Starting phenix.real_space_refine on Sat Aug 23 02:54:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fjf_50502/08_2025/9fjf_50502.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fjf_50502/08_2025/9fjf_50502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fjf_50502/08_2025/9fjf_50502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fjf_50502/08_2025/9fjf_50502.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fjf_50502/08_2025/9fjf_50502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fjf_50502/08_2025/9fjf_50502.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.008 sd= 1.041 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 42 5.16 5 C 5922 2.51 5 N 1519 2.21 5 O 1824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9307 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3166 Classifications: {'peptide': 391} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 370} Chain: "B" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3854 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 33, 'TRANS': 453} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1014 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "D" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 888 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain breaks: 1 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 68 Unusual residues: {'MES': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 78 Unusual residues: {'MES': 3, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 2.54, per 1000 atoms: 0.27 Number of scatterers: 9307 At special positions: 0 Unit cell: (89.725, 114.7, 135.975, 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 42 16.00 O 1824 8.00 N 1519 7.00 C 5922 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 329 " distance=2.04 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 318 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 103 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 501 " - " ASN A 45 " " NAG A 502 " - " ASN A 224 " " NAG A 503 " - " ASN A 304 " " NAG A 504 " - " ASN A 105 " " NAG B 501 " - " ASN B 59 " " NAG B 502 " - " ASN B 146 " " NAG B 503 " - " ASN B 270 " " NAG E 1 " - " ASN A 68 " " NAG F 1 " - " ASN A 206 " " NAG G 1 " - " ASN A 249 " " NAG H 1 " - " ASN A 325 " " NAG I 1 " - " ASN A 412 " " NAG J 1 " - " ASN B 19 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 384.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2082 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 20.3% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.619A pdb=" N LYS A 55 " --> pdb=" O ASP A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 removed outlier: 4.058A pdb=" N LEU A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 77' Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 137 through 149 removed outlier: 3.824A pdb=" N LEU A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN A 148 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 163 removed outlier: 3.943A pdb=" N LYS A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 183 through 190 removed outlier: 3.904A pdb=" N VAL A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 346 through 353 removed outlier: 4.077A pdb=" N VAL A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE A 353 " --> pdb=" O PHE A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 429 removed outlier: 3.867A pdb=" N SER A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N MET A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 94 removed outlier: 3.562A pdb=" N ALA B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 109 removed outlier: 3.655A pdb=" N TYR B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 removed outlier: 3.507A pdb=" N THR B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS B 157 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 165 removed outlier: 3.758A pdb=" N LEU B 165 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 203 through 210 Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.637A pdb=" N LYS B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.846A pdb=" N ASP B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 271 removed outlier: 3.561A pdb=" N ALA B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 296 removed outlier: 3.630A pdb=" N ALA B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS B 293 " --> pdb=" O PRO B 289 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 294 " --> pdb=" O HIS B 290 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL B 295 " --> pdb=" O TRP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 331 removed outlier: 4.346A pdb=" N HIS B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ARG B 329 " --> pdb=" O GLY B 325 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU B 330 " --> pdb=" O GLU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 371 removed outlier: 3.786A pdb=" N MET B 361 " --> pdb=" O TRP B 357 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN B 362 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER B 364 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 414 through 427 removed outlier: 4.325A pdb=" N TYR B 418 " --> pdb=" O GLN B 414 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE B 423 " --> pdb=" O HIS B 419 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE B 426 " --> pdb=" O HIS B 422 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.505A pdb=" N TYR C 31 " --> pdb=" O THR C 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 86 removed outlier: 3.805A pdb=" N PHE A 66 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 61 " --> pdb=" O SER A 414 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER A 414 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 67 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N VAL A 408 " --> pdb=" O PHE A 67 " (cutoff:3.500A) removed outlier: 11.924A pdb=" N VAL A 69 " --> pdb=" O PHE A 406 " (cutoff:3.500A) removed outlier: 14.579A pdb=" N PHE A 406 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET A 404 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE A 385 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N TYR A 410 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N PHE A 383 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASN A 412 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS A 381 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER A 414 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA A 379 " --> pdb=" O SER A 414 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LYS A 378 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 380 " --> pdb=" O PHE A 366 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE A 366 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LYS A 296 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N PHE A 281 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 213 through 215 removed outlier: 3.800A pdb=" N TYR A 213 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 111 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N THR A 108 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N PHE A 102 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N SER A 110 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE A 100 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL A 60 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 61 " --> pdb=" O SER A 414 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER A 414 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 67 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N VAL A 408 " --> pdb=" O PHE A 67 " (cutoff:3.500A) removed outlier: 11.924A pdb=" N VAL A 69 " --> pdb=" O PHE A 406 " (cutoff:3.500A) removed outlier: 14.579A pdb=" N PHE A 406 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET A 404 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE A 385 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N TYR A 410 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N PHE A 383 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASN A 412 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS A 381 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER A 414 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA A 379 " --> pdb=" O SER A 414 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 135 Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA5, first strand: chain 'B' and resid 17 through 19 removed outlier: 3.529A pdb=" N CYS B 18 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU B 385 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.629A pdb=" N TRP B 494 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 449 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 459 " --> pdb=" O VAL B 447 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 447 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN B 432 " --> pdb=" O MET B 450 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 436 through 437 removed outlier: 3.832A pdb=" N LYS B 473 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU B 69 " --> pdb=" O LYS B 473 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 173 through 177 removed outlier: 3.911A pdb=" N SER B 177 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 118 " --> pdb=" O PHE B 81 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 308 through 311 Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.912A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 46 through 47 removed outlier: 3.828A pdb=" N ALA C 92 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL C 126 " --> pdb=" O ALA C 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 49 through 50 removed outlier: 3.602A pdb=" N CYS C 50 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR C 59 " --> pdb=" O CYS C 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 20 through 23 removed outlier: 3.926A pdb=" N THR D 68 " --> pdb=" O GLN D 81 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 57 through 59 removed outlier: 3.578A pdb=" N ASN D 58 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR D 50 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) 229 hydrogen bonds defined for protein. 600 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: 1.55 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1930 1.33 - 1.45: 2447 1.45 - 1.58: 5085 1.58 - 1.70: 0 1.70 - 1.83: 63 Bond restraints: 9525 Sorted by residual: bond pdb=" C HIS A 357 " pdb=" N PRO A 358 " ideal model delta sigma weight residual 1.328 1.406 -0.077 1.26e-02 6.30e+03 3.76e+01 bond pdb=" N VAL A 229 " pdb=" CA VAL A 229 " ideal model delta sigma weight residual 1.458 1.493 -0.036 9.00e-03 1.23e+04 1.56e+01 bond pdb=" N SER B 400 " pdb=" CA SER B 400 " ideal model delta sigma weight residual 1.453 1.489 -0.036 9.20e-03 1.18e+04 1.51e+01 bond pdb=" N VAL C 128 " pdb=" CA VAL C 128 " ideal model delta sigma weight residual 1.457 1.492 -0.035 9.00e-03 1.23e+04 1.50e+01 bond pdb=" CA PRO A 56 " pdb=" C PRO A 56 " ideal model delta sigma weight residual 1.514 1.536 -0.021 5.50e-03 3.31e+04 1.49e+01 ... (remaining 9520 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 11127 1.49 - 2.98: 1493 2.98 - 4.47: 303 4.47 - 5.96: 31 5.96 - 7.45: 3 Bond angle restraints: 12957 Sorted by residual: angle pdb=" N ARG C 100 " pdb=" CA ARG C 100 " pdb=" C ARG C 100 " ideal model delta sigma weight residual 112.88 107.75 5.13 1.29e+00 6.01e-01 1.58e+01 angle pdb=" CA VAL A 112 " pdb=" C VAL A 112 " pdb=" O VAL A 112 " ideal model delta sigma weight residual 121.63 117.78 3.85 9.90e-01 1.02e+00 1.52e+01 angle pdb=" N PRO B 150 " pdb=" CA PRO B 150 " pdb=" C PRO B 150 " ideal model delta sigma weight residual 111.13 116.89 -5.76 1.49e+00 4.50e-01 1.49e+01 angle pdb=" N HIS B 274 " pdb=" CA HIS B 274 " pdb=" C HIS B 274 " ideal model delta sigma weight residual 114.39 108.80 5.59 1.45e+00 4.76e-01 1.48e+01 angle pdb=" CA GLU A 354 " pdb=" C GLU A 354 " pdb=" O GLU A 354 " ideal model delta sigma weight residual 121.94 117.53 4.41 1.15e+00 7.56e-01 1.47e+01 ... (remaining 12952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.68: 5416 21.68 - 43.35: 385 43.35 - 65.03: 88 65.03 - 86.70: 17 86.70 - 108.38: 9 Dihedral angle restraints: 5915 sinusoidal: 2658 harmonic: 3257 Sorted by residual: dihedral pdb=" CB CYS A 274 " pdb=" SG CYS A 274 " pdb=" SG CYS A 329 " pdb=" CB CYS A 329 " ideal model delta sinusoidal sigma weight residual -86.00 -162.61 76.61 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 95 " pdb=" CB CYS D 95 " ideal model delta sinusoidal sigma weight residual -86.00 -120.33 34.33 1 1.00e+01 1.00e-02 1.67e+01 dihedral pdb=" O4 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C5 BMA I 3 " pdb=" O5 BMA I 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.67 108.38 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 5912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1271 0.108 - 0.217: 182 0.217 - 0.325: 11 0.325 - 0.433: 1 0.433 - 0.541: 3 Chirality restraints: 1468 Sorted by residual: chirality pdb=" C1 MAN I 5 " pdb=" O6 BMA I 3 " pdb=" C2 MAN I 5 " pdb=" O5 MAN I 5 " both_signs ideal model delta sigma weight residual False 2.40 1.94 0.46 2.00e-02 2.50e+03 5.25e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.08e+02 chirality pdb=" C1 MAN I 4 " pdb=" O3 BMA I 3 " pdb=" C2 MAN I 4 " pdb=" O5 MAN I 4 " both_signs ideal model delta sigma weight residual False 2.40 2.17 0.23 2.00e-02 2.50e+03 1.28e+02 ... (remaining 1465 not shown) Planarity restraints: 1638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " -0.284 2.00e-02 2.50e+03 2.43e-01 7.41e+02 pdb=" C7 NAG J 2 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " 0.427 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " -0.280 2.00e-02 2.50e+03 2.37e-01 7.02e+02 pdb=" C7 NAG I 2 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " -0.176 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " 0.407 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.271 2.00e-02 2.50e+03 2.33e-01 6.79e+02 pdb=" C7 NAG I 1 " 0.059 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " 0.012 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.395 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " -0.196 2.00e-02 2.50e+03 ... (remaining 1635 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1673 2.78 - 3.31: 7955 3.31 - 3.84: 12841 3.84 - 4.37: 14329 4.37 - 4.90: 26055 Nonbonded interactions: 62853 Sorted by model distance: nonbonded pdb=" O MET B 123 " pdb=" OH TYR B 135 " model vdw 2.248 3.040 nonbonded pdb=" NH2 ARG B 47 " pdb=" OG SER D 56 " model vdw 2.254 3.120 nonbonded pdb=" O3 NAG A 501 " pdb=" O7 NAG A 501 " model vdw 2.303 3.040 nonbonded pdb=" OE1 GLU B 41 " pdb=" O HOH B 601 " model vdw 2.303 3.040 nonbonded pdb=" NE2 GLN D 1 " pdb=" O GLN D 3 " model vdw 2.315 3.120 ... (remaining 62848 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 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.690 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.009 0.077 9553 Z= 0.617 Angle : 1.080 10.851 13036 Z= 0.730 Chirality : 0.074 0.541 1468 Planarity : 0.015 0.243 1625 Dihedral : 15.892 108.379 3818 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.10 % Allowed : 14.36 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.24), residues: 1112 helix: -1.01 (0.40), residues: 146 sheet: -0.33 (0.32), residues: 271 loop : -1.92 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 382 TYR 0.025 0.001 TYR C 105 PHE 0.013 0.001 PHE A 269 TRP 0.016 0.001 TRP C 116 HIS 0.005 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00856 ( 9525) covalent geometry : angle 1.05352 (12957) SS BOND : bond 0.00387 ( 5) SS BOND : angle 0.99859 ( 10) hydrogen bonds : bond 0.24728 ( 221) hydrogen bonds : angle 7.15292 ( 600) link_ALPHA1-3 : bond 0.01169 ( 1) link_ALPHA1-3 : angle 2.23106 ( 3) link_ALPHA1-6 : bond 0.00085 ( 1) link_ALPHA1-6 : angle 3.89702 ( 3) link_BETA1-4 : bond 0.00901 ( 8) link_BETA1-4 : angle 2.19252 ( 24) link_NAG-ASN : bond 0.00825 ( 13) link_NAG-ASN : angle 4.05045 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.7940 (mt) cc_final: 0.7528 (mt) REVERT: A 100 ILE cc_start: 0.8155 (mm) cc_final: 0.7928 (mm) REVERT: B 408 LYS cc_start: 0.8253 (mtmm) cc_final: 0.7933 (mtpp) REVERT: C 83 MET cc_start: 0.6419 (mmm) cc_final: 0.6062 (mmm) REVERT: C 95 TYR cc_start: 0.7630 (m-80) cc_final: 0.7094 (m-10) outliers start: 1 outliers final: 1 residues processed: 117 average time/residue: 0.0993 time to fit residues: 16.2927 Evaluate side-chains 97 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.0370 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN A 357 HIS B 226 GLN B 442 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.178917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.151033 restraints weight = 11423.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.146303 restraints weight = 23100.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.144625 restraints weight = 22875.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.142143 restraints weight = 16078.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.143002 restraints weight = 16142.711| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9553 Z= 0.152 Angle : 0.696 19.210 13036 Z= 0.339 Chirality : 0.046 0.260 1468 Planarity : 0.005 0.080 1625 Dihedral : 9.733 72.777 1751 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.38 % Allowed : 14.77 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.24), residues: 1112 helix: -0.41 (0.39), residues: 157 sheet: -0.24 (0.31), residues: 278 loop : -1.97 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 262 TYR 0.016 0.001 TYR A 410 PHE 0.011 0.001 PHE A 66 TRP 0.011 0.001 TRP B 494 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9525) covalent geometry : angle 0.63666 (12957) SS BOND : bond 0.00363 ( 5) SS BOND : angle 0.71437 ( 10) hydrogen bonds : bond 0.06081 ( 221) hydrogen bonds : angle 5.36852 ( 600) link_ALPHA1-3 : bond 0.01472 ( 1) link_ALPHA1-3 : angle 1.80990 ( 3) link_ALPHA1-6 : bond 0.01218 ( 1) link_ALPHA1-6 : angle 1.42341 ( 3) link_BETA1-4 : bond 0.00801 ( 8) link_BETA1-4 : angle 2.14908 ( 24) link_NAG-ASN : bond 0.00872 ( 13) link_NAG-ASN : angle 4.90124 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 54 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6905 (tt0) REVERT: A 76 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7276 (mm) REVERT: A 100 ILE cc_start: 0.8279 (mm) cc_final: 0.8034 (mm) REVERT: A 267 TYR cc_start: 0.8470 (m-80) cc_final: 0.8218 (m-80) REVERT: B 104 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9080 (tt) REVERT: C 102 GLN cc_start: 0.8820 (mp10) cc_final: 0.8429 (mm-40) outliers start: 23 outliers final: 10 residues processed: 117 average time/residue: 0.0812 time to fit residues: 14.1892 Evaluate side-chains 105 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 442 ASN Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 69 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 85 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 7 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 442 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.177193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.134462 restraints weight = 11332.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.130668 restraints weight = 12191.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.130864 restraints weight = 10392.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.130864 restraints weight = 9385.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.130864 restraints weight = 9366.267| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9553 Z= 0.148 Angle : 0.631 12.633 13036 Z= 0.315 Chirality : 0.044 0.239 1468 Planarity : 0.005 0.072 1625 Dihedral : 8.692 63.653 1751 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.58 % Allowed : 15.29 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.23), residues: 1112 helix: -0.39 (0.39), residues: 153 sheet: -0.18 (0.31), residues: 272 loop : -2.04 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 382 TYR 0.015 0.001 TYR A 410 PHE 0.012 0.001 PHE B 411 TRP 0.012 0.001 TRP B 179 HIS 0.003 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9525) covalent geometry : angle 0.59306 (12957) SS BOND : bond 0.00345 ( 5) SS BOND : angle 0.65482 ( 10) hydrogen bonds : bond 0.05802 ( 221) hydrogen bonds : angle 5.04100 ( 600) link_ALPHA1-3 : bond 0.01346 ( 1) link_ALPHA1-3 : angle 1.40994 ( 3) link_ALPHA1-6 : bond 0.00973 ( 1) link_ALPHA1-6 : angle 1.30862 ( 3) link_BETA1-4 : bond 0.00582 ( 8) link_BETA1-4 : angle 1.88609 ( 24) link_NAG-ASN : bond 0.00806 ( 13) link_NAG-ASN : angle 3.70325 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 GLU cc_start: 0.7033 (tm-30) cc_final: 0.6675 (tt0) REVERT: A 76 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7170 (mm) REVERT: A 100 ILE cc_start: 0.8205 (mm) cc_final: 0.7960 (mm) REVERT: A 267 TYR cc_start: 0.8724 (m-80) cc_final: 0.8488 (m-80) REVERT: B 104 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9073 (tt) REVERT: B 166 GLN cc_start: 0.8232 (tp40) cc_final: 0.7648 (tt0) REVERT: B 310 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8409 (m) REVERT: B 443 ASP cc_start: 0.8255 (t0) cc_final: 0.7903 (t0) REVERT: C 102 GLN cc_start: 0.8803 (mp10) cc_final: 0.8520 (mm-40) outliers start: 25 outliers final: 13 residues processed: 116 average time/residue: 0.0866 time to fit residues: 14.7791 Evaluate side-chains 109 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 69 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 97 optimal weight: 0.0050 chunk 101 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 60 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.174774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.150725 restraints weight = 11355.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.146636 restraints weight = 23770.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.144238 restraints weight = 26413.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.140548 restraints weight = 23491.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.140271 restraints weight = 22121.406| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9553 Z= 0.159 Angle : 0.630 9.248 13036 Z= 0.319 Chirality : 0.045 0.217 1468 Planarity : 0.005 0.064 1625 Dihedral : 7.520 52.500 1748 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.20 % Allowed : 14.36 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (0.23), residues: 1112 helix: -0.38 (0.40), residues: 153 sheet: -0.32 (0.30), residues: 271 loop : -2.12 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 382 TYR 0.017 0.001 TYR A 410 PHE 0.012 0.001 PHE B 411 TRP 0.011 0.001 TRP B 494 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9525) covalent geometry : angle 0.59968 (12957) SS BOND : bond 0.00368 ( 5) SS BOND : angle 0.70841 ( 10) hydrogen bonds : bond 0.05769 ( 221) hydrogen bonds : angle 4.90978 ( 600) link_ALPHA1-3 : bond 0.01333 ( 1) link_ALPHA1-3 : angle 1.40682 ( 3) link_ALPHA1-6 : bond 0.00830 ( 1) link_ALPHA1-6 : angle 1.37519 ( 3) link_BETA1-4 : bond 0.00568 ( 8) link_BETA1-4 : angle 1.94480 ( 24) link_NAG-ASN : bond 0.00716 ( 13) link_NAG-ASN : angle 3.24512 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 54 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6698 (tt0) REVERT: A 76 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7277 (mm) REVERT: A 100 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8049 (mm) REVERT: B 166 GLN cc_start: 0.8313 (tp40) cc_final: 0.7715 (tt0) REVERT: B 443 ASP cc_start: 0.8212 (t0) cc_final: 0.7777 (t0) REVERT: C 102 GLN cc_start: 0.8850 (mp10) cc_final: 0.8581 (mm-40) REVERT: C 114 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7054 (tp) outliers start: 31 outliers final: 19 residues processed: 120 average time/residue: 0.0820 time to fit residues: 14.5870 Evaluate side-chains 115 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 69 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 78 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 71 optimal weight: 0.0570 chunk 95 optimal weight: 6.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.177142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.153322 restraints weight = 11362.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.149916 restraints weight = 21911.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.131362 restraints weight = 25431.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.129856 restraints weight = 19290.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.130183 restraints weight = 14734.975| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9553 Z= 0.119 Angle : 0.572 8.262 13036 Z= 0.285 Chirality : 0.043 0.213 1468 Planarity : 0.004 0.060 1625 Dihedral : 7.082 53.630 1748 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.58 % Allowed : 16.32 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.23), residues: 1112 helix: -0.24 (0.40), residues: 154 sheet: -0.35 (0.30), residues: 276 loop : -2.10 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.017 0.001 TYR A 410 PHE 0.012 0.001 PHE B 411 TRP 0.017 0.001 TRP B 179 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9525) covalent geometry : angle 0.54328 (12957) SS BOND : bond 0.00289 ( 5) SS BOND : angle 0.62092 ( 10) hydrogen bonds : bond 0.04512 ( 221) hydrogen bonds : angle 4.67365 ( 600) link_ALPHA1-3 : bond 0.01363 ( 1) link_ALPHA1-3 : angle 1.17149 ( 3) link_ALPHA1-6 : bond 0.00689 ( 1) link_ALPHA1-6 : angle 1.41327 ( 3) link_BETA1-4 : bond 0.00540 ( 8) link_BETA1-4 : angle 1.61682 ( 24) link_NAG-ASN : bond 0.00593 ( 13) link_NAG-ASN : angle 3.07740 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 GLU cc_start: 0.7063 (tm-30) cc_final: 0.6711 (tt0) REVERT: A 76 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7024 (mm) REVERT: A 100 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7889 (mm) REVERT: A 115 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7592 (mtpt) REVERT: B 123 MET cc_start: 0.6465 (mtp) cc_final: 0.6085 (mtp) REVERT: B 443 ASP cc_start: 0.8338 (t0) cc_final: 0.7827 (t0) REVERT: C 102 GLN cc_start: 0.8863 (mp10) cc_final: 0.8614 (mm-40) outliers start: 25 outliers final: 15 residues processed: 111 average time/residue: 0.0843 time to fit residues: 13.9323 Evaluate side-chains 106 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 69 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 0.0970 chunk 95 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 42 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.178136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.156700 restraints weight = 11423.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.133937 restraints weight = 23810.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.131384 restraints weight = 21488.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.129831 restraints weight = 17898.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.130819 restraints weight = 14139.319| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9553 Z= 0.108 Angle : 0.537 7.363 13036 Z= 0.269 Chirality : 0.042 0.206 1468 Planarity : 0.004 0.056 1625 Dihedral : 6.743 56.622 1748 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.10 % Allowed : 16.01 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.24), residues: 1112 helix: -0.05 (0.40), residues: 154 sheet: -0.38 (0.30), residues: 286 loop : -2.07 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.015 0.001 TYR A 410 PHE 0.009 0.001 PHE B 411 TRP 0.009 0.001 TRP B 494 HIS 0.003 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 9525) covalent geometry : angle 0.51404 (12957) SS BOND : bond 0.00254 ( 5) SS BOND : angle 0.57555 ( 10) hydrogen bonds : bond 0.04037 ( 221) hydrogen bonds : angle 4.50333 ( 600) link_ALPHA1-3 : bond 0.01350 ( 1) link_ALPHA1-3 : angle 1.08053 ( 3) link_ALPHA1-6 : bond 0.00592 ( 1) link_ALPHA1-6 : angle 1.50227 ( 3) link_BETA1-4 : bond 0.00521 ( 8) link_BETA1-4 : angle 1.41302 ( 24) link_NAG-ASN : bond 0.00533 ( 13) link_NAG-ASN : angle 2.65747 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 GLU cc_start: 0.7072 (tm-30) cc_final: 0.6744 (tt0) REVERT: A 76 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7026 (mm) REVERT: A 100 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7895 (mm) REVERT: A 115 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7701 (mtpt) REVERT: A 214 VAL cc_start: 0.8227 (t) cc_final: 0.7855 (p) REVERT: B 333 ASN cc_start: 0.7255 (m110) cc_final: 0.6779 (m-40) REVERT: B 443 ASP cc_start: 0.8227 (t0) cc_final: 0.7791 (t0) outliers start: 30 outliers final: 17 residues processed: 110 average time/residue: 0.0812 time to fit residues: 13.4129 Evaluate side-chains 104 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 51 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 84 optimal weight: 0.8980 chunk 12 optimal weight: 0.2980 chunk 65 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.176328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.146009 restraints weight = 11174.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.143215 restraints weight = 21919.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.142264 restraints weight = 22397.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.140934 restraints weight = 13229.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.141772 restraints weight = 11909.046| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9553 Z= 0.128 Angle : 0.566 7.213 13036 Z= 0.285 Chirality : 0.043 0.197 1468 Planarity : 0.004 0.057 1625 Dihedral : 6.721 58.015 1748 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.58 % Allowed : 16.63 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.23), residues: 1112 helix: -0.09 (0.40), residues: 154 sheet: -0.30 (0.30), residues: 282 loop : -2.12 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.016 0.001 TYR A 410 PHE 0.014 0.001 PHE B 411 TRP 0.015 0.001 TRP B 179 HIS 0.003 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9525) covalent geometry : angle 0.54144 (12957) SS BOND : bond 0.00317 ( 5) SS BOND : angle 0.59763 ( 10) hydrogen bonds : bond 0.04772 ( 221) hydrogen bonds : angle 4.50735 ( 600) link_ALPHA1-3 : bond 0.01324 ( 1) link_ALPHA1-3 : angle 1.08392 ( 3) link_ALPHA1-6 : bond 0.00543 ( 1) link_ALPHA1-6 : angle 1.45512 ( 3) link_BETA1-4 : bond 0.00504 ( 8) link_BETA1-4 : angle 1.53457 ( 24) link_NAG-ASN : bond 0.00583 ( 13) link_NAG-ASN : angle 2.79413 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7244 (mm) REVERT: A 100 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8049 (mm) REVERT: B 333 ASN cc_start: 0.7292 (m110) cc_final: 0.6829 (m-40) REVERT: B 443 ASP cc_start: 0.8126 (t0) cc_final: 0.7680 (t0) outliers start: 25 outliers final: 20 residues processed: 105 average time/residue: 0.0857 time to fit residues: 13.3607 Evaluate side-chains 109 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 51 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 94 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.176282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.152624 restraints weight = 11299.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.149418 restraints weight = 24271.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.133400 restraints weight = 26943.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.129189 restraints weight = 18799.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.128837 restraints weight = 14518.157| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9553 Z= 0.125 Angle : 0.557 6.746 13036 Z= 0.281 Chirality : 0.043 0.193 1468 Planarity : 0.004 0.054 1625 Dihedral : 6.649 58.862 1748 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.79 % Allowed : 16.63 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.23), residues: 1112 helix: -0.09 (0.40), residues: 153 sheet: -0.42 (0.30), residues: 287 loop : -2.15 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.016 0.001 TYR A 410 PHE 0.023 0.001 PHE A 256 TRP 0.011 0.001 TRP B 378 HIS 0.003 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9525) covalent geometry : angle 0.53349 (12957) SS BOND : bond 0.00305 ( 5) SS BOND : angle 0.67938 ( 10) hydrogen bonds : bond 0.04690 ( 221) hydrogen bonds : angle 4.48203 ( 600) link_ALPHA1-3 : bond 0.01334 ( 1) link_ALPHA1-3 : angle 0.96564 ( 3) link_ALPHA1-6 : bond 0.00568 ( 1) link_ALPHA1-6 : angle 1.40443 ( 3) link_BETA1-4 : bond 0.00516 ( 8) link_BETA1-4 : angle 1.54160 ( 24) link_NAG-ASN : bond 0.00560 ( 13) link_NAG-ASN : angle 2.69992 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7039 (mm) REVERT: A 100 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7903 (mm) REVERT: A 406 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.7417 (m-80) REVERT: B 333 ASN cc_start: 0.7327 (m110) cc_final: 0.6922 (m-40) REVERT: B 443 ASP cc_start: 0.8309 (t0) cc_final: 0.7880 (t0) outliers start: 27 outliers final: 22 residues processed: 106 average time/residue: 0.0875 time to fit residues: 13.8922 Evaluate side-chains 109 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 82 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 24 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 8 optimal weight: 0.0770 chunk 86 optimal weight: 0.0570 chunk 81 optimal weight: 0.7980 chunk 1 optimal weight: 0.0970 chunk 60 optimal weight: 1.9990 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.179191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.151057 restraints weight = 11277.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.148380 restraints weight = 21441.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.135369 restraints weight = 23421.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.131657 restraints weight = 18382.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.131903 restraints weight = 13831.145| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9553 Z= 0.097 Angle : 0.510 6.276 13036 Z= 0.256 Chirality : 0.042 0.192 1468 Planarity : 0.004 0.054 1625 Dihedral : 6.364 59.291 1748 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.96 % Allowed : 17.25 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.24), residues: 1112 helix: 0.08 (0.41), residues: 155 sheet: -0.28 (0.30), residues: 288 loop : -2.09 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 100 TYR 0.014 0.001 TYR A 410 PHE 0.008 0.001 PHE B 411 TRP 0.018 0.001 TRP B 179 HIS 0.003 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 9525) covalent geometry : angle 0.49125 (12957) SS BOND : bond 0.00234 ( 5) SS BOND : angle 0.54740 ( 10) hydrogen bonds : bond 0.03555 ( 221) hydrogen bonds : angle 4.36839 ( 600) link_ALPHA1-3 : bond 0.01320 ( 1) link_ALPHA1-3 : angle 0.92293 ( 3) link_ALPHA1-6 : bond 0.00509 ( 1) link_ALPHA1-6 : angle 1.43577 ( 3) link_BETA1-4 : bond 0.00512 ( 8) link_BETA1-4 : angle 1.34807 ( 24) link_NAG-ASN : bond 0.00484 ( 13) link_NAG-ASN : angle 2.33849 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.6977 (mm) REVERT: A 100 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7833 (mm) REVERT: A 115 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7867 (mtpt) REVERT: A 214 VAL cc_start: 0.8216 (t) cc_final: 0.7844 (p) REVERT: A 256 PHE cc_start: 0.8242 (m-80) cc_final: 0.7984 (m-10) REVERT: B 44 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.6189 (ttm170) REVERT: B 333 ASN cc_start: 0.7341 (m110) cc_final: 0.6934 (m-40) REVERT: B 443 ASP cc_start: 0.8151 (t0) cc_final: 0.7696 (t0) outliers start: 19 outliers final: 13 residues processed: 99 average time/residue: 0.0893 time to fit residues: 13.0519 Evaluate side-chains 98 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.173833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.146945 restraints weight = 11151.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.144603 restraints weight = 23048.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.141000 restraints weight = 21711.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.139483 restraints weight = 20690.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.139487 restraints weight = 16914.694| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9553 Z= 0.170 Angle : 0.617 8.339 13036 Z= 0.314 Chirality : 0.044 0.184 1468 Planarity : 0.005 0.055 1625 Dihedral : 6.682 59.093 1748 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.96 % Allowed : 17.46 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.10 (0.23), residues: 1112 helix: -0.28 (0.40), residues: 154 sheet: -0.53 (0.30), residues: 282 loop : -2.16 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 382 TYR 0.017 0.002 TYR A 410 PHE 0.019 0.002 PHE A 269 TRP 0.016 0.001 TRP B 179 HIS 0.004 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9525) covalent geometry : angle 0.59273 (12957) SS BOND : bond 0.00393 ( 5) SS BOND : angle 0.73537 ( 10) hydrogen bonds : bond 0.05790 ( 221) hydrogen bonds : angle 4.54019 ( 600) link_ALPHA1-3 : bond 0.01159 ( 1) link_ALPHA1-3 : angle 0.93185 ( 3) link_ALPHA1-6 : bond 0.00546 ( 1) link_ALPHA1-6 : angle 1.35796 ( 3) link_BETA1-4 : bond 0.00493 ( 8) link_BETA1-4 : angle 1.66890 ( 24) link_NAG-ASN : bond 0.00628 ( 13) link_NAG-ASN : angle 2.91017 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7279 (mm) REVERT: A 100 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.8038 (mm) REVERT: B 333 ASN cc_start: 0.7271 (m110) cc_final: 0.6875 (m-40) REVERT: B 443 ASP cc_start: 0.8136 (t0) cc_final: 0.7676 (t0) outliers start: 19 outliers final: 13 residues processed: 98 average time/residue: 0.0810 time to fit residues: 12.0281 Evaluate side-chains 98 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 16 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 0.0000 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.176885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.145732 restraints weight = 10932.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.142793 restraints weight = 22009.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.141481 restraints weight = 22794.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.138384 restraints weight = 20314.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.139677 restraints weight = 16702.116| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9553 Z= 0.126 Angle : 0.565 6.656 13036 Z= 0.287 Chirality : 0.043 0.185 1468 Planarity : 0.004 0.054 1625 Dihedral : 6.567 59.787 1748 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.17 % Allowed : 17.56 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (0.23), residues: 1112 helix: -0.23 (0.40), residues: 155 sheet: -0.49 (0.30), residues: 297 loop : -2.12 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.016 0.001 TYR A 410 PHE 0.020 0.001 PHE A 269 TRP 0.015 0.001 TRP B 179 HIS 0.003 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9525) covalent geometry : angle 0.54345 (12957) SS BOND : bond 0.00331 ( 5) SS BOND : angle 0.64796 ( 10) hydrogen bonds : bond 0.04708 ( 221) hydrogen bonds : angle 4.47465 ( 600) link_ALPHA1-3 : bond 0.01351 ( 1) link_ALPHA1-3 : angle 0.94908 ( 3) link_ALPHA1-6 : bond 0.00583 ( 1) link_ALPHA1-6 : angle 1.33639 ( 3) link_BETA1-4 : bond 0.00513 ( 8) link_BETA1-4 : angle 1.57945 ( 24) link_NAG-ASN : bond 0.00563 ( 13) link_NAG-ASN : angle 2.60425 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1586.64 seconds wall clock time: 28 minutes 15.22 seconds (1695.22 seconds total)