Starting phenix.real_space_refine on Mon Jul 28 11:59:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dng_27566/07_2025/8dng_27566_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dng_27566/07_2025/8dng_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dng_27566/07_2025/8dng_27566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dng_27566/07_2025/8dng_27566.map" model { file = "/net/cci-nas-00/data/ceres_data/8dng_27566/07_2025/8dng_27566_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dng_27566/07_2025/8dng_27566_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.57, per 1000 atoms: 0.64 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: 2.36 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.84 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: 3.17 Time building geometry restraints manager: 2.84 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: 0.03 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.120 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:13.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.810 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (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 TRP 0.007 0.001 TRP G 308 HIS 0.003 0.001 HIS G 372 PHE 0.008 0.001 PHE A 301 TYR 0.016 0.001 TYR G 248 ARG 0.008 0.000 ARG G 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 12) link_NAG-ASN : angle 2.05681 ( 36) hydrogen bonds : bond 0.19445 ( 393) hydrogen bonds : angle 7.05026 ( 1101) SS BOND : bond 0.00307 ( 18) SS BOND : angle 1.41215 ( 36) covalent geometry : bond 0.00370 (10365) covalent geometry : angle 0.60900 (14085) *********************** 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 : 1.077 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: 0.7835 (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: 0.7836 time to fit residues: 185.9522 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 : 1.021 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 chunk 61 optimal weight: 0.0770 chunk 75 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.189948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.162796 restraints weight = 10471.823| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.80 r_work: 0.3675 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10395 Z= 0.135 Angle : 0.620 11.143 14157 Z= 0.316 Chirality : 0.048 0.270 1758 Planarity : 0.004 0.038 1767 Dihedral : 6.205 57.226 1659 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.55 % Allowed : 19.85 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.23), residues: 1296 helix: 1.76 (0.26), residues: 411 sheet: 0.38 (0.31), residues: 273 loop : -0.96 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 308 HIS 0.002 0.001 HIS D 102 PHE 0.012 0.001 PHE G 253 TYR 0.016 0.001 TYR D 438 ARG 0.006 0.001 ARG G 375 Details of bonding type rmsd link_NAG-ASN : bond 0.00851 ( 12) link_NAG-ASN : angle 2.29835 ( 36) hydrogen bonds : bond 0.03926 ( 393) hydrogen bonds : angle 5.09495 ( 1101) SS BOND : bond 0.00642 ( 18) SS BOND : angle 1.44763 ( 36) covalent geometry : bond 0.00304 (10365) covalent geometry : angle 0.60630 (14085) *********************** 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 : 1.152 Fit side-chains REVERT: A 45 LYS cc_start: 0.7824 (mtmt) cc_final: 0.7053 (mmpt) REVERT: A 77 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7234 (tt0) REVERT: A 197 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.6228 (tt) REVERT: A 220 ASP cc_start: 0.7541 (p0) cc_final: 0.6934 (m-30) REVERT: A 226 MET cc_start: 0.8458 (ttm) cc_final: 0.8223 (ttm) REVERT: A 320 ASN cc_start: 0.7439 (t0) cc_final: 0.7108 (m110) REVERT: A 322 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7225 (mt) REVERT: D 45 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7341 (mtpt) REVERT: D 138 MET cc_start: 0.6683 (ttp) cc_final: 0.5545 (tpp) REVERT: D 189 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.6505 (mtmt) REVERT: D 320 ASN cc_start: 0.7280 (t0) cc_final: 0.6939 (m110) REVERT: D 322 LEU cc_start: 0.7939 (mm) cc_final: 0.7465 (mt) REVERT: D 325 ASN cc_start: 0.7942 (m-40) cc_final: 0.7475 (t0) REVERT: D 388 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8261 (mm) REVERT: D 391 THR cc_start: 0.8464 (m) cc_final: 0.8181 (t) REVERT: G 45 LYS cc_start: 0.7880 (mtmt) cc_final: 0.7205 (mmpt) REVERT: G 77 GLU cc_start: 0.7556 (mm-30) cc_final: 0.6990 (tt0) REVERT: G 290 GLN cc_start: 0.8414 (mm-40) cc_final: 0.8187 (mp10) REVERT: G 322 LEU cc_start: 0.7913 (mm) cc_final: 0.7471 (mt) REVERT: G 337 SER cc_start: 0.8460 (t) cc_final: 0.8232 (p) REVERT: G 342 GLN cc_start: 0.7747 (mt0) cc_final: 0.7180 (tt0) REVERT: G 371 SER cc_start: 0.7683 (OUTLIER) cc_final: 0.7189 (p) outliers start: 53 outliers final: 15 residues processed: 165 average time/residue: 0.9284 time to fit residues: 169.7732 Evaluate side-chains 128 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 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 334 THR 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 82 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 342 GLN G 229 GLN G 303 ASN G 468 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.185797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.158655 restraints weight = 10648.050| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.81 r_work: 0.3649 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10395 Z= 0.144 Angle : 0.589 10.348 14157 Z= 0.297 Chirality : 0.047 0.276 1758 Planarity : 0.003 0.037 1767 Dihedral : 5.519 56.357 1643 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.38 % Allowed : 20.62 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.23), residues: 1296 helix: 1.56 (0.25), residues: 411 sheet: 0.11 (0.32), residues: 258 loop : -0.88 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 308 HIS 0.003 0.001 HIS G 372 PHE 0.008 0.001 PHE G 235 TYR 0.013 0.001 TYR D 275 ARG 0.004 0.001 ARG G 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00591 ( 12) link_NAG-ASN : angle 2.29818 ( 36) hydrogen bonds : bond 0.03797 ( 393) hydrogen bonds : angle 4.78679 ( 1101) SS BOND : bond 0.00501 ( 18) SS BOND : angle 1.51143 ( 36) covalent geometry : bond 0.00338 (10365) covalent geometry : angle 0.57381 (14085) *********************** 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 180 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 129 time to evaluate : 1.513 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8082 (mttm) cc_final: 0.7835 (mttm) REVERT: A 45 LYS cc_start: 0.7821 (mtmt) cc_final: 0.7051 (mmpt) REVERT: A 77 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7225 (tt0) REVERT: A 197 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.6106 (tt) REVERT: A 220 ASP cc_start: 0.7606 (p0) cc_final: 0.6999 (m-30) REVERT: A 261 SER cc_start: 0.8827 (OUTLIER) cc_final: 0.8555 (m) REVERT: A 320 ASN cc_start: 0.7391 (t0) cc_final: 0.6994 (m110) REVERT: A 322 LEU cc_start: 0.7655 (mm) cc_final: 0.7237 (mt) REVERT: A 342 GLN cc_start: 0.8137 (mt0) cc_final: 0.7548 (tt0) REVERT: A 371 SER cc_start: 0.7794 (OUTLIER) cc_final: 0.7222 (p) REVERT: D 138 MET cc_start: 0.6575 (ttp) cc_final: 0.5414 (tpp) REVERT: D 320 ASN cc_start: 0.7303 (t0) cc_final: 0.6952 (m110) REVERT: D 322 LEU cc_start: 0.8011 (mm) cc_final: 0.7544 (mt) REVERT: D 325 ASN cc_start: 0.7979 (m-40) cc_final: 0.7483 (t0) REVERT: D 337 SER cc_start: 0.8709 (OUTLIER) cc_final: 0.8503 (p) REVERT: D 391 THR cc_start: 0.8549 (m) cc_final: 0.8239 (t) REVERT: G 45 LYS cc_start: 0.7826 (mtmt) cc_final: 0.7210 (mmpt) REVERT: G 77 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7008 (tt0) REVERT: G 290 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8202 (mp10) REVERT: G 322 LEU cc_start: 0.7907 (mm) cc_final: 0.7484 (mt) REVERT: G 325 ASN cc_start: 0.7899 (m-40) cc_final: 0.7510 (m110) REVERT: G 336 ARG cc_start: 0.8060 (mmm-85) cc_final: 0.7393 (tpt170) REVERT: G 337 SER cc_start: 0.8464 (t) cc_final: 0.8185 (p) REVERT: G 342 GLN cc_start: 0.7848 (mt0) cc_final: 0.7301 (tt0) REVERT: G 362 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7267 (mttp) REVERT: G 371 SER cc_start: 0.7592 (OUTLIER) cc_final: 0.7078 (p) outliers start: 51 outliers final: 21 residues processed: 170 average time/residue: 1.1323 time to fit residues: 211.2690 Evaluate side-chains 140 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 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 76 MET Chi-restraints excluded: chain D residue 102 HIS 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 328 ILE Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain G residue 362 LYS 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 105 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 7 optimal weight: 0.3980 chunk 4 optimal weight: 0.1980 chunk 65 optimal weight: 0.3980 chunk 119 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 G 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.188574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.161018 restraints weight = 10546.897| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.85 r_work: 0.3669 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10395 Z= 0.106 Angle : 0.551 13.500 14157 Z= 0.276 Chirality : 0.046 0.279 1758 Planarity : 0.003 0.034 1767 Dihedral : 5.468 56.174 1643 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.12 % Allowed : 20.79 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.23), residues: 1296 helix: 1.70 (0.26), residues: 411 sheet: 0.18 (0.33), residues: 240 loop : -0.79 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 308 HIS 0.005 0.001 HIS A 372 PHE 0.007 0.001 PHE A 376 TYR 0.016 0.001 TYR D 438 ARG 0.003 0.000 ARG D 375 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 12) link_NAG-ASN : angle 2.65365 ( 36) hydrogen bonds : bond 0.03248 ( 393) hydrogen bonds : angle 4.55274 ( 1101) SS BOND : bond 0.00283 ( 18) SS BOND : angle 1.24926 ( 36) covalent geometry : bond 0.00239 (10365) covalent geometry : angle 0.53186 (14085) *********************** 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 173 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 time to evaluate : 1.140 Fit side-chains REVERT: A 32 LYS cc_start: 0.8082 (mttm) cc_final: 0.7854 (mttm) REVERT: A 45 LYS cc_start: 0.7842 (mtmt) cc_final: 0.7042 (mmtt) REVERT: A 77 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7212 (tt0) REVERT: A 197 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.6148 (tt) REVERT: A 220 ASP cc_start: 0.7567 (p0) cc_final: 0.6931 (m-30) REVERT: A 261 SER cc_start: 0.8813 (OUTLIER) cc_final: 0.8550 (m) REVERT: A 320 ASN cc_start: 0.7322 (t0) cc_final: 0.6954 (m110) REVERT: A 322 LEU cc_start: 0.7658 (mm) cc_final: 0.7272 (mt) REVERT: A 342 GLN cc_start: 0.8126 (mt0) cc_final: 0.7556 (tt0) REVERT: A 371 SER cc_start: 0.7779 (OUTLIER) cc_final: 0.7214 (p) REVERT: D 45 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7128 (mmtt) REVERT: D 56 ASP cc_start: 0.7003 (OUTLIER) cc_final: 0.6790 (t70) REVERT: D 138 MET cc_start: 0.6491 (ttp) cc_final: 0.5346 (tpp) REVERT: D 192 CYS cc_start: 0.6124 (OUTLIER) cc_final: 0.5583 (m) REVERT: D 320 ASN cc_start: 0.7186 (t0) cc_final: 0.6874 (m110) REVERT: D 322 LEU cc_start: 0.7999 (mm) cc_final: 0.7502 (mt) REVERT: D 325 ASN cc_start: 0.7895 (m-40) cc_final: 0.7449 (t0) REVERT: D 342 GLN cc_start: 0.8413 (mt0) cc_final: 0.7753 (pt0) REVERT: D 391 THR cc_start: 0.8458 (m) cc_final: 0.8168 (t) REVERT: D 393 GLN cc_start: 0.7786 (pt0) cc_final: 0.7542 (pt0) REVERT: G 45 LYS cc_start: 0.7762 (mtmt) cc_final: 0.7215 (mmpt) REVERT: G 77 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7004 (tt0) REVERT: G 289 GLN cc_start: 0.8413 (mm110) cc_final: 0.8169 (mp10) REVERT: G 290 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8190 (mp10) REVERT: G 322 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7494 (mt) REVERT: G 325 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.7261 (m110) REVERT: G 336 ARG cc_start: 0.8075 (mmm-85) cc_final: 0.7425 (tpt170) REVERT: G 337 SER cc_start: 0.8466 (t) cc_final: 0.8159 (p) REVERT: G 342 GLN cc_start: 0.7826 (mt0) cc_final: 0.7295 (tt0) REVERT: G 362 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.7190 (mttp) REVERT: G 371 SER cc_start: 0.7554 (OUTLIER) cc_final: 0.7051 (p) outliers start: 48 outliers final: 19 residues processed: 161 average time/residue: 0.8438 time to fit residues: 151.0641 Evaluate side-chains 146 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 197 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 355 CYS 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 449 VAL Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 102 HIS 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 421 VAL Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 325 ASN Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 362 LYS Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain G residue 390 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 93 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 4 optimal weight: 0.0020 chunk 109 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- 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 D 229 GLN G 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.183986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.156852 restraints weight = 10510.607| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.80 r_work: 0.3627 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10395 Z= 0.136 Angle : 0.561 9.743 14157 Z= 0.281 Chirality : 0.047 0.279 1758 Planarity : 0.003 0.034 1767 Dihedral : 5.410 56.574 1643 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.90 % Allowed : 20.19 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.23), residues: 1296 helix: 1.56 (0.26), residues: 411 sheet: -0.08 (0.31), residues: 258 loop : -0.79 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 308 HIS 0.002 0.001 HIS A 372 PHE 0.009 0.001 PHE G 235 TYR 0.014 0.001 TYR A 275 ARG 0.002 0.000 ARG G 353 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 12) link_NAG-ASN : angle 2.33946 ( 36) hydrogen bonds : bond 0.03301 ( 393) hydrogen bonds : angle 4.60519 ( 1101) SS BOND : bond 0.00247 ( 18) SS BOND : angle 1.35295 ( 36) covalent geometry : bond 0.00324 (10365) covalent geometry : angle 0.54557 (14085) *********************** 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 178 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 121 time to evaluate : 1.220 Fit side-chains REVERT: A 32 LYS cc_start: 0.8065 (mttm) cc_final: 0.7849 (mttm) REVERT: A 45 LYS cc_start: 0.7838 (mtmt) cc_final: 0.7029 (mmtt) REVERT: A 77 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7234 (tt0) REVERT: A 146 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7519 (mttp) REVERT: A 197 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.6029 (tt) REVERT: A 220 ASP cc_start: 0.7637 (p0) cc_final: 0.7042 (m-30) REVERT: A 261 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8515 (m) REVERT: A 320 ASN cc_start: 0.7412 (t0) cc_final: 0.7132 (m110) REVERT: A 322 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7271 (mt) REVERT: A 342 GLN cc_start: 0.8201 (mt0) cc_final: 0.7597 (tt0) REVERT: A 371 SER cc_start: 0.7798 (OUTLIER) cc_final: 0.7202 (p) REVERT: D 56 ASP cc_start: 0.7019 (OUTLIER) cc_final: 0.6796 (t70) REVERT: D 138 MET cc_start: 0.6459 (ttp) cc_final: 0.5698 (tpp) REVERT: D 175 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7412 (mp) REVERT: D 189 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.6648 (mtmt) REVERT: D 192 CYS cc_start: 0.6303 (OUTLIER) cc_final: 0.5685 (m) REVERT: D 320 ASN cc_start: 0.7161 (t0) cc_final: 0.6844 (m110) REVERT: D 322 LEU cc_start: 0.8015 (mm) cc_final: 0.7520 (mt) REVERT: D 325 ASN cc_start: 0.8023 (m-40) cc_final: 0.7684 (t0) REVERT: D 393 GLN cc_start: 0.7833 (pt0) cc_final: 0.7578 (pt0) REVERT: G 45 LYS cc_start: 0.7801 (mtmt) cc_final: 0.7276 (mmpt) REVERT: G 77 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7037 (tt0) REVERT: G 197 LEU cc_start: 0.6390 (OUTLIER) cc_final: 0.6079 (tt) REVERT: G 290 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8158 (mp10) REVERT: G 322 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7393 (mt) REVERT: G 325 ASN cc_start: 0.7886 (OUTLIER) cc_final: 0.7493 (m110) REVERT: G 336 ARG cc_start: 0.8118 (mmm-85) cc_final: 0.7455 (tpt170) REVERT: G 337 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.8141 (p) REVERT: G 342 GLN cc_start: 0.7861 (mt0) cc_final: 0.7328 (tt0) outliers start: 57 outliers final: 21 residues processed: 164 average time/residue: 1.4710 time to fit residues: 266.4549 Evaluate side-chains 148 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 261 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 371 SER 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 56 ASP 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 334 THR 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 169 VAL Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 325 ASN 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 390 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 113 optimal weight: 2.9990 chunk 15 optimal weight: 0.0870 chunk 97 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 56 optimal weight: 0.0050 chunk 79 optimal weight: 0.9990 chunk 22 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.2950 ------------------------------------------------------------------------------- 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 D 229 GLN G 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.185940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.158520 restraints weight = 10628.580| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.85 r_work: 0.3652 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10395 Z= 0.100 Angle : 0.522 9.556 14157 Z= 0.264 Chirality : 0.046 0.279 1758 Planarity : 0.003 0.034 1767 Dihedral : 5.244 55.959 1643 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.78 % Allowed : 21.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.23), residues: 1296 helix: 1.69 (0.25), residues: 420 sheet: 0.04 (0.33), residues: 240 loop : -0.76 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 308 HIS 0.004 0.001 HIS A 372 PHE 0.007 0.001 PHE A 376 TYR 0.015 0.001 TYR D 438 ARG 0.002 0.000 ARG G 353 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 12) link_NAG-ASN : angle 2.28002 ( 36) hydrogen bonds : bond 0.03013 ( 393) hydrogen bonds : angle 4.42486 ( 1101) SS BOND : bond 0.00358 ( 18) SS BOND : angle 1.14489 ( 36) covalent geometry : bond 0.00225 (10365) covalent geometry : angle 0.50743 (14085) *********************** 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 174 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 130 time to evaluate : 1.188 Fit side-chains REVERT: A 32 LYS cc_start: 0.8047 (mttm) cc_final: 0.7836 (mttm) REVERT: A 45 LYS cc_start: 0.7750 (mtmt) cc_final: 0.7064 (mmtt) REVERT: A 77 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7192 (tt0) REVERT: A 197 LEU cc_start: 0.6449 (OUTLIER) cc_final: 0.6139 (tt) REVERT: A 220 ASP cc_start: 0.7662 (p0) cc_final: 0.7044 (m-30) REVERT: A 261 SER cc_start: 0.8806 (OUTLIER) cc_final: 0.8507 (m) REVERT: A 320 ASN cc_start: 0.7380 (t0) cc_final: 0.7091 (m110) REVERT: A 322 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7287 (mt) REVERT: A 342 GLN cc_start: 0.8189 (mt0) cc_final: 0.7594 (tt0) REVERT: A 371 SER cc_start: 0.7822 (OUTLIER) cc_final: 0.7245 (p) REVERT: D 56 ASP cc_start: 0.6979 (OUTLIER) cc_final: 0.6720 (t70) REVERT: D 138 MET cc_start: 0.6296 (ttp) cc_final: 0.5176 (tpp) REVERT: D 189 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.6653 (mtmt) REVERT: D 192 CYS cc_start: 0.6003 (OUTLIER) cc_final: 0.5476 (m) REVERT: D 197 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6211 (tt) REVERT: D 320 ASN cc_start: 0.7121 (t0) cc_final: 0.6826 (m110) REVERT: D 322 LEU cc_start: 0.8021 (mm) cc_final: 0.7523 (mt) REVERT: D 325 ASN cc_start: 0.7886 (m-40) cc_final: 0.7539 (t0) REVERT: D 336 ARG cc_start: 0.7892 (mtm-85) cc_final: 0.7081 (tpt170) REVERT: D 348 MET cc_start: 0.8204 (ttm) cc_final: 0.7792 (ttp) REVERT: D 354 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7210 (mp0) REVERT: D 391 THR cc_start: 0.8462 (m) cc_final: 0.8195 (p) REVERT: D 393 GLN cc_start: 0.7822 (pt0) cc_final: 0.7581 (pt0) REVERT: G 45 LYS cc_start: 0.7730 (mtmt) cc_final: 0.7228 (mmpt) REVERT: G 77 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7042 (tt0) REVERT: G 290 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8182 (mp10) REVERT: G 322 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7402 (mt) REVERT: G 325 ASN cc_start: 0.7635 (OUTLIER) cc_final: 0.7261 (m110) REVERT: G 327 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: G 336 ARG cc_start: 0.8148 (mmm-85) cc_final: 0.7464 (tpt170) REVERT: G 337 SER cc_start: 0.8431 (t) cc_final: 0.8085 (p) REVERT: G 342 GLN cc_start: 0.7820 (mt0) cc_final: 0.7333 (tt0) REVERT: G 445 ILE cc_start: 0.5340 (OUTLIER) cc_final: 0.4972 (pp) outliers start: 44 outliers final: 24 residues processed: 163 average time/residue: 0.9401 time to fit residues: 168.7352 Evaluate side-chains 152 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 1.357 ------------------------------------------------------------------------------- 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 261 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 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 56 ASP Chi-restraints excluded: chain D residue 69 SER 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 192 CYS Chi-restraints excluded: chain D residue 197 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 421 VAL Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 325 ASN Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 327 GLU 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 390 VAL Chi-restraints excluded: chain G residue 445 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.0770 chunk 42 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 79 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 84 optimal weight: 0.0970 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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 D 229 GLN G 229 GLN G 302 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.187985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.160822 restraints weight = 10698.337| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.84 r_work: 0.3657 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2557 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= 0.101 Angle : 0.525 9.544 14157 Z= 0.263 Chirality : 0.046 0.278 1758 Planarity : 0.003 0.032 1767 Dihedral : 5.136 56.227 1643 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.81 % Allowed : 21.56 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.23), residues: 1296 helix: 1.73 (0.25), residues: 420 sheet: 0.09 (0.33), residues: 240 loop : -0.74 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 308 HIS 0.003 0.001 HIS A 372 PHE 0.006 0.001 PHE A 376 TYR 0.014 0.001 TYR D 438 ARG 0.006 0.000 ARG G 375 Details of bonding type rmsd link_NAG-ASN : bond 0.00557 ( 12) link_NAG-ASN : angle 2.24334 ( 36) hydrogen bonds : bond 0.02978 ( 393) hydrogen bonds : angle 4.36465 ( 1101) SS BOND : bond 0.00260 ( 18) SS BOND : angle 1.05958 ( 36) covalent geometry : bond 0.00231 (10365) covalent geometry : angle 0.51140 (14085) *********************** 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: 56 poor density : 120 time to evaluate : 1.117 Fit side-chains REVERT: A 45 LYS cc_start: 0.7748 (mtmt) cc_final: 0.7091 (mmtt) REVERT: A 77 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7183 (tt0) REVERT: A 197 LEU cc_start: 0.6450 (OUTLIER) cc_final: 0.6140 (tt) REVERT: A 220 ASP cc_start: 0.7670 (p0) cc_final: 0.7013 (t0) REVERT: A 261 SER cc_start: 0.8806 (OUTLIER) cc_final: 0.8517 (m) REVERT: A 320 ASN cc_start: 0.7381 (t0) cc_final: 0.7092 (m110) REVERT: A 322 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7176 (mt) REVERT: A 342 GLN cc_start: 0.8217 (mt0) cc_final: 0.7606 (tt0) REVERT: A 371 SER cc_start: 0.7711 (OUTLIER) cc_final: 0.7121 (p) REVERT: D 138 MET cc_start: 0.6184 (ttp) cc_final: 0.5057 (tpp) REVERT: D 140 ASN cc_start: 0.6626 (t0) cc_final: 0.6190 (m110) REVERT: D 189 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.6655 (mtmt) REVERT: D 192 CYS cc_start: 0.6040 (OUTLIER) cc_final: 0.5456 (m) REVERT: D 320 ASN cc_start: 0.7060 (t0) cc_final: 0.6791 (m110) REVERT: D 322 LEU cc_start: 0.8011 (mm) cc_final: 0.7507 (mt) REVERT: D 325 ASN cc_start: 0.7861 (m-40) cc_final: 0.7528 (t0) REVERT: D 336 ARG cc_start: 0.7933 (mtm-85) cc_final: 0.7098 (tpt170) REVERT: D 342 GLN cc_start: 0.8409 (mt0) cc_final: 0.7838 (tt0) REVERT: D 348 MET cc_start: 0.8198 (ttm) cc_final: 0.7795 (ttp) REVERT: D 354 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7124 (mp0) REVERT: D 391 THR cc_start: 0.8438 (m) cc_final: 0.8185 (p) REVERT: D 393 GLN cc_start: 0.7797 (pt0) cc_final: 0.7552 (pt0) REVERT: G 45 LYS cc_start: 0.7717 (mtmt) cc_final: 0.7222 (mmpt) REVERT: G 77 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7023 (tt0) REVERT: G 103 ASP cc_start: 0.6850 (m-30) cc_final: 0.6639 (m-30) REVERT: G 290 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8206 (mp10) REVERT: G 322 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7394 (mt) REVERT: G 325 ASN cc_start: 0.7593 (OUTLIER) cc_final: 0.7216 (m110) REVERT: G 336 ARG cc_start: 0.8158 (mmm-85) cc_final: 0.7450 (tpt170) REVERT: G 337 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.8090 (p) REVERT: G 342 GLN cc_start: 0.7841 (mt0) cc_final: 0.7383 (tt0) REVERT: G 445 ILE cc_start: 0.5093 (OUTLIER) cc_final: 0.4813 (pp) outliers start: 56 outliers final: 27 residues processed: 160 average time/residue: 0.8227 time to fit residues: 146.1614 Evaluate side-chains 151 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 190 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 261 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 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 69 SER Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 169 VAL 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 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 404 SER 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 322 LEU Chi-restraints excluded: chain G residue 325 ASN 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 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 120 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN D 100 ASN D 229 GLN G 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.184761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.157484 restraints weight = 10554.776| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.83 r_work: 0.3635 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10395 Z= 0.124 Angle : 0.554 9.553 14157 Z= 0.276 Chirality : 0.047 0.280 1758 Planarity : 0.003 0.033 1767 Dihedral : 5.212 56.357 1643 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.12 % Allowed : 22.16 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.23), residues: 1296 helix: 1.59 (0.25), residues: 420 sheet: 0.01 (0.33), residues: 240 loop : -0.79 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 308 HIS 0.003 0.001 HIS A 372 PHE 0.007 0.001 PHE G 301 TYR 0.019 0.001 TYR A 135 ARG 0.006 0.000 ARG G 375 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 12) link_NAG-ASN : angle 2.26347 ( 36) hydrogen bonds : bond 0.03210 ( 393) hydrogen bonds : angle 4.49056 ( 1101) SS BOND : bond 0.00263 ( 18) SS BOND : angle 1.40396 ( 36) covalent geometry : bond 0.00297 (10365) covalent geometry : angle 0.53927 (14085) *********************** 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 165 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 117 time to evaluate : 1.029 Fit side-chains REVERT: A 45 LYS cc_start: 0.7777 (mtmt) cc_final: 0.7124 (mmtt) REVERT: A 77 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7235 (tt0) REVERT: A 146 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7479 (mttp) REVERT: A 197 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6188 (tt) REVERT: A 220 ASP cc_start: 0.7694 (p0) cc_final: 0.7065 (m-30) REVERT: A 261 SER cc_start: 0.8816 (OUTLIER) cc_final: 0.8517 (m) REVERT: A 320 ASN cc_start: 0.7406 (t0) cc_final: 0.7114 (m110) REVERT: A 322 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7230 (mt) REVERT: A 342 GLN cc_start: 0.8252 (mt0) cc_final: 0.7646 (tt0) REVERT: A 371 SER cc_start: 0.7778 (OUTLIER) cc_final: 0.7175 (p) REVERT: D 138 MET cc_start: 0.6171 (ttp) cc_final: 0.5067 (tpp) REVERT: D 140 ASN cc_start: 0.6650 (t0) cc_final: 0.6223 (m110) REVERT: D 189 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.6649 (mtmt) REVERT: D 192 CYS cc_start: 0.6019 (OUTLIER) cc_final: 0.5455 (m) REVERT: D 320 ASN cc_start: 0.7008 (t0) cc_final: 0.6739 (m110) REVERT: D 322 LEU cc_start: 0.8063 (mm) cc_final: 0.7555 (mt) REVERT: D 325 ASN cc_start: 0.7983 (m-40) cc_final: 0.7688 (t0) REVERT: D 336 ARG cc_start: 0.7903 (mtm-85) cc_final: 0.7097 (tpt170) REVERT: D 342 GLN cc_start: 0.8433 (mt0) cc_final: 0.7850 (tt0) REVERT: D 354 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7184 (mp0) REVERT: D 391 THR cc_start: 0.8344 (m) cc_final: 0.8094 (p) REVERT: D 393 GLN cc_start: 0.7844 (pt0) cc_final: 0.7590 (pt0) REVERT: G 45 LYS cc_start: 0.7753 (mtmt) cc_final: 0.7276 (mmpt) REVERT: G 77 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7017 (tt0) REVERT: G 290 GLN cc_start: 0.8462 (mm-40) cc_final: 0.8209 (mp10) REVERT: G 322 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7410 (mt) REVERT: G 325 ASN cc_start: 0.7696 (OUTLIER) cc_final: 0.7329 (m110) REVERT: G 336 ARG cc_start: 0.8156 (mmm-85) cc_final: 0.7496 (tpt170) REVERT: G 337 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.8085 (p) REVERT: G 342 GLN cc_start: 0.7859 (mt0) cc_final: 0.7410 (tt0) REVERT: G 445 ILE cc_start: 0.5115 (OUTLIER) cc_final: 0.4902 (pp) outliers start: 48 outliers final: 28 residues processed: 153 average time/residue: 1.1915 time to fit residues: 201.0276 Evaluate side-chains 156 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 146 LYS 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 355 CYS Chi-restraints excluded: chain A residue 371 SER 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 76 MET Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 169 VAL 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 334 THR Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 404 SER 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 322 LEU Chi-restraints excluded: chain G residue 325 ASN 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 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 18 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN G 229 GLN ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.183103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.155209 restraints weight = 10664.279| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.87 r_work: 0.3616 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10395 Z= 0.141 Angle : 0.574 9.577 14157 Z= 0.286 Chirality : 0.047 0.284 1758 Planarity : 0.003 0.033 1767 Dihedral : 5.305 56.410 1643 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.12 % Allowed : 22.16 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.22), residues: 1296 helix: 1.44 (0.25), residues: 420 sheet: -0.12 (0.32), residues: 240 loop : -0.84 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 308 HIS 0.003 0.001 HIS A 372 PHE 0.008 0.001 PHE G 301 TYR 0.016 0.001 TYR G 135 ARG 0.004 0.000 ARG G 375 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 12) link_NAG-ASN : angle 2.29124 ( 36) hydrogen bonds : bond 0.03336 ( 393) hydrogen bonds : angle 4.58853 ( 1101) SS BOND : bond 0.00247 ( 18) SS BOND : angle 1.43457 ( 36) covalent geometry : bond 0.00343 (10365) covalent geometry : angle 0.55931 (14085) *********************** 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 169 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 121 time to evaluate : 1.164 Fit side-chains REVERT: A 45 LYS cc_start: 0.7738 (mtmt) cc_final: 0.6978 (mmtt) REVERT: A 77 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7140 (tt0) REVERT: A 197 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.5993 (tt) REVERT: A 220 ASP cc_start: 0.7717 (p0) cc_final: 0.6880 (m-30) REVERT: A 261 SER cc_start: 0.8833 (OUTLIER) cc_final: 0.8518 (m) REVERT: A 320 ASN cc_start: 0.7451 (t0) cc_final: 0.7066 (m110) REVERT: A 322 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7069 (mt) REVERT: A 336 ARG cc_start: 0.7916 (mtm-85) cc_final: 0.7227 (tpt170) REVERT: A 371 SER cc_start: 0.7662 (OUTLIER) cc_final: 0.7053 (p) REVERT: D 138 MET cc_start: 0.6103 (ttp) cc_final: 0.5420 (tpp) REVERT: D 140 ASN cc_start: 0.6747 (t0) cc_final: 0.6220 (m110) REVERT: D 175 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7322 (mp) REVERT: D 189 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.6582 (mtmt) REVERT: D 192 CYS cc_start: 0.5941 (OUTLIER) cc_final: 0.5369 (m) REVERT: D 322 LEU cc_start: 0.7938 (mm) cc_final: 0.7397 (mt) REVERT: D 336 ARG cc_start: 0.7844 (mtm-85) cc_final: 0.7064 (tpt170) REVERT: D 342 GLN cc_start: 0.8425 (mt0) cc_final: 0.7709 (tt0) REVERT: D 354 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7201 (mp0) REVERT: D 391 THR cc_start: 0.8363 (m) cc_final: 0.8102 (p) REVERT: D 393 GLN cc_start: 0.7797 (pt0) cc_final: 0.7554 (pt0) REVERT: G 45 LYS cc_start: 0.7736 (mtmt) cc_final: 0.7219 (mmpt) REVERT: G 77 GLU cc_start: 0.7483 (mm-30) cc_final: 0.6942 (tt0) REVERT: G 175 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7620 (mp) REVERT: G 290 GLN cc_start: 0.8414 (mm-40) cc_final: 0.8166 (mp10) REVERT: G 322 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7341 (mt) REVERT: G 325 ASN cc_start: 0.7788 (m-40) cc_final: 0.7386 (m110) REVERT: G 336 ARG cc_start: 0.8150 (mmm-85) cc_final: 0.7445 (tpt170) REVERT: G 337 SER cc_start: 0.8449 (OUTLIER) cc_final: 0.8063 (p) REVERT: G 342 GLN cc_start: 0.7902 (mt0) cc_final: 0.7344 (tt0) REVERT: G 445 ILE cc_start: 0.4944 (OUTLIER) cc_final: 0.4717 (pp) outliers start: 48 outliers final: 24 residues processed: 155 average time/residue: 1.0221 time to fit residues: 174.1098 Evaluate side-chains 145 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 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 355 CYS Chi-restraints excluded: chain A residue 371 SER 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 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 334 THR 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 169 VAL Chi-restraints excluded: chain G residue 175 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 64 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 342 GLN D 229 GLN G 229 GLN ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.182931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.155106 restraints weight = 10699.754| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.88 r_work: 0.3613 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10395 Z= 0.138 Angle : 0.570 9.599 14157 Z= 0.285 Chirality : 0.047 0.286 1758 Planarity : 0.003 0.032 1767 Dihedral : 5.294 56.265 1643 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.52 % Allowed : 23.20 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.22), residues: 1296 helix: 1.33 (0.25), residues: 420 sheet: -0.22 (0.32), residues: 240 loop : -0.88 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 308 HIS 0.002 0.001 HIS G 372 PHE 0.007 0.001 PHE G 301 TYR 0.026 0.001 TYR G 135 ARG 0.004 0.000 ARG G 375 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 12) link_NAG-ASN : angle 2.30737 ( 36) hydrogen bonds : bond 0.03328 ( 393) hydrogen bonds : angle 4.60085 ( 1101) SS BOND : bond 0.00267 ( 18) SS BOND : angle 1.38152 ( 36) covalent geometry : bond 0.00332 (10365) covalent geometry : angle 0.55503 (14085) ********************** 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 160 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 1.033 Fit side-chains REVERT: A 45 LYS cc_start: 0.7658 (mtmt) cc_final: 0.6985 (mmtt) REVERT: A 77 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7176 (tt0) REVERT: A 197 LEU cc_start: 0.6404 (OUTLIER) cc_final: 0.6012 (tt) REVERT: A 220 ASP cc_start: 0.7649 (p0) cc_final: 0.7211 (p0) REVERT: A 261 SER cc_start: 0.8884 (OUTLIER) cc_final: 0.8540 (m) REVERT: A 320 ASN cc_start: 0.7489 (t0) cc_final: 0.7078 (m110) REVERT: A 322 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7039 (mt) REVERT: A 336 ARG cc_start: 0.7889 (mtm-85) cc_final: 0.7252 (tpt170) REVERT: A 371 SER cc_start: 0.7638 (OUTLIER) cc_final: 0.6984 (p) REVERT: D 138 MET cc_start: 0.5985 (ttp) cc_final: 0.5371 (tpp) REVERT: D 140 ASN cc_start: 0.6656 (t0) cc_final: 0.6129 (m110) REVERT: D 175 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7321 (mp) REVERT: D 189 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6440 (mtmt) REVERT: D 192 CYS cc_start: 0.5926 (OUTLIER) cc_final: 0.5348 (m) REVERT: D 225 SER cc_start: 0.8565 (m) cc_final: 0.7930 (p) REVERT: D 289 GLN cc_start: 0.8294 (mm110) cc_final: 0.8070 (mm110) REVERT: D 320 ASN cc_start: 0.7094 (t0) cc_final: 0.6762 (m110) REVERT: D 322 LEU cc_start: 0.7912 (mm) cc_final: 0.7360 (mt) REVERT: D 336 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7082 (tpt170) REVERT: D 342 GLN cc_start: 0.8418 (mt0) cc_final: 0.7722 (tt0) REVERT: D 354 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7204 (mp0) REVERT: D 391 THR cc_start: 0.8358 (m) cc_final: 0.8086 (p) REVERT: D 393 GLN cc_start: 0.7792 (pt0) cc_final: 0.7551 (pt0) REVERT: G 45 LYS cc_start: 0.7714 (mtmt) cc_final: 0.7209 (mmpt) REVERT: G 77 GLU cc_start: 0.7475 (mm-30) cc_final: 0.6947 (tt0) REVERT: G 175 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7643 (mp) REVERT: G 290 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8150 (mp10) REVERT: G 322 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7218 (mt) REVERT: G 336 ARG cc_start: 0.8121 (mmm-85) cc_final: 0.7409 (tpt170) REVERT: G 337 SER cc_start: 0.8427 (OUTLIER) cc_final: 0.8030 (p) REVERT: G 342 GLN cc_start: 0.7900 (mt0) cc_final: 0.7321 (tt0) REVERT: G 445 ILE cc_start: 0.5097 (OUTLIER) cc_final: 0.4751 (pp) outliers start: 41 outliers final: 24 residues processed: 151 average time/residue: 1.0525 time to fit residues: 175.2040 Evaluate side-chains 153 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 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 371 SER 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 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 334 THR 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 169 VAL Chi-restraints excluded: chain G residue 175 LEU 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 Chi-restraints excluded: chain G residue 445 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 13 optimal weight: 0.0010 chunk 121 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN G 229 GLN ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.183573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.155818 restraints weight = 10590.751| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.86 r_work: 0.3622 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10395 Z= 0.126 Angle : 0.561 9.605 14157 Z= 0.281 Chirality : 0.047 0.286 1758 Planarity : 0.003 0.031 1767 Dihedral : 5.204 56.180 1643 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.44 % Allowed : 23.28 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1296 helix: 1.37 (0.25), residues: 420 sheet: -0.24 (0.32), residues: 240 loop : -0.86 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 308 HIS 0.003 0.001 HIS A 372 PHE 0.007 0.001 PHE G 301 TYR 0.023 0.001 TYR G 135 ARG 0.011 0.000 ARG G 375 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 12) link_NAG-ASN : angle 2.27509 ( 36) hydrogen bonds : bond 0.03222 ( 393) hydrogen bonds : angle 4.56997 ( 1101) SS BOND : bond 0.00224 ( 18) SS BOND : angle 1.33313 ( 36) covalent geometry : bond 0.00301 (10365) covalent geometry : angle 0.54600 (14085) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8002.46 seconds wall clock time: 144 minutes 58.57 seconds (8698.57 seconds total)