through 342 or resid 348 through 444)) selection = (chain 'B' and (resid 3 through 236 or resid 249 through 288 or resid 295 throug \ h 444)) selection = (chain 'C' and (resid 3 through 112 or resid 126 through 162 or resid 175 throug \ h 236 or resid 249 through 310 or (resid 311 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name NE or name NH1 or name NH2)) or \ resid 312 through 342 or resid 348 through 444)) selection = (chain 'F' and (resid 3 through 112 or resid 126 through 162 or resid 175 throug \ h 236 or resid 249 through 310 or (resid 311 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name NE or name NH1 or name NH2)) or \ resid 312 through 342 or resid 348 through 444)) } 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: 2.520 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: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 42.300 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 : 0.004 0.045 15914 Z= 0.247 Angle : 0.589 10.355 21435 Z= 0.339 Chirality : 0.045 0.179 2370 Planarity : 0.004 0.051 2727 Dihedral : 11.450 86.880 5978 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.58 % Allowed : 4.04 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.32 (0.18), residues: 1893 helix: 0.06 (0.15), residues: 989 sheet: 0.35 (0.30), residues: 323 loop : -0.76 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 287 HIS 0.004 0.001 HIS B 424 PHE 0.018 0.002 PHE D 216 TYR 0.021 0.002 TYR A 197 ARG 0.003 0.000 ARG D 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 198 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8357 (mtmm) REVERT: A 129 MET cc_start: 0.9140 (mtp) cc_final: 0.8917 (mmt) REVERT: A 276 LYS cc_start: 0.9267 (tttt) cc_final: 0.9027 (tttm) REVERT: A 364 ARG cc_start: 0.9004 (ptt-90) cc_final: 0.8792 (ptp90) REVERT: A 442 GLU cc_start: 0.8406 (tt0) cc_final: 0.8169 (tt0) REVERT: B 195 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8668 (mp) REVERT: B 201 MET cc_start: 0.8354 (mmt) cc_final: 0.7735 (mtm) REVERT: B 209 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8011 (mm-30) REVERT: D 17 MET cc_start: 0.9323 (mtp) cc_final: 0.9109 (mtm) REVERT: D 99 GLN cc_start: 0.8275 (tt0) cc_final: 0.8026 (tp40) REVERT: D 212 PHE cc_start: 0.9706 (t80) cc_final: 0.9367 (t80) REVERT: C 106 MET cc_start: 0.8476 (mtt) cc_final: 0.7914 (tmm) REVERT: C 126 MET cc_start: 0.9249 (mtm) cc_final: 0.8782 (tmm) REVERT: C 342 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.8094 (p90) REVERT: F 436 MET cc_start: 0.7153 (mtp) cc_final: 0.6444 (mmm) outliers start: 44 outliers final: 11 residues processed: 234 average time/residue: 0.3297 time to fit residues: 108.5823 Evaluate side-chains 123 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 30.0000 chunk 146 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 0.0670 chunk 78 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 175 optimal weight: 20.0000 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN D 99 GLN C 32 HIS C 324 ASN F 32 HIS F 262 GLN F 312 GLN F 315 GLN F 424 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15914 Z= 0.236 Angle : 0.500 13.788 21435 Z= 0.262 Chirality : 0.042 0.170 2370 Planarity : 0.003 0.031 2727 Dihedral : 7.483 85.967 2213 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.87 % Allowed : 8.49 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.19), residues: 1893 helix: 1.53 (0.16), residues: 989 sheet: 0.43 (0.30), residues: 328 loop : -0.52 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 158 HIS 0.004 0.001 HIS B 424 PHE 0.014 0.001 PHE C 100 TYR 0.014 0.001 TYR A 197 ARG 0.003 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 121 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.9168 (mtp) cc_final: 0.8960 (mmt) REVERT: A 206 ARG cc_start: 0.8245 (mmm-85) cc_final: 0.7947 (tpt90) REVERT: A 442 GLU cc_start: 0.8274 (tt0) cc_final: 0.8034 (tt0) REVERT: B 209 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8156 (mm-30) REVERT: B 230 PHE cc_start: 0.8576 (t80) cc_final: 0.8019 (t80) REVERT: D 35 TYR cc_start: 0.8959 (OUTLIER) cc_final: 0.8477 (m-10) REVERT: D 136 GLN cc_start: 0.9067 (tm-30) cc_final: 0.8754 (pp30) REVERT: D 212 PHE cc_start: 0.9692 (t80) cc_final: 0.9394 (t80) REVERT: C 106 MET cc_start: 0.8457 (mtt) cc_final: 0.7948 (tmm) REVERT: C 126 MET cc_start: 0.9280 (mtm) cc_final: 0.8899 (tmm) REVERT: C 342 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.8033 (p90) REVERT: F 436 MET cc_start: 0.7227 (mtp) cc_final: 0.6486 (mmm) outliers start: 32 outliers final: 16 residues processed: 145 average time/residue: 0.3189 time to fit residues: 66.4356 Evaluate side-chains 117 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain D residue 35 TYR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 175 optimal weight: 9.9990 chunk 189 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 140 optimal weight: 9.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15914 Z= 0.313 Angle : 0.504 12.371 21435 Z= 0.263 Chirality : 0.042 0.178 2370 Planarity : 0.003 0.028 2727 Dihedral : 7.320 81.122 2199 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.17 % Allowed : 8.49 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.20), residues: 1893 helix: 2.03 (0.16), residues: 988 sheet: 0.36 (0.30), residues: 328 loop : -0.40 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 158 HIS 0.005 0.001 HIS B 424 PHE 0.026 0.001 PHE A 230 TYR 0.017 0.001 TYR A 197 ARG 0.005 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 108 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.8027 (mtm-85) REVERT: A 206 ARG cc_start: 0.8324 (mmm-85) cc_final: 0.7994 (tpt90) REVERT: B 209 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8186 (mm-30) REVERT: B 230 PHE cc_start: 0.8722 (t80) cc_final: 0.8258 (t80) REVERT: D 35 TYR cc_start: 0.9051 (OUTLIER) cc_final: 0.8499 (m-10) REVERT: D 212 PHE cc_start: 0.9701 (t80) cc_final: 0.9371 (t80) REVERT: C 106 MET cc_start: 0.8509 (mtt) cc_final: 0.7958 (tmm) REVERT: C 126 MET cc_start: 0.9332 (mtm) cc_final: 0.8909 (pmm) REVERT: C 342 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.8023 (p90) REVERT: C 406 LEU cc_start: 0.9231 (tt) cc_final: 0.8902 (tt) REVERT: F 436 MET cc_start: 0.7262 (mtp) cc_final: 0.6496 (mmm) outliers start: 37 outliers final: 23 residues processed: 138 average time/residue: 0.3080 time to fit residues: 62.1426 Evaluate side-chains 121 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain D residue 35 TYR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 173 optimal weight: 8.9990 chunk 132 optimal weight: 0.0770 chunk 91 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 117 optimal weight: 30.0000 chunk 176 optimal weight: 10.0000 chunk 186 optimal weight: 20.0000 chunk 92 optimal weight: 0.9980 chunk 167 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 overall best weight: 1.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15914 Z= 0.312 Angle : 0.498 10.596 21435 Z= 0.261 Chirality : 0.042 0.178 2370 Planarity : 0.003 0.027 2727 Dihedral : 7.237 80.471 2198 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.17 % Allowed : 8.38 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.20), residues: 1893 helix: 2.19 (0.17), residues: 989 sheet: 0.27 (0.30), residues: 328 loop : -0.27 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 158 HIS 0.005 0.001 HIS B 424 PHE 0.028 0.001 PHE A 230 TYR 0.017 0.001 TYR A 197 ARG 0.005 0.000 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 98 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8040 (mtm-85) REVERT: A 129 MET cc_start: 0.8916 (mmt) cc_final: 0.8529 (mpp) REVERT: A 206 ARG cc_start: 0.8316 (mmm-85) cc_final: 0.7987 (tpt90) REVERT: B 209 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8270 (mm-30) REVERT: B 230 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.8421 (t80) REVERT: D 35 TYR cc_start: 0.9044 (OUTLIER) cc_final: 0.8503 (m-10) REVERT: D 212 PHE cc_start: 0.9700 (t80) cc_final: 0.9431 (t80) REVERT: C 106 MET cc_start: 0.8498 (mtt) cc_final: 0.7956 (tmm) REVERT: C 126 MET cc_start: 0.9299 (mtm) cc_final: 0.8920 (pmm) REVERT: C 342 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.8022 (p90) REVERT: C 436 MET cc_start: 0.8587 (mtt) cc_final: 0.8249 (mtt) REVERT: F 436 MET cc_start: 0.7164 (mtp) cc_final: 0.6402 (mmm) outliers start: 37 outliers final: 24 residues processed: 128 average time/residue: 0.2946 time to fit residues: 55.8498 Evaluate side-chains 119 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 91 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain D residue 35 TYR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 155 optimal weight: 30.0000 chunk 105 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 138 optimal weight: 9.9990 chunk 76 optimal weight: 0.6980 chunk 159 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 0 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 167 optimal weight: 30.0000 chunk 47 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15914 Z= 0.186 Angle : 0.464 11.197 21435 Z= 0.238 Chirality : 0.041 0.163 2370 Planarity : 0.003 0.025 2727 Dihedral : 6.710 82.592 2198 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.64 % Allowed : 9.49 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.20), residues: 1893 helix: 2.34 (0.17), residues: 989 sheet: 0.30 (0.29), residues: 333 loop : -0.15 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 158 HIS 0.002 0.001 HIS B 424 PHE 0.030 0.001 PHE A 230 TYR 0.018 0.001 TYR B 278 ARG 0.005 0.000 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.8001 (mtm-85) REVERT: A 129 MET cc_start: 0.8918 (mmt) cc_final: 0.8559 (mpp) REVERT: A 206 ARG cc_start: 0.8296 (mmm-85) cc_final: 0.7979 (tpt90) REVERT: A 224 ARG cc_start: 0.7892 (ttm-80) cc_final: 0.7514 (ttm-80) REVERT: B 209 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8240 (mm-30) REVERT: B 230 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8481 (t80) REVERT: D 35 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.8525 (m-10) REVERT: D 212 PHE cc_start: 0.9695 (t80) cc_final: 0.9437 (t80) REVERT: C 106 MET cc_start: 0.8458 (mtt) cc_final: 0.7938 (tmm) REVERT: C 126 MET cc_start: 0.9294 (mtm) cc_final: 0.8866 (tmm) REVERT: C 342 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.8017 (p90) REVERT: C 436 MET cc_start: 0.8595 (mtt) cc_final: 0.8233 (mtt) REVERT: F 436 MET cc_start: 0.7140 (mtp) cc_final: 0.6427 (mmm) outliers start: 28 outliers final: 19 residues processed: 125 average time/residue: 0.2971 time to fit residues: 55.1090 Evaluate side-chains 120 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain D residue 35 TYR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 62 optimal weight: 0.0870 chunk 168 optimal weight: 0.0270 chunk 36 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 186 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 98 optimal weight: 0.0170 overall best weight: 0.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15914 Z= 0.120 Angle : 0.462 13.009 21435 Z= 0.232 Chirality : 0.040 0.282 2370 Planarity : 0.002 0.027 2727 Dihedral : 6.072 83.639 2196 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.46 % Allowed : 10.25 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.20), residues: 1893 helix: 2.49 (0.17), residues: 988 sheet: 0.40 (0.30), residues: 333 loop : -0.05 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 158 HIS 0.002 0.000 HIS B 424 PHE 0.033 0.001 PHE A 230 TYR 0.013 0.001 TYR A 197 ARG 0.006 0.000 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.8917 (mmt) cc_final: 0.8640 (mpp) REVERT: A 206 ARG cc_start: 0.8284 (mmm-85) cc_final: 0.7977 (tpt90) REVERT: A 224 ARG cc_start: 0.7889 (ttm-80) cc_final: 0.7490 (ttm-80) REVERT: A 232 LYS cc_start: 0.8948 (tptp) cc_final: 0.8739 (tptp) REVERT: B 209 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8081 (mm-30) REVERT: B 234 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7224 (t80) REVERT: D 196 LEU cc_start: 0.8793 (pt) cc_final: 0.8533 (pp) REVERT: D 212 PHE cc_start: 0.9671 (t80) cc_final: 0.9454 (t80) REVERT: C 106 MET cc_start: 0.8435 (mtt) cc_final: 0.7950 (tmm) REVERT: C 126 MET cc_start: 0.9317 (mtm) cc_final: 0.8879 (tmm) REVERT: C 342 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7986 (p90) REVERT: F 436 MET cc_start: 0.7123 (mtp) cc_final: 0.6398 (mmm) outliers start: 25 outliers final: 15 residues processed: 121 average time/residue: 0.2792 time to fit residues: 50.8727 Evaluate side-chains 112 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 342 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 180 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 106 optimal weight: 0.0020 chunk 136 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 chunk 186 optimal weight: 0.3980 chunk 116 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 overall best weight: 3.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 15914 Z= 0.476 Angle : 0.590 12.628 21435 Z= 0.302 Chirality : 0.045 0.265 2370 Planarity : 0.003 0.039 2727 Dihedral : 7.424 88.577 2194 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.93 % Allowed : 10.19 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.20), residues: 1893 helix: 2.23 (0.17), residues: 988 sheet: 0.14 (0.29), residues: 337 loop : -0.09 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 287 HIS 0.006 0.001 HIS B 424 PHE 0.032 0.002 PHE A 230 TYR 0.017 0.002 TYR A 197 ARG 0.005 0.001 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 99 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.8901 (mmt) cc_final: 0.8520 (mpp) REVERT: A 206 ARG cc_start: 0.8391 (mmm-85) cc_final: 0.8008 (tpt90) REVERT: D 35 TYR cc_start: 0.9125 (OUTLIER) cc_final: 0.8438 (m-10) REVERT: D 212 PHE cc_start: 0.9688 (t80) cc_final: 0.9480 (t80) REVERT: C 106 MET cc_start: 0.8458 (mtt) cc_final: 0.7923 (tmm) REVERT: C 126 MET cc_start: 0.9265 (mtm) cc_final: 0.8902 (pmm) REVERT: C 188 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.8354 (t80) REVERT: C 342 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7951 (p90) REVERT: F 326 MET cc_start: 0.7581 (mmm) cc_final: 0.7304 (mmm) REVERT: F 436 MET cc_start: 0.7145 (mtp) cc_final: 0.6437 (mmm) outliers start: 33 outliers final: 26 residues processed: 127 average time/residue: 0.2812 time to fit residues: 53.6714 Evaluate side-chains 124 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 95 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 35 TYR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 115 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 111 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 118 optimal weight: 30.0000 chunk 126 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 146 optimal weight: 9.9990 chunk 169 optimal weight: 20.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15914 Z= 0.238 Angle : 0.505 13.869 21435 Z= 0.256 Chirality : 0.042 0.423 2370 Planarity : 0.003 0.030 2727 Dihedral : 7.137 88.746 2194 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.87 % Allowed : 10.54 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.20), residues: 1893 helix: 2.38 (0.17), residues: 988 sheet: 0.18 (0.29), residues: 333 loop : -0.04 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 158 HIS 0.004 0.001 HIS B 424 PHE 0.050 0.001 PHE B 230 TYR 0.015 0.001 TYR A 197 ARG 0.005 0.000 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 97 time to evaluate : 1.981 Fit side-chains revert: symmetry clash REVERT: A 129 MET cc_start: 0.8915 (mmt) cc_final: 0.8517 (mpp) REVERT: A 206 ARG cc_start: 0.8314 (mmm-85) cc_final: 0.7919 (tpt90) REVERT: B 234 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.7196 (t80) REVERT: D 35 TYR cc_start: 0.9025 (OUTLIER) cc_final: 0.8427 (m-10) REVERT: C 106 MET cc_start: 0.8460 (mtt) cc_final: 0.7935 (tmm) REVERT: C 126 MET cc_start: 0.9268 (mtm) cc_final: 0.8856 (tmm) REVERT: C 342 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7980 (p90) REVERT: F 436 MET cc_start: 0.7173 (mtp) cc_final: 0.6449 (mmm) outliers start: 32 outliers final: 21 residues processed: 124 average time/residue: 0.3053 time to fit residues: 56.4872 Evaluate side-chains 115 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 91 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 35 TYR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 342 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 178 optimal weight: 0.7980 chunk 162 optimal weight: 30.0000 chunk 173 optimal weight: 0.3980 chunk 104 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15914 Z= 0.239 Angle : 0.512 16.289 21435 Z= 0.257 Chirality : 0.042 0.406 2370 Planarity : 0.003 0.035 2727 Dihedral : 6.945 84.712 2194 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.52 % Allowed : 10.90 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.20), residues: 1893 helix: 2.40 (0.17), residues: 990 sheet: 0.12 (0.29), residues: 338 loop : -0.05 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 158 HIS 0.004 0.001 HIS B 424 PHE 0.050 0.001 PHE B 230 TYR 0.015 0.001 TYR A 197 ARG 0.011 0.000 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 93 time to evaluate : 1.834 Fit side-chains revert: symmetry clash REVERT: A 129 MET cc_start: 0.8910 (mmt) cc_final: 0.8515 (mpp) REVERT: A 206 ARG cc_start: 0.8316 (mmm-85) cc_final: 0.7918 (tpt90) REVERT: A 224 ARG cc_start: 0.7845 (ttm-80) cc_final: 0.7442 (tpp80) REVERT: A 309 ARG cc_start: 0.8346 (ttp80) cc_final: 0.7416 (tmm-80) REVERT: A 386 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7778 (p0) REVERT: B 234 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.7209 (t80) REVERT: D 35 TYR cc_start: 0.8985 (OUTLIER) cc_final: 0.8489 (m-10) REVERT: C 106 MET cc_start: 0.8464 (mtt) cc_final: 0.7938 (tmm) REVERT: C 126 MET cc_start: 0.9281 (mtm) cc_final: 0.8856 (tmm) REVERT: C 326 MET cc_start: 0.8098 (mmm) cc_final: 0.7843 (mmm) REVERT: C 342 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7994 (p90) REVERT: F 436 MET cc_start: 0.7170 (mtp) cc_final: 0.6445 (mmm) outliers start: 26 outliers final: 22 residues processed: 115 average time/residue: 0.2738 time to fit residues: 48.3160 Evaluate side-chains 117 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 35 TYR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 342 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 30.0000 chunk 86 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 192 optimal weight: 20.0000 chunk 176 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.106 15914 Z= 0.748 Angle : 0.741 14.259 21435 Z= 0.379 Chirality : 0.051 0.404 2370 Planarity : 0.005 0.059 2727 Dihedral : 7.373 85.451 2194 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.82 % Allowed : 10.78 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.20), residues: 1893 helix: 1.74 (0.16), residues: 996 sheet: -0.08 (0.29), residues: 337 loop : -0.43 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 402 HIS 0.008 0.002 HIS B 424 PHE 0.067 0.002 PHE B 230 TYR 0.022 0.002 TYR A 197 ARG 0.012 0.001 ARG A 309 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 90 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.8883 (mmt) cc_final: 0.8442 (mpp) REVERT: A 206 ARG cc_start: 0.8474 (mmm-85) cc_final: 0.8061 (tpt90) REVERT: A 222 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7875 (mm-30) REVERT: D 35 TYR cc_start: 0.9211 (OUTLIER) cc_final: 0.8736 (m-10) REVERT: C 106 MET cc_start: 0.8382 (mtt) cc_final: 0.7885 (tmm) REVERT: C 126 MET cc_start: 0.9292 (mtm) cc_final: 0.8900 (pmm) REVERT: C 342 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7498 (p90) REVERT: F 436 MET cc_start: 0.7237 (mtp) cc_final: 0.6601 (mmm) outliers start: 31 outliers final: 26 residues processed: 116 average time/residue: 0.3123 time to fit residues: 54.5969 Evaluate side-chains 116 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 88 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 35 TYR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 342 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 163 optimal weight: 20.0000 chunk 46 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 153 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.139856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.077915 restraints weight = 37436.114| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.75 r_work: 0.3064 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15914 Z= 0.227 Angle : 0.531 15.382 21435 Z= 0.269 Chirality : 0.042 0.393 2370 Planarity : 0.003 0.042 2727 Dihedral : 6.147 79.518 2194 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.41 % Allowed : 11.01 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.20), residues: 1893 helix: 2.19 (0.17), residues: 989 sheet: -0.06 (0.29), residues: 335 loop : -0.16 (0.28), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 158 HIS 0.003 0.001 HIS B 424 PHE 0.031 0.001 PHE A 226 TYR 0.017 0.001 TYR A 197 ARG 0.010 0.000 ARG A 309 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3518.40 seconds wall clock time: 63 minutes 27.03 seconds (3807.03 seconds total)