Starting phenix.real_space_refine on Wed Feb 4 10:57:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dng_27566/02_2026/8dng_27566_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dng_27566/02_2026/8dng_27566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dng_27566/02_2026/8dng_27566_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dng_27566/02_2026/8dng_27566_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dng_27566/02_2026/8dng_27566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dng_27566/02_2026/8dng_27566.map" } resolution = 3.0 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= -0.001 sd= 0.048 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 66 5.16 5 C 6465 2.51 5 N 1656 2.21 5 O 2031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10218 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3350 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 16, 'TRANS': 419} Chain breaks: 1 Chain: "D" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3350 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 16, 'TRANS': 419} Chain breaks: 1 Chain: "G" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3350 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 16, 'TRANS': 419} Chain breaks: 1 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.22, per 1000 atoms: 0.22 Number of scatterers: 10218 At special positions: 0 Unit cell: (100.58, 105.28, 99.64, 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 66 16.00 O 2031 8.00 N 1656 7.00 C 6465 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 114 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 71 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 114 " distance=2.04 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 340 " distance=2.03 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 363 " distance=2.03 Simple disulfide: pdb=" SG CYS D 387 " - pdb=" SG CYS D 392 " distance=2.03 Simple disulfide: pdb=" SG CYS D 394 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS G 71 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 331 " - pdb=" SG CYS G 340 " distance=2.03 Simple disulfide: pdb=" SG CYS G 355 " - pdb=" SG CYS G 363 " distance=2.03 Simple disulfide: pdb=" SG CYS G 387 " - pdb=" SG CYS G 392 " distance=2.03 Simple disulfide: pdb=" SG CYS G 394 " - pdb=" SG CYS G 417 " distance=2.04 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 NAG-ASN " NAG A 501 " - " ASN A 67 " " NAG A 502 " - " ASN A 99 " " NAG A 503 " - " ASN A 414 " " NAG A 504 " - " ASN A 464 " " NAG D 501 " - " ASN D 67 " " NAG D 502 " - " ASN D 99 " " NAG D 503 " - " ASN D 414 " " NAG D 504 " - " ASN D 464 " " NAG G 501 " - " ASN G 67 " " NAG G 502 " - " ASN G 99 " " NAG G 503 " - " ASN G 414 " " NAG G 504 " - " ASN G 464 " Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 479.0 milliseconds 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 15 sheets defined 38.0% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 29 through 37 removed outlier: 3.570A pdb=" N LYS A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.568A pdb=" N SER A 69 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLN A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS A 71 " --> pdb=" O MET A 68 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 removed outlier: 3.611A pdb=" N ASN A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Proline residue: A 89 - end of helix removed outlier: 3.720A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 146 removed outlier: 3.849A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 191 through 211 Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.734A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 437 through 441 Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.894A pdb=" N SER A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 37 Processing helix chain 'D' and resid 65 through 69 removed outlier: 3.506A pdb=" N SER D 69 " --> pdb=" O SER D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 100 Proline residue: D 89 - end of helix removed outlier: 3.643A pdb=" N ILE D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN D 100 " --> pdb=" O ILE D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 146 removed outlier: 3.785A pdb=" N LYS D 139 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASN D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN D 143 " --> pdb=" O LYS D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 154 Processing helix chain 'D' and resid 175 through 182 Processing helix chain 'D' and resid 191 through 211 Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 238 through 247 removed outlier: 3.701A pdb=" N LEU D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 349 through 357 Processing helix chain 'D' and resid 359 through 363 removed outlier: 3.605A pdb=" N LYS D 362 " --> pdb=" O SER D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 441 Processing helix chain 'D' and resid 452 through 468 removed outlier: 3.919A pdb=" N SER D 457 " --> pdb=" O LYS D 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 37 removed outlier: 3.602A pdb=" N LYS G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 72 removed outlier: 5.194A pdb=" N GLN G 70 " --> pdb=" O ASN G 67 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR G 72 " --> pdb=" O SER G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 99 removed outlier: 3.746A pdb=" N ASN G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) Proline residue: G 89 - end of helix removed outlier: 3.707A pdb=" N ILE G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TYR G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 146 removed outlier: 3.897A pdb=" N LYS G 139 " --> pdb=" O TYR G 135 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASN G 140 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN G 143 " --> pdb=" O LYS G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 153 Processing helix chain 'G' and resid 175 through 182 Processing helix chain 'G' and resid 191 through 211 Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 233 through 236 Processing helix chain 'G' and resid 238 through 247 removed outlier: 3.591A pdb=" N LEU G 242 " --> pdb=" O ASN G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 259 Processing helix chain 'G' and resid 349 through 357 Processing helix chain 'G' and resid 358 through 363 removed outlier: 5.647A pdb=" N GLU G 361 " --> pdb=" O GLY G 358 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS G 362 " --> pdb=" O SER G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 441 Processing helix chain 'G' and resid 452 through 468 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.601A pdb=" N TYR A 170 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LYS A 40 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU A 297 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL A 42 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR A 46 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA A 291 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 10.388A pdb=" N ILE A 48 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 9.662A pdb=" N GLN A 289 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N SER A 50 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N GLU A 287 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N LEU A 285 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N THR A 54 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 9.643A pdb=" N ASP A 56 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N TYR A 281 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N VAL A 58 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N ARG A 279 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N LYS A 60 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N ILE A 277 " --> pdb=" O LYS A 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 275 through 298 current: chain 'A' and resid 332 through 333 Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.337A pdb=" N MET A 226 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR A 263 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N ILE A 277 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N LYS A 60 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N ARG A 279 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N VAL A 58 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N TYR A 281 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 9.643A pdb=" N ASP A 56 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N THR A 54 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N LEU A 285 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N GLU A 287 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N SER A 50 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 9.662A pdb=" N GLN A 289 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 10.388A pdb=" N ILE A 48 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA A 291 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR A 46 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL A 42 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU A 297 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LYS A 40 " --> pdb=" O LEU A 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 60 current: chain 'A' and resid 322 through 326 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 removed outlier: 3.563A pdb=" N HIS A 102 " --> pdb=" O CYS A 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 302 removed outlier: 5.951A pdb=" N ARG A 365 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 removed outlier: 3.520A pdb=" N LEU A 383 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 393 through 394 removed outlier: 6.363A pdb=" N ILE A 426 " --> pdb=" O MET D 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 158 through 162 removed outlier: 17.171A pdb=" N THR D 168 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 11.788A pdb=" N THR D 54 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 11.260A pdb=" N TYR D 170 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASP D 56 " --> pdb=" O TYR D 170 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N PHE D 172 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL D 58 " --> pdb=" O PHE D 172 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LYS D 40 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LEU D 297 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL D 42 " --> pdb=" O GLU D 295 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR D 46 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA D 291 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N ILE D 48 " --> pdb=" O GLN D 289 " (cutoff:3.500A) removed outlier: 9.588A pdb=" N GLN D 289 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 9.647A pdb=" N SER D 50 " --> pdb=" O GLU D 287 " (cutoff:3.500A) removed outlier: 9.310A pdb=" N GLU D 287 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 10.754A pdb=" N LEU D 285 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 9.095A pdb=" N THR D 54 " --> pdb=" O PRO D 283 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N ASP D 56 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N TYR D 281 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 9.672A pdb=" N VAL D 58 " --> pdb=" O ARG D 279 " (cutoff:3.500A) removed outlier: 9.505A pdb=" N ARG D 279 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 9.501A pdb=" N LYS D 60 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 9.848A pdb=" N ILE D 277 " --> pdb=" O LYS D 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 275 through 298 current: chain 'D' and resid 332 through 333 Processing sheet with id=AA9, first strand: chain 'D' and resid 226 through 227 removed outlier: 4.279A pdb=" N MET D 226 " --> pdb=" O GLY D 264 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR D 263 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE D 277 " --> pdb=" O ILE D 267 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL D 269 " --> pdb=" O TYR D 275 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TYR D 275 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 9.848A pdb=" N ILE D 277 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 9.501A pdb=" N LYS D 60 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 9.505A pdb=" N ARG D 279 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 9.672A pdb=" N VAL D 58 " --> pdb=" O ARG D 279 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N TYR D 281 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N ASP D 56 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 9.095A pdb=" N THR D 54 " --> pdb=" O PRO D 283 " (cutoff:3.500A) removed outlier: 10.754A pdb=" N LEU D 285 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 9.310A pdb=" N GLU D 287 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 9.647A pdb=" N SER D 50 " --> pdb=" O GLU D 287 " (cutoff:3.500A) removed outlier: 9.588A pdb=" N GLN D 289 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N ILE D 48 " --> pdb=" O GLN D 289 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA D 291 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR D 46 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL D 42 " --> pdb=" O GLU D 295 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LEU D 297 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LYS D 40 " --> pdb=" O LEU D 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 38 through 60 current: chain 'D' and resid 322 through 326 Processing sheet with id=AB1, first strand: chain 'D' and resid 301 through 302 Processing sheet with id=AB2, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AB3, first strand: chain 'D' and resid 399 through 401 removed outlier: 3.513A pdb=" N ARG D 399 " --> pdb=" O CYS D 394 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N CYS D 392 " --> pdb=" O ILE D 401 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN D 393 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE D 426 " --> pdb=" O MET G 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 158 through 161 removed outlier: 4.496A pdb=" N TYR G 170 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS G 40 " --> pdb=" O LEU G 297 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU G 297 " --> pdb=" O LYS G 40 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL G 42 " --> pdb=" O GLU G 295 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR G 46 " --> pdb=" O ALA G 291 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA G 291 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 10.377A pdb=" N ILE G 48 " --> pdb=" O GLN G 289 " (cutoff:3.500A) removed outlier: 9.801A pdb=" N GLN G 289 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 9.587A pdb=" N SER G 50 " --> pdb=" O GLU G 287 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N GLU G 287 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 10.578A pdb=" N LEU G 285 " --> pdb=" O PRO G 52 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N THR G 54 " --> pdb=" O PRO G 283 " (cutoff:3.500A) removed outlier: 9.588A pdb=" N ASP G 56 " --> pdb=" O TYR G 281 " (cutoff:3.500A) removed outlier: 9.455A pdb=" N TYR G 281 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 9.716A pdb=" N VAL G 58 " --> pdb=" O ARG G 279 " (cutoff:3.500A) removed outlier: 9.511A pdb=" N ARG G 279 " --> pdb=" O VAL G 58 " (cutoff:3.500A) removed outlier: 9.503A pdb=" N LYS G 60 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 9.933A pdb=" N ILE G 277 " --> pdb=" O LYS G 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 275 through 298 current: chain 'G' and resid 332 through 333 Processing sheet with id=AB5, first strand: chain 'G' and resid 226 through 227 removed outlier: 4.309A pdb=" N MET G 226 " --> pdb=" O GLY G 264 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR G 263 " --> pdb=" O TYR G 281 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE G 277 " --> pdb=" O ILE G 267 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL G 269 " --> pdb=" O TYR G 275 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TYR G 275 " --> pdb=" O VAL G 269 " (cutoff:3.500A) removed outlier: 9.933A pdb=" N ILE G 277 " --> pdb=" O LYS G 60 " (cutoff:3.500A) removed outlier: 9.503A pdb=" N LYS G 60 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 9.511A pdb=" N ARG G 279 " --> pdb=" O VAL G 58 " (cutoff:3.500A) removed outlier: 9.716A pdb=" N VAL G 58 " --> pdb=" O ARG G 279 " (cutoff:3.500A) removed outlier: 9.455A pdb=" N TYR G 281 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 9.588A pdb=" N ASP G 56 " --> pdb=" O TYR G 281 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N THR G 54 " --> pdb=" O PRO G 283 " (cutoff:3.500A) removed outlier: 10.578A pdb=" N LEU G 285 " --> pdb=" O PRO G 52 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N GLU G 287 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 9.587A pdb=" N SER G 50 " --> pdb=" O GLU G 287 " (cutoff:3.500A) removed outlier: 9.801A pdb=" N GLN G 289 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 10.377A pdb=" N ILE G 48 " --> pdb=" O GLN G 289 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA G 291 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR G 46 " --> pdb=" O ALA G 291 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL G 42 " --> pdb=" O GLU G 295 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU G 297 " --> pdb=" O LYS G 40 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS G 40 " --> pdb=" O LEU G 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 38 through 60 current: chain 'G' and resid 322 through 326 Processing sheet with id=AB6, first strand: chain 'G' and resid 301 through 303 402 hydrogen bonds defined for protein. 1101 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: 1.39 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3287 1.35 - 1.47: 2231 1.47 - 1.59: 4751 1.59 - 1.71: 0 1.71 - 1.83: 96 Bond restraints: 10365 Sorted by residual: bond pdb=" N VAL G 369 " pdb=" CA VAL G 369 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.08e-02 8.57e+03 1.25e+01 bond pdb=" N SER G 370 " pdb=" CA SER G 370 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.21e-02 6.83e+03 7.43e+00 bond pdb=" N VAL G 368 " pdb=" CA VAL G 368 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.29e-02 6.01e+03 7.37e+00 bond pdb=" N VAL A 369 " pdb=" CA VAL A 369 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.31e+00 bond pdb=" N CYS G 104 " pdb=" CA CYS G 104 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.23e-02 6.61e+03 6.52e+00 ... (remaining 10360 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 13676 1.60 - 3.19: 345 3.19 - 4.79: 53 4.79 - 6.38: 7 6.38 - 7.98: 4 Bond angle restraints: 14085 Sorted by residual: angle pdb=" N VAL G 369 " pdb=" CA VAL G 369 " pdb=" C VAL G 369 " ideal model delta sigma weight residual 113.42 108.90 4.52 1.17e+00 7.31e-01 1.49e+01 angle pdb=" CA SER G 370 " pdb=" C SER G 370 " pdb=" O SER G 370 " ideal model delta sigma weight residual 121.72 118.10 3.62 1.18e+00 7.18e-01 9.42e+00 angle pdb=" CA GLU A 163 " pdb=" CB GLU A 163 " pdb=" CG GLU A 163 " ideal model delta sigma weight residual 114.10 120.23 -6.13 2.00e+00 2.50e-01 9.38e+00 angle pdb=" CA GLU G 406 " pdb=" CB GLU G 406 " pdb=" CG GLU G 406 " ideal model delta sigma weight residual 114.10 120.12 -6.02 2.00e+00 2.50e-01 9.06e+00 angle pdb=" CA ARG A 399 " pdb=" C ARG A 399 " pdb=" O ARG A 399 " ideal model delta sigma weight residual 121.58 118.12 3.46 1.16e+00 7.43e-01 8.92e+00 ... (remaining 14080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5781 17.95 - 35.89: 557 35.89 - 53.84: 151 53.84 - 71.79: 36 71.79 - 89.74: 12 Dihedral angle restraints: 6537 sinusoidal: 2709 harmonic: 3828 Sorted by residual: dihedral pdb=" CB CYS A 71 " pdb=" SG CYS A 71 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -160.15 74.15 1 1.00e+01 1.00e-02 6.98e+01 dihedral pdb=" CB CYS D 71 " pdb=" SG CYS D 71 " pdb=" SG CYS D 192 " pdb=" CB CYS D 192 " ideal model delta sinusoidal sigma weight residual -86.00 -159.92 73.92 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS G 394 " pdb=" SG CYS G 394 " pdb=" SG CYS G 417 " pdb=" CB CYS G 417 " ideal model delta sinusoidal sigma weight residual -86.00 -156.13 70.13 1 1.00e+01 1.00e-02 6.34e+01 ... (remaining 6534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1242 0.043 - 0.086: 321 0.086 - 0.129: 183 0.129 - 0.172: 10 0.172 - 0.215: 2 Chirality restraints: 1758 Sorted by residual: chirality pdb=" CA CYS A 394 " pdb=" N CYS A 394 " pdb=" C CYS A 394 " pdb=" CB CYS A 394 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA VAL A 369 " pdb=" N VAL A 369 " pdb=" C VAL A 369 " pdb=" CB VAL A 369 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA VAL D 105 " pdb=" N VAL D 105 " pdb=" C VAL D 105 " pdb=" CB VAL D 105 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.14e-01 ... (remaining 1755 not shown) Planarity restraints: 1779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS D 102 " 0.023 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C HIS D 102 " -0.081 2.00e-02 2.50e+03 pdb=" O HIS D 102 " 0.030 2.00e-02 2.50e+03 pdb=" N ASP D 103 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 393 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C GLN A 393 " -0.032 2.00e-02 2.50e+03 pdb=" O GLN A 393 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS A 394 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 190 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO D 191 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 191 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 191 " 0.026 5.00e-02 4.00e+02 ... (remaining 1776 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 142 2.60 - 3.18: 9281 3.18 - 3.75: 15647 3.75 - 4.33: 21809 4.33 - 4.90: 35569 Nonbonded interactions: 82448 Sorted by model distance: nonbonded pdb=" O HIS A 372 " pdb=" ND1 HIS A 372 " model vdw 2.029 3.120 nonbonded pdb=" O HIS G 372 " pdb=" ND1 HIS G 372 " model vdw 2.051 3.120 nonbonded pdb=" N GLU D 361 " pdb=" OE1 GLU D 361 " model vdw 2.094 3.120 nonbonded pdb=" N GLU A 361 " pdb=" OE1 GLU A 361 " model vdw 2.121 3.120 nonbonded pdb=" N GLU D 287 " pdb=" OE1 GLU D 287 " model vdw 2.157 3.120 ... (remaining 82443 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.020 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:5.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10395 Z= 0.193 Angle : 0.620 7.979 14157 Z= 0.338 Chirality : 0.047 0.215 1758 Planarity : 0.003 0.047 1767 Dihedral : 15.289 89.737 4011 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.15 % Allowed : 23.20 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.46 (0.24), residues: 1296 helix: 1.98 (0.27), residues: 411 sheet: 0.46 (0.31), residues: 270 loop : -0.96 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 399 TYR 0.016 0.001 TYR G 248 PHE 0.008 0.001 PHE A 301 TRP 0.007 0.001 TRP G 308 HIS 0.003 0.001 HIS G 372 Details of bonding type rmsd covalent geometry : bond 0.00370 (10365) covalent geometry : angle 0.60900 (14085) SS BOND : bond 0.00307 ( 18) SS BOND : angle 1.41215 ( 36) hydrogen bonds : bond 0.19445 ( 393) hydrogen bonds : angle 7.05026 ( 1101) link_NAG-ASN : bond 0.00270 ( 12) link_NAG-ASN : angle 2.05681 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 34 SER cc_start: 0.7653 (p) cc_final: 0.7451 (p) REVERT: A 45 LYS cc_start: 0.7215 (mtmt) cc_final: 0.6217 (mmtt) REVERT: A 77 GLU cc_start: 0.6555 (mm-30) cc_final: 0.5755 (tt0) REVERT: A 138 MET cc_start: 0.6163 (tpt) cc_final: 0.5917 (tpt) REVERT: A 177 ASP cc_start: 0.6962 (t0) cc_final: 0.6700 (p0) REVERT: A 220 ASP cc_start: 0.6667 (p0) cc_final: 0.5817 (m-30) REVERT: A 226 MET cc_start: 0.8083 (ttm) cc_final: 0.7744 (ttm) REVERT: A 290 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7719 (mp10) REVERT: A 320 ASN cc_start: 0.7367 (t0) cc_final: 0.6939 (m110) REVERT: A 322 LEU cc_start: 0.7050 (mm) cc_final: 0.6583 (mt) REVERT: A 342 GLN cc_start: 0.7510 (mt0) cc_final: 0.6488 (tt0) REVERT: A 375 ARG cc_start: 0.7734 (mtt90) cc_final: 0.7395 (mtt90) REVERT: A 380 ASN cc_start: 0.7659 (OUTLIER) cc_final: 0.7369 (m-40) REVERT: D 102 HIS cc_start: 0.4305 (OUTLIER) cc_final: 0.3580 (m-70) REVERT: D 138 MET cc_start: 0.5861 (ttp) cc_final: 0.4080 (mmm) REVERT: D 146 LYS cc_start: 0.7379 (ttmt) cc_final: 0.7132 (mttp) REVERT: D 177 ASP cc_start: 0.6923 (t0) cc_final: 0.6680 (p0) REVERT: D 214 PHE cc_start: 0.8291 (m-80) cc_final: 0.8070 (m-80) REVERT: D 290 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7774 (mp10) REVERT: D 320 ASN cc_start: 0.7212 (t0) cc_final: 0.6867 (m110) REVERT: D 322 LEU cc_start: 0.7443 (mm) cc_final: 0.6988 (mt) REVERT: D 325 ASN cc_start: 0.7836 (m-40) cc_final: 0.7388 (t160) REVERT: D 391 THR cc_start: 0.8484 (m) cc_final: 0.8180 (p) REVERT: D 393 GLN cc_start: 0.7546 (pt0) cc_final: 0.7346 (pp30) REVERT: D 396 THR cc_start: 0.7037 (OUTLIER) cc_final: 0.6593 (p) REVERT: G 45 LYS cc_start: 0.7340 (mtmt) cc_final: 0.6448 (mmpt) REVERT: G 77 GLU cc_start: 0.6440 (mm-30) cc_final: 0.5623 (tt0) REVERT: G 136 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6661 (mt-10) REVERT: G 140 ASN cc_start: 0.6982 (t0) cc_final: 0.6527 (t0) REVERT: G 146 LYS cc_start: 0.7455 (ttmt) cc_final: 0.7115 (mtmm) REVERT: G 226 MET cc_start: 0.7807 (ttp) cc_final: 0.7410 (ttm) REVERT: G 290 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7701 (mp10) REVERT: G 322 LEU cc_start: 0.7197 (mm) cc_final: 0.6620 (mt) REVERT: G 337 SER cc_start: 0.8428 (OUTLIER) cc_final: 0.7965 (p) REVERT: G 342 GLN cc_start: 0.7024 (mt0) cc_final: 0.6037 (tt0) REVERT: G 379 SER cc_start: 0.7572 (OUTLIER) cc_final: 0.7218 (p) REVERT: G 380 ASN cc_start: 0.7539 (m110) cc_final: 0.7245 (m110) REVERT: G 426 ILE cc_start: 0.7091 (mt) cc_final: 0.6758 (mp) outliers start: 25 outliers final: 8 residues processed: 213 average time/residue: 0.2987 time to fit residues: 71.0973 Evaluate side-chains 140 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 337 SER Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 379 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.0270 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 229 GLN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN D 229 GLN ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 HIS G 145 ASN G 229 GLN G 303 ASN G 325 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.190674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.163175 restraints weight = 10553.045| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.84 r_work: 0.3665 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10395 Z= 0.134 Angle : 0.616 11.392 14157 Z= 0.314 Chirality : 0.047 0.268 1758 Planarity : 0.004 0.036 1767 Dihedral : 6.216 57.261 1659 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.55 % Allowed : 19.93 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.33 (0.23), residues: 1296 helix: 1.77 (0.26), residues: 411 sheet: 0.39 (0.31), residues: 273 loop : -0.96 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 375 TYR 0.015 0.001 TYR D 438 PHE 0.012 0.001 PHE G 253 TRP 0.005 0.001 TRP G 308 HIS 0.002 0.000 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00304 (10365) covalent geometry : angle 0.60243 (14085) SS BOND : bond 0.00433 ( 18) SS BOND : angle 1.46582 ( 36) hydrogen bonds : bond 0.04163 ( 393) hydrogen bonds : angle 5.11095 ( 1101) link_NAG-ASN : bond 0.00798 ( 12) link_NAG-ASN : angle 2.28360 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 123 time to evaluate : 0.323 Fit side-chains REVERT: A 45 LYS cc_start: 0.7844 (mtmt) cc_final: 0.7063 (mmpt) REVERT: A 77 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7256 (tt0) REVERT: A 197 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6250 (tt) REVERT: A 220 ASP cc_start: 0.7571 (p0) cc_final: 0.6955 (m-30) REVERT: A 226 MET cc_start: 0.8460 (ttm) cc_final: 0.8245 (ttm) REVERT: A 320 ASN cc_start: 0.7462 (t0) cc_final: 0.7125 (m110) REVERT: A 322 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7234 (mt) REVERT: A 371 SER cc_start: 0.7905 (OUTLIER) cc_final: 0.7368 (p) REVERT: D 45 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7367 (mtpt) REVERT: D 138 MET cc_start: 0.6712 (ttp) cc_final: 0.5566 (tpp) REVERT: D 189 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6582 (mtmt) REVERT: D 320 ASN cc_start: 0.7339 (t0) cc_final: 0.7048 (m110) REVERT: D 322 LEU cc_start: 0.7942 (mm) cc_final: 0.7458 (mt) REVERT: D 325 ASN cc_start: 0.7973 (m-40) cc_final: 0.7516 (t0) REVERT: D 388 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8286 (mm) REVERT: D 391 THR cc_start: 0.8457 (m) cc_final: 0.8174 (t) REVERT: G 45 LYS cc_start: 0.7905 (mtmt) cc_final: 0.7229 (mmpt) REVERT: G 77 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7015 (tt0) REVERT: G 226 MET cc_start: 0.8355 (ttp) cc_final: 0.8143 (ttm) REVERT: G 290 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8188 (mp10) REVERT: G 322 LEU cc_start: 0.7920 (mm) cc_final: 0.7478 (mt) REVERT: G 337 SER cc_start: 0.8466 (t) cc_final: 0.8238 (p) REVERT: G 342 GLN cc_start: 0.7778 (mt0) cc_final: 0.7210 (tt0) REVERT: G 371 SER cc_start: 0.7665 (OUTLIER) cc_final: 0.7179 (p) outliers start: 53 outliers final: 14 residues processed: 165 average time/residue: 0.3649 time to fit residues: 66.1802 Evaluate side-chains 132 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 440 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 16 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 4 optimal weight: 0.0980 chunk 106 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 114 optimal weight: 0.0980 chunk 123 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 229 GLN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN D 229 GLN D 305 ASN D 342 GLN ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 GLN G 303 ASN G 468 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.182374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.154472 restraints weight = 10696.516| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.87 r_work: 0.3611 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10395 Z= 0.178 Angle : 0.633 11.154 14157 Z= 0.317 Chirality : 0.049 0.272 1758 Planarity : 0.004 0.036 1767 Dihedral : 5.701 56.390 1643 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.07 % Allowed : 20.27 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.16 (0.22), residues: 1296 helix: 1.21 (0.25), residues: 417 sheet: -0.08 (0.31), residues: 258 loop : -1.01 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 399 TYR 0.018 0.002 TYR D 275 PHE 0.011 0.001 PHE G 235 TRP 0.003 0.001 TRP A 308 HIS 0.007 0.001 HIS G 372 Details of bonding type rmsd covalent geometry : bond 0.00425 (10365) covalent geometry : angle 0.61763 (14085) SS BOND : bond 0.00359 ( 18) SS BOND : angle 1.61047 ( 36) hydrogen bonds : bond 0.03988 ( 393) hydrogen bonds : angle 4.91742 ( 1101) link_NAG-ASN : bond 0.00543 ( 12) link_NAG-ASN : angle 2.37817 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 129 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8080 (mttm) cc_final: 0.7811 (mttm) REVERT: A 45 LYS cc_start: 0.7829 (mtmt) cc_final: 0.7010 (mmpt) REVERT: A 77 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7202 (tt0) REVERT: A 197 LEU cc_start: 0.6446 (OUTLIER) cc_final: 0.6103 (tt) REVERT: A 220 ASP cc_start: 0.7674 (p0) cc_final: 0.7039 (m-30) REVERT: A 261 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8529 (m) REVERT: A 320 ASN cc_start: 0.7476 (t0) cc_final: 0.7043 (m110) REVERT: A 322 LEU cc_start: 0.7641 (mm) cc_final: 0.7258 (mt) REVERT: A 342 GLN cc_start: 0.8207 (mt0) cc_final: 0.7559 (tt0) REVERT: A 371 SER cc_start: 0.7877 (OUTLIER) cc_final: 0.7270 (p) REVERT: D 138 MET cc_start: 0.6646 (ttp) cc_final: 0.5889 (tpp) REVERT: D 320 ASN cc_start: 0.7316 (t0) cc_final: 0.6943 (m110) REVERT: D 322 LEU cc_start: 0.8008 (mm) cc_final: 0.7536 (mt) REVERT: D 337 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8506 (p) REVERT: D 391 THR cc_start: 0.8480 (m) cc_final: 0.8144 (t) REVERT: G 45 LYS cc_start: 0.7847 (mtmt) cc_final: 0.7179 (mmpt) REVERT: G 77 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6970 (tt0) REVERT: G 226 MET cc_start: 0.8301 (ttp) cc_final: 0.8074 (ttm) REVERT: G 289 GLN cc_start: 0.8370 (mm110) cc_final: 0.8101 (mp10) REVERT: G 290 GLN cc_start: 0.8405 (mm-40) cc_final: 0.8114 (mp10) REVERT: G 322 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7418 (mt) REVERT: G 336 ARG cc_start: 0.8114 (mmm-85) cc_final: 0.7367 (tpt170) REVERT: G 337 SER cc_start: 0.8490 (t) cc_final: 0.8180 (p) REVERT: G 342 GLN cc_start: 0.7815 (mt0) cc_final: 0.7221 (tt0) REVERT: G 371 SER cc_start: 0.7613 (OUTLIER) cc_final: 0.7065 (p) outliers start: 59 outliers final: 27 residues processed: 175 average time/residue: 0.3597 time to fit residues: 69.2769 Evaluate side-chains 144 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 440 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 229 GLN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN D 305 ASN G 229 GLN G 325 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.178685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.151515 restraints weight = 10649.020| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.81 r_work: 0.3563 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10395 Z= 0.226 Angle : 0.687 12.061 14157 Z= 0.341 Chirality : 0.050 0.288 1758 Planarity : 0.004 0.040 1767 Dihedral : 6.086 57.131 1643 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 6.27 % Allowed : 19.42 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.56 (0.22), residues: 1296 helix: 0.85 (0.25), residues: 408 sheet: -0.57 (0.29), residues: 273 loop : -1.08 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 399 TYR 0.019 0.002 TYR D 275 PHE 0.010 0.002 PHE G 235 TRP 0.002 0.001 TRP A 308 HIS 0.002 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00561 (10365) covalent geometry : angle 0.66646 (14085) SS BOND : bond 0.00346 ( 18) SS BOND : angle 1.74984 ( 36) hydrogen bonds : bond 0.04074 ( 393) hydrogen bonds : angle 5.05490 ( 1101) link_NAG-ASN : bond 0.00493 ( 12) link_NAG-ASN : angle 2.99347 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 127 time to evaluate : 0.393 Fit side-chains REVERT: A 32 LYS cc_start: 0.8098 (mttm) cc_final: 0.7879 (mttm) REVERT: A 45 LYS cc_start: 0.7867 (mtmt) cc_final: 0.6987 (mmpt) REVERT: A 77 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7293 (tt0) REVERT: A 220 ASP cc_start: 0.7830 (p0) cc_final: 0.6946 (m-30) REVERT: A 261 SER cc_start: 0.8866 (OUTLIER) cc_final: 0.8530 (m) REVERT: A 320 ASN cc_start: 0.7567 (t0) cc_final: 0.7083 (m110) REVERT: A 322 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7219 (mt) REVERT: A 371 SER cc_start: 0.7835 (OUTLIER) cc_final: 0.7148 (p) REVERT: D 45 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.6980 (mmtt) REVERT: D 138 MET cc_start: 0.6675 (ttp) cc_final: 0.5849 (tpp) REVERT: D 175 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7468 (mp) REVERT: D 189 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.6653 (mtmt) REVERT: D 192 CYS cc_start: 0.6383 (OUTLIER) cc_final: 0.5824 (m) REVERT: D 271 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7801 (mt) REVERT: D 320 ASN cc_start: 0.7232 (t0) cc_final: 0.6856 (m110) REVERT: D 322 LEU cc_start: 0.8059 (mm) cc_final: 0.7552 (mt) REVERT: D 336 ARG cc_start: 0.7819 (mtm-85) cc_final: 0.7114 (tpt170) REVERT: D 337 SER cc_start: 0.8672 (OUTLIER) cc_final: 0.8409 (p) REVERT: D 391 THR cc_start: 0.8476 (m) cc_final: 0.8152 (t) REVERT: D 393 GLN cc_start: 0.7914 (pt0) cc_final: 0.7668 (pt0) REVERT: G 45 LYS cc_start: 0.7921 (mtmt) cc_final: 0.7183 (mmpt) REVERT: G 77 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7074 (tt0) REVERT: G 231 ILE cc_start: 0.8252 (mt) cc_final: 0.8021 (mm) REVERT: G 289 GLN cc_start: 0.8332 (mm110) cc_final: 0.8106 (mp10) REVERT: G 322 LEU cc_start: 0.7829 (mm) cc_final: 0.7381 (mt) REVERT: G 336 ARG cc_start: 0.8107 (mmm-85) cc_final: 0.7379 (tpt170) REVERT: G 337 SER cc_start: 0.8492 (OUTLIER) cc_final: 0.8199 (p) REVERT: G 342 GLN cc_start: 0.7902 (mt0) cc_final: 0.7230 (tt0) REVERT: G 354 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7779 (mp0) REVERT: G 371 SER cc_start: 0.7655 (OUTLIER) cc_final: 0.7047 (p) outliers start: 73 outliers final: 33 residues processed: 183 average time/residue: 0.3627 time to fit residues: 73.0819 Evaluate side-chains 163 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 337 SER Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 440 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 30 optimal weight: 0.0070 chunk 62 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN D 229 GLN D 305 ASN G 229 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.181718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.154632 restraints weight = 10662.988| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.83 r_work: 0.3611 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10395 Z= 0.121 Angle : 0.563 10.166 14157 Z= 0.283 Chirality : 0.047 0.289 1758 Planarity : 0.003 0.035 1767 Dihedral : 5.597 55.726 1643 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.73 % Allowed : 22.16 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.22), residues: 1296 helix: 1.27 (0.25), residues: 402 sheet: -0.48 (0.31), residues: 240 loop : -0.93 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 353 TYR 0.016 0.001 TYR D 438 PHE 0.008 0.001 PHE G 253 TRP 0.004 0.001 TRP G 308 HIS 0.003 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00284 (10365) covalent geometry : angle 0.54744 (14085) SS BOND : bond 0.00231 ( 18) SS BOND : angle 1.25977 ( 36) hydrogen bonds : bond 0.03347 ( 393) hydrogen bonds : angle 4.67701 ( 1101) link_NAG-ASN : bond 0.00513 ( 12) link_NAG-ASN : angle 2.38743 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 116 time to evaluate : 0.356 Fit side-chains REVERT: A 32 LYS cc_start: 0.8056 (mttm) cc_final: 0.7852 (mttm) REVERT: A 45 LYS cc_start: 0.7764 (mtmt) cc_final: 0.6933 (mmtt) REVERT: A 77 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7178 (tt0) REVERT: A 220 ASP cc_start: 0.7744 (p0) cc_final: 0.7321 (p0) REVERT: A 261 SER cc_start: 0.8883 (OUTLIER) cc_final: 0.8517 (m) REVERT: A 320 ASN cc_start: 0.7484 (t0) cc_final: 0.7042 (m110) REVERT: A 322 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7074 (mt) REVERT: A 371 SER cc_start: 0.7792 (OUTLIER) cc_final: 0.7170 (p) REVERT: D 138 MET cc_start: 0.6387 (ttp) cc_final: 0.5623 (tpp) REVERT: D 140 ASN cc_start: 0.6635 (t0) cc_final: 0.6090 (m110) REVERT: D 175 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7375 (mp) REVERT: D 192 CYS cc_start: 0.6144 (OUTLIER) cc_final: 0.5522 (m) REVERT: D 320 ASN cc_start: 0.7247 (t0) cc_final: 0.6871 (m110) REVERT: D 322 LEU cc_start: 0.8000 (mm) cc_final: 0.7455 (mt) REVERT: D 336 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7054 (tpt170) REVERT: D 337 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.8340 (p) REVERT: D 393 GLN cc_start: 0.7859 (pt0) cc_final: 0.7621 (pt0) REVERT: G 45 LYS cc_start: 0.7737 (mtmt) cc_final: 0.7155 (mmpt) REVERT: G 77 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7083 (tt0) REVERT: G 231 ILE cc_start: 0.8242 (mt) cc_final: 0.8001 (mm) REVERT: G 289 GLN cc_start: 0.8321 (mm110) cc_final: 0.8095 (mp10) REVERT: G 290 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8112 (mp10) REVERT: G 322 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7303 (mt) REVERT: G 336 ARG cc_start: 0.8075 (mmm-85) cc_final: 0.7388 (tpt170) REVERT: G 337 SER cc_start: 0.8406 (OUTLIER) cc_final: 0.8087 (p) REVERT: G 342 GLN cc_start: 0.7881 (mt0) cc_final: 0.7239 (tt0) REVERT: G 371 SER cc_start: 0.7681 (OUTLIER) cc_final: 0.7083 (p) outliers start: 55 outliers final: 22 residues processed: 159 average time/residue: 0.3314 time to fit residues: 58.5131 Evaluate side-chains 143 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 337 SER Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain G residue 390 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 96 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 78 optimal weight: 0.1980 chunk 113 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 342 GLN D 100 ASN D 229 GLN D 305 ASN G 229 GLN G 325 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.183123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.155474 restraints weight = 10759.413| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.87 r_work: 0.3626 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10395 Z= 0.109 Angle : 0.535 9.621 14157 Z= 0.270 Chirality : 0.046 0.286 1758 Planarity : 0.003 0.033 1767 Dihedral : 5.329 56.133 1643 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.47 % Allowed : 22.42 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.22), residues: 1296 helix: 1.53 (0.26), residues: 402 sheet: -0.36 (0.32), residues: 240 loop : -0.88 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 375 TYR 0.015 0.001 TYR D 438 PHE 0.007 0.001 PHE A 376 TRP 0.002 0.001 TRP G 308 HIS 0.004 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00254 (10365) covalent geometry : angle 0.52043 (14085) SS BOND : bond 0.00280 ( 18) SS BOND : angle 1.11137 ( 36) hydrogen bonds : bond 0.03122 ( 393) hydrogen bonds : angle 4.47691 ( 1101) link_NAG-ASN : bond 0.00517 ( 12) link_NAG-ASN : angle 2.35600 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 118 time to evaluate : 0.329 Fit side-chains REVERT: A 45 LYS cc_start: 0.7692 (mtmt) cc_final: 0.6939 (mmtt) REVERT: A 77 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7091 (tt0) REVERT: A 197 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.6051 (tt) REVERT: A 220 ASP cc_start: 0.7754 (p0) cc_final: 0.7311 (p0) REVERT: A 261 SER cc_start: 0.8885 (OUTLIER) cc_final: 0.8531 (m) REVERT: A 320 ASN cc_start: 0.7453 (t0) cc_final: 0.6983 (m110) REVERT: A 322 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7084 (mt) REVERT: A 336 ARG cc_start: 0.7887 (mtm-85) cc_final: 0.7189 (tpt170) REVERT: A 342 GLN cc_start: 0.8233 (mt0) cc_final: 0.7572 (tt0) REVERT: A 371 SER cc_start: 0.7722 (OUTLIER) cc_final: 0.7113 (p) REVERT: D 138 MET cc_start: 0.6185 (ttp) cc_final: 0.5458 (tpp) REVERT: D 140 ASN cc_start: 0.6573 (t0) cc_final: 0.6059 (m110) REVERT: D 175 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7383 (mp) REVERT: D 192 CYS cc_start: 0.6143 (OUTLIER) cc_final: 0.5513 (m) REVERT: D 320 ASN cc_start: 0.7190 (t0) cc_final: 0.6845 (m110) REVERT: D 322 LEU cc_start: 0.8002 (mm) cc_final: 0.7441 (mt) REVERT: D 336 ARG cc_start: 0.7846 (mtm-85) cc_final: 0.7083 (tpt170) REVERT: D 337 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8306 (p) REVERT: D 342 GLN cc_start: 0.8407 (mt0) cc_final: 0.7748 (tt0) REVERT: D 354 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7114 (mp0) REVERT: D 393 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7549 (pt0) REVERT: G 45 LYS cc_start: 0.7679 (mtmt) cc_final: 0.7163 (mmpt) REVERT: G 77 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7032 (tt0) REVERT: G 231 ILE cc_start: 0.8271 (mt) cc_final: 0.8040 (mm) REVERT: G 289 GLN cc_start: 0.8327 (mm110) cc_final: 0.8109 (mp10) REVERT: G 290 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8135 (mp10) REVERT: G 322 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7336 (mt) REVERT: G 336 ARG cc_start: 0.8102 (mmm-85) cc_final: 0.7398 (tpt170) REVERT: G 337 SER cc_start: 0.8406 (OUTLIER) cc_final: 0.8053 (p) REVERT: G 342 GLN cc_start: 0.7811 (mt0) cc_final: 0.7238 (tt0) REVERT: G 354 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7712 (mp0) outliers start: 52 outliers final: 22 residues processed: 158 average time/residue: 0.3380 time to fit residues: 58.8678 Evaluate side-chains 144 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 337 SER Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 390 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 0.0040 chunk 114 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 71 optimal weight: 0.0970 chunk 11 optimal weight: 2.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN D 229 GLN D 305 ASN G 219 GLN G 229 GLN G 302 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.184032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.156411 restraints weight = 10652.014| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.86 r_work: 0.3625 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10395 Z= 0.104 Angle : 0.524 9.610 14157 Z= 0.263 Chirality : 0.046 0.285 1758 Planarity : 0.003 0.033 1767 Dihedral : 5.146 55.982 1643 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.47 % Allowed : 22.68 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.07 (0.23), residues: 1296 helix: 1.64 (0.26), residues: 402 sheet: -0.26 (0.32), residues: 240 loop : -0.84 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 353 TYR 0.014 0.001 TYR D 438 PHE 0.007 0.001 PHE A 376 TRP 0.003 0.001 TRP G 308 HIS 0.002 0.000 HIS G 372 Details of bonding type rmsd covalent geometry : bond 0.00240 (10365) covalent geometry : angle 0.50949 (14085) SS BOND : bond 0.00222 ( 18) SS BOND : angle 1.10098 ( 36) hydrogen bonds : bond 0.03037 ( 393) hydrogen bonds : angle 4.39325 ( 1101) link_NAG-ASN : bond 0.00570 ( 12) link_NAG-ASN : angle 2.24101 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 124 time to evaluate : 0.281 Fit side-chains REVERT: A 45 LYS cc_start: 0.7679 (mtmt) cc_final: 0.7037 (mmtt) REVERT: A 77 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7145 (tt0) REVERT: A 197 LEU cc_start: 0.6499 (OUTLIER) cc_final: 0.6139 (tt) REVERT: A 220 ASP cc_start: 0.7699 (p0) cc_final: 0.7251 (p0) REVERT: A 261 SER cc_start: 0.8884 (OUTLIER) cc_final: 0.8543 (m) REVERT: A 320 ASN cc_start: 0.7450 (t0) cc_final: 0.7089 (m110) REVERT: A 322 LEU cc_start: 0.7626 (mm) cc_final: 0.7158 (mt) REVERT: A 336 ARG cc_start: 0.7924 (mtm-85) cc_final: 0.7311 (tpt170) REVERT: D 138 MET cc_start: 0.6171 (ttp) cc_final: 0.5477 (tpp) REVERT: D 140 ASN cc_start: 0.6591 (t0) cc_final: 0.6101 (m110) REVERT: D 175 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7401 (mp) REVERT: D 192 CYS cc_start: 0.5998 (OUTLIER) cc_final: 0.5341 (m) REVERT: D 320 ASN cc_start: 0.7152 (t0) cc_final: 0.6856 (m110) REVERT: D 322 LEU cc_start: 0.8038 (mm) cc_final: 0.7495 (mt) REVERT: D 336 ARG cc_start: 0.7870 (mtm-85) cc_final: 0.7145 (tpt170) REVERT: D 342 GLN cc_start: 0.8442 (mt0) cc_final: 0.7818 (tt0) REVERT: D 354 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7134 (mp0) REVERT: D 393 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7581 (pt0) REVERT: G 45 LYS cc_start: 0.7691 (mtmt) cc_final: 0.7231 (mmpt) REVERT: G 77 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7032 (tt0) REVERT: G 290 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8208 (mp10) REVERT: G 322 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7281 (mt) REVERT: G 336 ARG cc_start: 0.8110 (mmm-85) cc_final: 0.7467 (tpt170) REVERT: G 337 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8046 (p) REVERT: G 342 GLN cc_start: 0.7829 (mt0) cc_final: 0.7324 (tt0) REVERT: G 445 ILE cc_start: 0.5187 (OUTLIER) cc_final: 0.4892 (pp) outliers start: 52 outliers final: 24 residues processed: 164 average time/residue: 0.3478 time to fit residues: 62.8754 Evaluate side-chains 145 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 337 SER Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 445 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 52 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 56 optimal weight: 0.0000 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 122 optimal weight: 0.0980 chunk 47 optimal weight: 0.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN D 229 GLN D 305 ASN G 219 GLN G 229 GLN ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.183118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.155367 restraints weight = 10637.612| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.86 r_work: 0.3613 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10395 Z= 0.116 Angle : 0.544 9.593 14157 Z= 0.271 Chirality : 0.046 0.285 1758 Planarity : 0.003 0.032 1767 Dihedral : 5.114 56.274 1643 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.21 % Allowed : 22.85 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.05 (0.23), residues: 1296 helix: 1.61 (0.25), residues: 402 sheet: -0.27 (0.32), residues: 240 loop : -0.84 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 353 TYR 0.014 0.001 TYR D 438 PHE 0.007 0.001 PHE G 214 TRP 0.002 0.001 TRP G 308 HIS 0.004 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00277 (10365) covalent geometry : angle 0.52973 (14085) SS BOND : bond 0.00212 ( 18) SS BOND : angle 1.12604 ( 36) hydrogen bonds : bond 0.03053 ( 393) hydrogen bonds : angle 4.40008 ( 1101) link_NAG-ASN : bond 0.00527 ( 12) link_NAG-ASN : angle 2.26077 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 114 time to evaluate : 0.292 Fit side-chains REVERT: A 45 LYS cc_start: 0.7689 (mtmt) cc_final: 0.7048 (mmtt) REVERT: A 77 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7195 (tt0) REVERT: A 197 LEU cc_start: 0.6509 (OUTLIER) cc_final: 0.6145 (tt) REVERT: A 220 ASP cc_start: 0.7693 (p0) cc_final: 0.7260 (p0) REVERT: A 261 SER cc_start: 0.8875 (OUTLIER) cc_final: 0.8527 (m) REVERT: A 320 ASN cc_start: 0.7490 (t0) cc_final: 0.7134 (m110) REVERT: A 322 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7159 (mt) REVERT: A 336 ARG cc_start: 0.7940 (mtm-85) cc_final: 0.7341 (tpt170) REVERT: A 354 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: D 138 MET cc_start: 0.6222 (ttp) cc_final: 0.5514 (tpp) REVERT: D 140 ASN cc_start: 0.6632 (t0) cc_final: 0.6144 (m110) REVERT: D 175 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7455 (mp) REVERT: D 320 ASN cc_start: 0.7106 (t0) cc_final: 0.6809 (m110) REVERT: D 322 LEU cc_start: 0.7989 (mm) cc_final: 0.7450 (mt) REVERT: D 336 ARG cc_start: 0.7838 (mtm-85) cc_final: 0.7124 (tpt170) REVERT: D 342 GLN cc_start: 0.8465 (mt0) cc_final: 0.7839 (tt0) REVERT: D 354 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7159 (mp0) REVERT: D 393 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7582 (pt0) REVERT: G 45 LYS cc_start: 0.7722 (mtmt) cc_final: 0.7267 (mmpt) REVERT: G 77 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7084 (tt0) REVERT: G 258 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7524 (tp30) REVERT: G 290 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8222 (mp10) REVERT: G 322 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7284 (mt) REVERT: G 336 ARG cc_start: 0.8160 (mmm-85) cc_final: 0.7515 (tpt170) REVERT: G 337 SER cc_start: 0.8404 (OUTLIER) cc_final: 0.8043 (p) REVERT: G 342 GLN cc_start: 0.7842 (mt0) cc_final: 0.7335 (tt0) REVERT: G 445 ILE cc_start: 0.5030 (OUTLIER) cc_final: 0.4786 (pp) outliers start: 49 outliers final: 26 residues processed: 151 average time/residue: 0.3792 time to fit residues: 62.9372 Evaluate side-chains 150 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 71 CYS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 258 GLU Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 337 SER Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 445 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 122 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 114 optimal weight: 0.0980 chunk 95 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 107 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN D 229 GLN D 305 ASN G 219 GLN G 229 GLN ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.182591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.154834 restraints weight = 10697.581| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.87 r_work: 0.3614 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10395 Z= 0.117 Angle : 0.539 9.599 14157 Z= 0.269 Chirality : 0.046 0.287 1758 Planarity : 0.003 0.032 1767 Dihedral : 5.012 56.274 1641 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.87 % Allowed : 23.28 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.01 (0.23), residues: 1296 helix: 1.41 (0.25), residues: 420 sheet: -0.29 (0.32), residues: 240 loop : -0.84 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 353 TYR 0.013 0.001 TYR D 438 PHE 0.007 0.001 PHE A 376 TRP 0.002 0.001 TRP G 308 HIS 0.002 0.000 HIS G 372 Details of bonding type rmsd covalent geometry : bond 0.00278 (10365) covalent geometry : angle 0.52587 (14085) SS BOND : bond 0.00218 ( 18) SS BOND : angle 1.03374 ( 36) hydrogen bonds : bond 0.03051 ( 393) hydrogen bonds : angle 4.39528 ( 1101) link_NAG-ASN : bond 0.00522 ( 12) link_NAG-ASN : angle 2.23442 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 115 time to evaluate : 0.385 Fit side-chains REVERT: A 45 LYS cc_start: 0.7638 (mtmt) cc_final: 0.6962 (mmtt) REVERT: A 77 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7094 (tt0) REVERT: A 197 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.6034 (tt) REVERT: A 220 ASP cc_start: 0.7591 (p0) cc_final: 0.7196 (p0) REVERT: A 261 SER cc_start: 0.8874 (OUTLIER) cc_final: 0.8503 (m) REVERT: A 320 ASN cc_start: 0.7457 (t0) cc_final: 0.7084 (m110) REVERT: A 322 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7087 (mt) REVERT: A 336 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7244 (tpt170) REVERT: A 354 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: D 71 CYS cc_start: 0.4401 (OUTLIER) cc_final: 0.4198 (t) REVERT: D 138 MET cc_start: 0.6047 (ttp) cc_final: 0.5043 (tpp) REVERT: D 140 ASN cc_start: 0.6586 (t0) cc_final: 0.6073 (m110) REVERT: D 175 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7422 (mp) REVERT: D 289 GLN cc_start: 0.8296 (mm110) cc_final: 0.8086 (mm110) REVERT: D 320 ASN cc_start: 0.7082 (t0) cc_final: 0.6766 (m110) REVERT: D 322 LEU cc_start: 0.7934 (mm) cc_final: 0.7380 (mt) REVERT: D 336 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7023 (tpt170) REVERT: D 342 GLN cc_start: 0.8434 (mt0) cc_final: 0.7771 (tt0) REVERT: D 354 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7108 (mp0) REVERT: D 393 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7524 (pt0) REVERT: G 45 LYS cc_start: 0.7682 (mtmt) cc_final: 0.7226 (mmpt) REVERT: G 77 GLU cc_start: 0.7445 (mm-30) cc_final: 0.6964 (tt0) REVERT: G 258 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7469 (tp30) REVERT: G 290 GLN cc_start: 0.8420 (mm-40) cc_final: 0.8127 (mp10) REVERT: G 322 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7211 (mt) REVERT: G 336 ARG cc_start: 0.8130 (mmm-85) cc_final: 0.7434 (tpt170) REVERT: G 337 SER cc_start: 0.8415 (OUTLIER) cc_final: 0.8007 (p) REVERT: G 342 GLN cc_start: 0.7780 (mt0) cc_final: 0.7228 (tt0) outliers start: 45 outliers final: 22 residues processed: 148 average time/residue: 0.4105 time to fit residues: 66.4108 Evaluate side-chains 144 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain D residue 71 CYS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 258 GLU Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 337 SER Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 390 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 85 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 69 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN D 229 GLN D 372 HIS G 219 GLN G 229 GLN G 303 ASN ** G 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.182819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.155189 restraints weight = 10548.711| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.84 r_work: 0.3612 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10395 Z= 0.122 Angle : 0.556 9.617 14157 Z= 0.277 Chirality : 0.047 0.288 1758 Planarity : 0.003 0.031 1767 Dihedral : 5.040 56.356 1641 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.26 % Allowed : 24.23 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.22), residues: 1296 helix: 1.37 (0.25), residues: 420 sheet: -0.32 (0.32), residues: 240 loop : -0.87 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 375 TYR 0.013 0.001 TYR D 438 PHE 0.007 0.001 PHE A 376 TRP 0.002 0.001 TRP G 308 HIS 0.004 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00294 (10365) covalent geometry : angle 0.54179 (14085) SS BOND : bond 0.00230 ( 18) SS BOND : angle 1.38906 ( 36) hydrogen bonds : bond 0.03218 ( 393) hydrogen bonds : angle 4.48355 ( 1101) link_NAG-ASN : bond 0.00503 ( 12) link_NAG-ASN : angle 2.23131 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 0.392 Fit side-chains REVERT: A 77 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7195 (tt0) REVERT: A 197 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.6133 (tt) REVERT: A 220 ASP cc_start: 0.7577 (p0) cc_final: 0.7171 (p0) REVERT: A 261 SER cc_start: 0.8892 (OUTLIER) cc_final: 0.8535 (m) REVERT: A 320 ASN cc_start: 0.7496 (t0) cc_final: 0.7112 (m110) REVERT: A 322 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7139 (mt) REVERT: A 336 ARG cc_start: 0.7892 (mtm-85) cc_final: 0.7293 (tpt170) REVERT: A 354 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7724 (mp0) REVERT: D 138 MET cc_start: 0.6129 (ttp) cc_final: 0.5172 (tpp) REVERT: D 140 ASN cc_start: 0.6699 (t0) cc_final: 0.6187 (m110) REVERT: D 175 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7444 (mp) REVERT: D 225 SER cc_start: 0.8510 (m) cc_final: 0.7898 (p) REVERT: D 320 ASN cc_start: 0.7099 (t0) cc_final: 0.6794 (m110) REVERT: D 322 LEU cc_start: 0.7947 (mm) cc_final: 0.7385 (mt) REVERT: D 336 ARG cc_start: 0.7791 (mtm-85) cc_final: 0.7084 (tpt170) REVERT: D 342 GLN cc_start: 0.8432 (mt0) cc_final: 0.7799 (tt0) REVERT: D 352 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6549 (tpt) REVERT: D 354 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7134 (mp0) REVERT: D 391 THR cc_start: 0.8373 (m) cc_final: 0.8124 (p) REVERT: D 393 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7600 (pt0) REVERT: G 45 LYS cc_start: 0.7735 (mtmt) cc_final: 0.7298 (mmpt) REVERT: G 77 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7072 (tt0) REVERT: G 258 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7366 (tp30) REVERT: G 290 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8218 (mp-120) REVERT: G 322 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7271 (mt) REVERT: G 336 ARG cc_start: 0.8168 (mmm-85) cc_final: 0.7510 (tpt170) REVERT: G 337 SER cc_start: 0.8399 (OUTLIER) cc_final: 0.8025 (p) REVERT: G 342 GLN cc_start: 0.7796 (mt0) cc_final: 0.7292 (tt0) outliers start: 38 outliers final: 21 residues processed: 141 average time/residue: 0.3540 time to fit residues: 54.8227 Evaluate side-chains 144 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 352 MET Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 258 GLU Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 337 SER Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain G residue 390 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 114 optimal weight: 0.0670 chunk 49 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 71 optimal weight: 0.0270 chunk 53 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN D 372 HIS G 229 GLN ** G 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.184002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.156296 restraints weight = 10646.768| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.85 r_work: 0.3627 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10395 Z= 0.109 Angle : 0.533 9.605 14157 Z= 0.266 Chirality : 0.046 0.287 1758 Planarity : 0.003 0.031 1767 Dihedral : 4.942 56.153 1641 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.18 % Allowed : 24.40 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.02 (0.23), residues: 1296 helix: 1.43 (0.25), residues: 420 sheet: -0.26 (0.33), residues: 240 loop : -0.82 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 353 TYR 0.013 0.001 TYR D 438 PHE 0.007 0.001 PHE G 253 TRP 0.005 0.001 TRP G 308 HIS 0.003 0.001 HIS G 372 Details of bonding type rmsd covalent geometry : bond 0.00257 (10365) covalent geometry : angle 0.51875 (14085) SS BOND : bond 0.00232 ( 18) SS BOND : angle 1.22012 ( 36) hydrogen bonds : bond 0.03072 ( 393) hydrogen bonds : angle 4.40121 ( 1101) link_NAG-ASN : bond 0.00506 ( 12) link_NAG-ASN : angle 2.19140 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2734.41 seconds wall clock time: 47 minutes 26.12 seconds (2846.12 seconds total)