Starting phenix.real_space_refine on Sat Jul 4 16:45:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wby_37427/07_2026/8wby_37427_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wby_37427/07_2026/8wby_37427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wby_37427/07_2026/8wby_37427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wby_37427/07_2026/8wby_37427.map" model { file = "/net/cci-nas-00/data/ceres_data/8wby_37427/07_2026/8wby_37427_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wby_37427/07_2026/8wby_37427_neut.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.080 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: 5 Type Number sf(0) Gaussians S 128 5.16 5 Cl 2 4.86 5 C 14424 2.51 5 N 3556 2.21 5 O 4122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22232 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 4794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4794 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 31, 'TRANS': 573} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 6095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6095 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 35, 'TRANS': 713} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 6095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6095 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 35, 'TRANS': 713} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 4794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4794 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 31, 'TRANS': 573} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 6 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'NAG': 1, 'WM8': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'NAG': 1, 'WM8': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.74, per 1000 atoms: 0.21 Number of scatterers: 22232 At special positions: 0 Unit cell: (136.875, 119.355, 189.435, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 128 16.00 O 4122 8.00 N 3556 7.00 C 14424 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 383 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.05 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.04 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 153 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 383 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM22098 O5 NAG G 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 702 " - " ASN A 258 " " NAG D 702 " - " ASN D 258 " " NAG E 1 " - " ASN B 53 " " NAG F 1 " - " ASN A 368 " " NAG G 1 " - " ASN C 90 " " NAG H 1 " - " ASN B 90 " " NAG I 1 " - " ASN B 103 " " NAG J 1 " - " ASN C 53 " " NAG K 1 " - " ASN C 432 " " NAG L 1 " - " ASN C 690 " " NAG M 1 " - " ASN C 103 " " NAG N 1 " - " ASN D 368 " " NAG O 1 " - " ASN B 690 " " NAG P 1 " - " ASN B 432 " " NAG S 1 " - " ASN B 322 " " NAG T 1 " - " ASN C 322 " Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 1.0 seconds 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5080 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 8 sheets defined 67.5% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 37 through 55 removed outlier: 3.753A pdb=" N VAL A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 67 removed outlier: 4.100A pdb=" N GLY A 66 " --> pdb=" O CYS A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 89 removed outlier: 4.104A pdb=" N PHE A 74 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ILE A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 91 through 97 Processing helix chain 'A' and resid 100 through 107 removed outlier: 4.514A pdb=" N TRP A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 142 removed outlier: 3.604A pdb=" N TYR A 128 " --> pdb=" O MET A 124 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.940A pdb=" N ASP A 152 " --> pdb=" O PRO A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 169 Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 194 through 212 Processing helix chain 'A' and resid 215 through 227 removed outlier: 3.904A pdb=" N LYS A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 243 removed outlier: 3.654A pdb=" N THR A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 256 removed outlier: 3.775A pdb=" N VAL A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 264 removed outlier: 3.672A pdb=" N LEU A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 280 Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 299 through 349 removed outlier: 3.639A pdb=" N VAL A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 371 removed outlier: 3.929A pdb=" N MET A 363 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A 371 " --> pdb=" O CYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 412 through 446 Proline residue: A 442 - end of helix Processing helix chain 'A' and resid 454 through 470 removed outlier: 3.756A pdb=" N GLY A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 475 Processing helix chain 'A' and resid 477 through 487 removed outlier: 3.946A pdb=" N SER A 487 " --> pdb=" O SER A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 508 removed outlier: 3.864A pdb=" N MET A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE A 503 " --> pdb=" O PHE A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 522 Processing helix chain 'A' and resid 527 through 536 removed outlier: 3.604A pdb=" N GLN A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 553 removed outlier: 3.657A pdb=" N LEU A 541 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A 543 " --> pdb=" O PRO A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 581 No H-bonds generated for 'chain 'A' and resid 579 through 581' Processing helix chain 'A' and resid 582 through 590 removed outlier: 3.664A pdb=" N VAL A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 587 " --> pdb=" O TYR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 608 removed outlier: 4.026A pdb=" N THR A 596 " --> pdb=" O VAL A 592 " (cutoff:3.500A) Proline residue: A 598 - end of helix removed outlier: 4.303A pdb=" N ALA A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 53 removed outlier: 3.728A pdb=" N GLU B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASP B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 79 removed outlier: 4.128A pdb=" N GLN B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.968A pdb=" N GLU B 87 " --> pdb=" O PRO B 84 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE B 88 " --> pdb=" O LEU B 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 84 through 88' Processing helix chain 'B' and resid 90 through 100 removed outlier: 3.511A pdb=" N LYS B 94 " --> pdb=" O ASN B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 129 Processing helix chain 'B' and resid 147 through 155 Processing helix chain 'B' and resid 157 through 193 Proline residue: B 178 - end of helix Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.537A pdb=" N TYR B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 249 removed outlier: 4.020A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 232 " --> pdb=" O HIS B 228 " (cutoff:3.500A) Proline residue: B 235 - end of helix removed outlier: 3.632A pdb=" N MET B 249 " --> pdb=" O ARG B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 275 through 281 removed outlier: 4.211A pdb=" N SER B 280 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 300 removed outlier: 3.592A pdb=" N MET B 297 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 298 " --> pdb=" O THR B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 318 removed outlier: 3.625A pdb=" N LYS B 309 " --> pdb=" O GLN B 305 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 removed outlier: 3.703A pdb=" N TRP B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN B 330 " --> pdb=" O GLY B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 385 removed outlier: 3.981A pdb=" N TYR B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'B' and resid 399 through 413 removed outlier: 3.502A pdb=" N ALA B 403 " --> pdb=" O GLY B 399 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 422 removed outlier: 3.547A pdb=" N GLY B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 447 removed outlier: 3.545A pdb=" N GLU B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 465 Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 498 through 502 Processing helix chain 'B' and resid 503 through 508 removed outlier: 3.715A pdb=" N SER B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 534 removed outlier: 3.514A pdb=" N THR B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 559 removed outlier: 3.694A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 572 Processing helix chain 'B' and resid 581 through 588 Processing helix chain 'B' and resid 588 through 599 Processing helix chain 'B' and resid 623 through 629 removed outlier: 3.564A pdb=" N ALA B 627 " --> pdb=" O SER B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 658 Processing helix chain 'B' and resid 696 through 714 removed outlier: 3.518A pdb=" N VAL B 700 " --> pdb=" O PRO B 696 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N SER B 709 " --> pdb=" O ARG B 705 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ARG B 710 " --> pdb=" O MET B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 767 removed outlier: 3.778A pdb=" N ILE B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 53 removed outlier: 4.257A pdb=" N ASP C 38 " --> pdb=" O HIS C 34 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 58 removed outlier: 3.529A pdb=" N ASN C 58 " --> pdb=" O THR C 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 55 through 58' Processing helix chain 'C' and resid 59 through 79 removed outlier: 3.967A pdb=" N ASN C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA C 65 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS C 68 " --> pdb=" O ASN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.512A pdb=" N SER C 106 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL C 107 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 Processing helix chain 'C' and resid 147 through 155 Processing helix chain 'C' and resid 157 through 193 Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.552A pdb=" N TYR C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 252 removed outlier: 3.768A pdb=" N LEU C 222 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C 232 " --> pdb=" O HIS C 228 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 3.822A pdb=" N ASN C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 251 " --> pdb=" O LYS C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 295 through 300 removed outlier: 4.076A pdb=" N ASP C 299 " --> pdb=" O ASP C 295 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C 300 " --> pdb=" O ALA C 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 295 through 300' Processing helix chain 'C' and resid 303 through 318 removed outlier: 4.075A pdb=" N ILE C 307 " --> pdb=" O ASP C 303 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 330 removed outlier: 3.661A pdb=" N TRP C 328 " --> pdb=" O THR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 385 removed outlier: 3.547A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR C 385 " --> pdb=" O TYR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 393 Processing helix chain 'C' and resid 399 through 413 removed outlier: 3.545A pdb=" N ALA C 403 " --> pdb=" O GLY C 399 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER C 409 " --> pdb=" O GLY C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 422 removed outlier: 3.590A pdb=" N GLY C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 447 removed outlier: 3.582A pdb=" N GLU C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 466 Processing helix chain 'C' and resid 472 through 484 Processing helix chain 'C' and resid 498 through 502 Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 512 through 534 removed outlier: 4.206A pdb=" N TYR C 516 " --> pdb=" O PHE C 512 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C 520 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE C 523 " --> pdb=" O THR C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 removed outlier: 3.508A pdb=" N LYS C 541 " --> pdb=" O PRO C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 559 removed outlier: 3.811A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG C 559 " --> pdb=" O PHE C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 572 Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 588 through 599 Processing helix chain 'C' and resid 623 through 629 removed outlier: 3.607A pdb=" N ALA C 627 " --> pdb=" O SER C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 658 Processing helix chain 'C' and resid 696 through 715 removed outlier: 3.533A pdb=" N VAL C 700 " --> pdb=" O PRO C 696 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N SER C 709 " --> pdb=" O ARG C 705 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG C 710 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE C 715 " --> pdb=" O ILE C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 767 removed outlier: 3.810A pdb=" N ILE C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 25 Processing helix chain 'D' and resid 37 through 55 removed outlier: 3.663A pdb=" N TYR D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 52 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY D 53 " --> pdb=" O CYS D 49 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL D 55 " --> pdb=" O GLY D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 67 removed outlier: 4.677A pdb=" N GLY D 66 " --> pdb=" O CYS D 62 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY D 67 " --> pdb=" O GLN D 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 67' Processing helix chain 'D' and resid 70 through 89 removed outlier: 3.632A pdb=" N PHE D 74 " --> pdb=" O PHE D 70 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ILE D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 91 through 97 Processing helix chain 'D' and resid 100 through 107 removed outlier: 4.175A pdb=" N TRP D 104 " --> pdb=" O SER D 100 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE D 107 " --> pdb=" O VAL D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 142 removed outlier: 4.494A pdb=" N LEU D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR D 128 " --> pdb=" O MET D 124 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N THR D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 152 removed outlier: 3.925A pdb=" N ASP D 152 " --> pdb=" O PRO D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 169 removed outlier: 3.590A pdb=" N SER D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 194 through 212 Processing helix chain 'D' and resid 215 through 227 removed outlier: 3.905A pdb=" N LYS D 221 " --> pdb=" O GLU D 217 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE D 225 " --> pdb=" O LYS D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 243 removed outlier: 3.505A pdb=" N THR D 235 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 256 removed outlier: 3.674A pdb=" N VAL D 252 " --> pdb=" O THR D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 264 Processing helix chain 'D' and resid 265 through 280 removed outlier: 3.936A pdb=" N LEU D 269 " --> pdb=" O PRO D 265 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP D 270 " --> pdb=" O ASP D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 291 Processing helix chain 'D' and resid 299 through 349 removed outlier: 3.710A pdb=" N SER D 303 " --> pdb=" O CYS D 299 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 344 " --> pdb=" O ASN D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 371 removed outlier: 3.694A pdb=" N ASP D 371 " --> pdb=" O CYS D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 408 Processing helix chain 'D' and resid 412 through 447 removed outlier: 3.932A pdb=" N TRP D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Proline residue: D 442 - end of helix Processing helix chain 'D' and resid 454 through 470 Processing helix chain 'D' and resid 471 through 475 Processing helix chain 'D' and resid 477 through 490 removed outlier: 3.772A pdb=" N TRP D 481 " --> pdb=" O SER D 477 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER D 487 " --> pdb=" O SER D 483 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY D 490 " --> pdb=" O ASP D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 508 removed outlier: 3.825A pdb=" N LEU D 495 " --> pdb=" O SER D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 522 removed outlier: 3.537A pdb=" N PHE D 514 " --> pdb=" O GLY D 510 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE D 522 " --> pdb=" O ILE D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 536 removed outlier: 3.669A pdb=" N GLN D 531 " --> pdb=" O ASN D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 542 removed outlier: 4.586A pdb=" N MET D 542 " --> pdb=" O SER D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 555 removed outlier: 3.970A pdb=" N LEU D 547 " --> pdb=" O LEU D 543 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE D 548 " --> pdb=" O ILE D 544 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE D 549 " --> pdb=" O ILE D 545 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N PHE D 550 " --> pdb=" O PHE D 546 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER D 555 " --> pdb=" O VAL D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 581 No H-bonds generated for 'chain 'D' and resid 579 through 581' Processing helix chain 'D' and resid 582 through 590 removed outlier: 3.513A pdb=" N VAL D 587 " --> pdb=" O TYR D 583 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA D 590 " --> pdb=" O VAL D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 596 removed outlier: 3.741A pdb=" N LEU D 595 " --> pdb=" O GLY D 591 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR D 596 " --> pdb=" O VAL D 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 591 through 596' Processing helix chain 'D' and resid 596 through 609 removed outlier: 4.720A pdb=" N TYR D 600 " --> pdb=" O THR D 596 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA D 601 " --> pdb=" O ILE D 597 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'B' and resid 262 through 263 removed outlier: 6.066A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 347 through 349 Processing sheet with id=AA4, first strand: chain 'B' and resid 670 through 673 Processing sheet with id=AA5, first strand: chain 'C' and resid 262 through 263 removed outlier: 6.038A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 347 through 350 Processing sheet with id=AA7, first strand: chain 'C' and resid 670 through 673 removed outlier: 6.510A pdb=" N ASP C 693 " --> pdb=" O ALA C 687 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 670 through 673 1171 hydrogen bonds defined for protein. 3438 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.13 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 3564 1.31 - 1.45: 6639 1.45 - 1.59: 12422 1.59 - 1.74: 1 1.74 - 1.88: 212 Bond restraints: 22838 Sorted by residual: bond pdb=" C5 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.413 1.541 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C5 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.413 1.538 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C5 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.413 1.537 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C5 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.413 1.536 -0.123 2.00e-02 2.50e+03 3.81e+01 bond pdb=" C5 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.413 1.536 -0.123 2.00e-02 2.50e+03 3.80e+01 ... (remaining 22833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 30511 2.62 - 5.24: 503 5.24 - 7.86: 58 7.86 - 10.48: 13 10.48 - 13.10: 3 Bond angle restraints: 31088 Sorted by residual: angle pdb=" N CYS B 133 " pdb=" CA CYS B 133 " pdb=" C CYS B 133 " ideal model delta sigma weight residual 109.23 118.25 -9.02 1.55e+00 4.16e-01 3.39e+01 angle pdb=" CB MET A 436 " pdb=" CG MET A 436 " pdb=" SD MET A 436 " ideal model delta sigma weight residual 112.70 125.80 -13.10 3.00e+00 1.11e-01 1.91e+01 angle pdb=" CB MET D 436 " pdb=" CG MET D 436 " pdb=" SD MET D 436 " ideal model delta sigma weight residual 112.70 125.03 -12.33 3.00e+00 1.11e-01 1.69e+01 angle pdb=" N VAL C 212 " pdb=" CA VAL C 212 " pdb=" C VAL C 212 " ideal model delta sigma weight residual 113.20 109.38 3.82 9.60e-01 1.09e+00 1.59e+01 angle pdb=" N PHE D 90 " pdb=" CA PHE D 90 " pdb=" C PHE D 90 " ideal model delta sigma weight residual 113.72 108.23 5.49 1.52e+00 4.33e-01 1.30e+01 ... (remaining 31083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.54: 12929 32.54 - 65.08: 700 65.08 - 97.63: 70 97.63 - 130.17: 63 130.17 - 162.71: 2 Dihedral angle restraints: 13764 sinusoidal: 5862 harmonic: 7902 Sorted by residual: dihedral pdb=" CA VAL C 739 " pdb=" C VAL C 739 " pdb=" N SER C 740 " pdb=" CA SER C 740 " ideal model delta harmonic sigma weight residual 180.00 153.88 26.12 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA ASN B 718 " pdb=" C ASN B 718 " pdb=" N ASP B 719 " pdb=" CA ASP B 719 " ideal model delta harmonic sigma weight residual 180.00 155.42 24.58 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA VAL B 739 " pdb=" C VAL B 739 " pdb=" N SER B 740 " pdb=" CA SER B 740 " ideal model delta harmonic sigma weight residual 180.00 156.93 23.07 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 13761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.453: 3479 0.453 - 0.907: 3 0.907 - 1.360: 1 1.360 - 1.813: 0 1.813 - 2.267: 1 Chirality restraints: 3484 Sorted by residual: chirality pdb=" C1 NAG D 702 " pdb=" ND2 ASN D 258 " pdb=" C2 NAG D 702 " pdb=" O5 NAG D 702 " both_signs ideal model delta sigma weight residual False -2.40 -0.13 -2.27 2.00e-01 2.50e+01 1.28e+02 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN C 432 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.17 -1.23 2.00e-01 2.50e+01 3.81e+01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 258 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.94e+01 ... (remaining 3481 not shown) Planarity restraints: 3920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 702 " -0.331 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG D 702 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG D 702 " -0.057 2.00e-02 2.50e+03 pdb=" N2 NAG D 702 " 0.507 2.00e-02 2.50e+03 pdb=" O7 NAG D 702 " -0.193 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 258 " -0.170 2.00e-02 2.50e+03 1.87e-01 4.35e+02 pdb=" CG ASN D 258 " 0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN D 258 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN D 258 " 0.310 2.00e-02 2.50e+03 pdb=" C1 NAG D 702 " -0.213 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 103 " 0.116 2.00e-02 2.50e+03 1.46e-01 2.66e+02 pdb=" CG ASN C 103 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN C 103 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 103 " -0.250 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " 0.167 2.00e-02 2.50e+03 ... (remaining 3917 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 491 2.69 - 3.24: 22722 3.24 - 3.79: 35294 3.79 - 4.35: 43651 4.35 - 4.90: 72494 Nonbonded interactions: 174652 Sorted by model distance: nonbonded pdb=" OG1 THR C 698 " pdb=" OE1 GLU C 699 " model vdw 2.136 3.040 nonbonded pdb=" OD2 ASP C 494 " pdb=" OG1 THR C 496 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR B 183 " pdb=" OD1 ASP B 509 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR C 183 " pdb=" OD1 ASP C 509 " model vdw 2.222 3.040 nonbonded pdb=" OD1 ASP B 382 " pdb=" OH TYR B 385 " model vdw 2.239 3.040 ... (remaining 174647 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' } 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: 1.650 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.890 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 : 0.010 0.204 22878 Z= 0.490 Angle : 0.898 42.852 31198 Z= 0.407 Chirality : 0.067 2.267 3484 Planarity : 0.007 0.287 3904 Dihedral : 20.705 162.710 8654 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.50 % Allowed : 26.66 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.17), residues: 2700 helix: 1.13 (0.13), residues: 1613 sheet: -0.62 (1.20), residues: 20 loop : -1.49 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 535 TYR 0.020 0.001 TYR B 41 PHE 0.023 0.002 PHE A 549 TRP 0.034 0.002 TRP D 416 HIS 0.006 0.001 HIS C 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00985 / 0.48 (22838) covalent geometry : angle 0.77746 / 0.38 (31088) SS BOND : bond 0.00626 / 0.24 ( 10) SS BOND : angle 1.36850 / 0.66 ( 20) hydrogen bonds : bond 0.14623 / 9.61 ( 1167) hydrogen bonds : angle 5.59089 / 4.01 ( 3438) link_BETA1-4 : bond 0.00559 / 0.33 ( 14) link_BETA1-4 : angle 1.22975 / 0.74 ( 42) link_NAG-ASN : bond 0.06399 / 2.85 ( 16) link_NAG-ASN : angle 11.44908 / 8.57 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 266 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7420 (m-90) cc_final: 0.7167 (m-90) REVERT: A 119 MET cc_start: 0.7598 (mmm) cc_final: 0.7231 (mmm) REVERT: A 245 LYS cc_start: 0.8155 (tptt) cc_final: 0.7884 (tptp) REVERT: B 288 LYS cc_start: 0.7557 (ttmt) cc_final: 0.7306 (ttmt) REVERT: C 556 ASN cc_start: 0.6935 (m110) cc_final: 0.6613 (m110) REVERT: D 42 MET cc_start: 0.7405 (mmt) cc_final: 0.7203 (mmp) REVERT: D 81 GLU cc_start: 0.6640 (mm-30) cc_final: 0.6412 (mm-30) outliers start: 12 outliers final: 5 residues processed: 272 average time/residue: 0.1390 time to fit residues: 62.4524 Evaluate side-chains 256 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 251 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain C residue 699 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 HIS C 121 ASN C 139 GLN C 718 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.198895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.119873 restraints weight = 29988.462| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.90 r_work: 0.3167 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22878 Z= 0.179 Angle : 0.725 15.200 31198 Z= 0.343 Chirality : 0.048 0.668 3484 Planarity : 0.005 0.071 3904 Dihedral : 15.420 152.792 3572 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.41 % Allowed : 23.21 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.17), residues: 2700 helix: 1.36 (0.13), residues: 1612 sheet: -0.69 (1.12), residues: 20 loop : -1.51 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 535 TYR 0.015 0.002 TYR B 41 PHE 0.021 0.002 PHE B 555 TRP 0.018 0.002 TRP D 416 HIS 0.005 0.001 HIS B 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (22838) covalent geometry : angle 0.69804 / 0.34 (31088) SS BOND : bond 0.00788 / 0.39 ( 10) SS BOND : angle 2.29821 / 1.39 ( 20) hydrogen bonds : bond 0.05538 / 3.71 ( 1167) hydrogen bonds : angle 4.20338 / 2.98 ( 3438) link_BETA1-4 : bond 0.00719 / 0.37 ( 14) link_BETA1-4 : angle 2.20421 / 1.20 ( 42) link_NAG-ASN : bond 0.00891 / 0.42 ( 16) link_NAG-ASN : angle 4.42359 / 2.90 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 265 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7373 (m-90) cc_final: 0.7114 (m-90) REVERT: A 119 MET cc_start: 0.7915 (mmm) cc_final: 0.7528 (mmm) REVERT: A 245 LYS cc_start: 0.8098 (tptt) cc_final: 0.7787 (tptp) REVERT: A 289 PHE cc_start: 0.7529 (m-80) cc_final: 0.7235 (m-80) REVERT: A 398 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8701 (tt) REVERT: B 45 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7766 (mm) REVERT: B 207 TYR cc_start: 0.8724 (m-80) cc_final: 0.8433 (m-80) REVERT: B 363 LYS cc_start: 0.8089 (mppt) cc_final: 0.7883 (mmmt) REVERT: B 564 GLU cc_start: 0.7768 (pm20) cc_final: 0.7529 (pm20) REVERT: B 725 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8707 (mp) REVERT: C 45 LEU cc_start: 0.8398 (mm) cc_final: 0.8129 (mm) REVERT: C 102 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8322 (mt0) REVERT: C 406 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8011 (tm-30) REVERT: C 556 ASN cc_start: 0.7146 (m110) cc_final: 0.6796 (m110) REVERT: C 699 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8142 (mp0) REVERT: D 81 GLU cc_start: 0.6693 (mm-30) cc_final: 0.6465 (mm-30) REVERT: D 308 ILE cc_start: 0.6739 (OUTLIER) cc_final: 0.6334 (tp) REVERT: D 398 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8484 (tt) outliers start: 81 outliers final: 33 residues processed: 325 average time/residue: 0.1378 time to fit residues: 74.0465 Evaluate side-chains 287 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 248 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 530 TRP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 699 GLU Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 507 TYR Chi-restraints excluded: chain D residue 520 PHE Chi-restraints excluded: chain D residue 585 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 2 optimal weight: 4.9990 chunk 179 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 106 optimal weight: 0.2980 chunk 222 optimal weight: 1.9990 chunk 257 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.201102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.123168 restraints weight = 30041.833| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.60 r_work: 0.3243 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22878 Z= 0.137 Angle : 0.662 14.094 31198 Z= 0.314 Chirality : 0.045 0.555 3484 Planarity : 0.004 0.059 3904 Dihedral : 13.607 141.516 3565 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.86 % Allowed : 24.10 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.17), residues: 2700 helix: 1.51 (0.13), residues: 1613 sheet: -0.94 (1.06), residues: 20 loop : -1.46 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.012 0.001 TYR B 41 PHE 0.022 0.001 PHE A 520 TRP 0.019 0.001 TRP D 416 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (22838) covalent geometry : angle 0.64083 / 0.31 (31088) SS BOND : bond 0.00518 / 0.19 ( 10) SS BOND : angle 2.23578 / 1.31 ( 20) hydrogen bonds : bond 0.04890 / 3.27 ( 1167) hydrogen bonds : angle 3.99429 / 2.83 ( 3438) link_BETA1-4 : bond 0.00525 / 0.27 ( 14) link_BETA1-4 : angle 2.16379 / 1.16 ( 42) link_NAG-ASN : bond 0.00483 / 0.29 ( 16) link_NAG-ASN : angle 3.53936 / 2.27 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 266 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.7130 (mp) cc_final: 0.6816 (mt) REVERT: A 119 MET cc_start: 0.7865 (mmm) cc_final: 0.7488 (mmm) REVERT: A 235 THR cc_start: 0.7660 (p) cc_final: 0.7441 (p) REVERT: A 245 LYS cc_start: 0.8130 (tptt) cc_final: 0.7830 (tptp) REVERT: A 289 PHE cc_start: 0.7524 (m-80) cc_final: 0.6823 (m-80) REVERT: A 398 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8748 (tt) REVERT: B 45 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7726 (mm) REVERT: B 169 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.7622 (mtt90) REVERT: B 207 TYR cc_start: 0.8720 (m-80) cc_final: 0.8341 (m-80) REVERT: B 361 CYS cc_start: 0.6736 (t) cc_final: 0.6176 (p) REVERT: B 408 MET cc_start: 0.8953 (mmt) cc_final: 0.8722 (mmp) REVERT: B 725 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8608 (mp) REVERT: C 45 LEU cc_start: 0.8314 (mm) cc_final: 0.7854 (mm) REVERT: C 556 ASN cc_start: 0.7066 (m110) cc_final: 0.6622 (m110) REVERT: C 699 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8198 (mp0) REVERT: D 119 MET cc_start: 0.7327 (tpt) cc_final: 0.7122 (tpt) REVERT: D 308 ILE cc_start: 0.6737 (OUTLIER) cc_final: 0.6304 (tp) REVERT: D 363 MET cc_start: 0.7497 (mmt) cc_final: 0.7294 (tpp) outliers start: 68 outliers final: 37 residues processed: 318 average time/residue: 0.1342 time to fit residues: 71.1075 Evaluate side-chains 296 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 253 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 699 GLU Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 507 TYR Chi-restraints excluded: chain D residue 520 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 144 optimal weight: 0.9990 chunk 263 optimal weight: 8.9990 chunk 212 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 246 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 218 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 HIS C 373 HIS C 718 ASN D 37 ASN D 364 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.200400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.125594 restraints weight = 30389.503| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.10 r_work: 0.3191 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22878 Z= 0.155 Angle : 0.665 12.240 31198 Z= 0.317 Chirality : 0.046 0.492 3484 Planarity : 0.004 0.060 3904 Dihedral : 12.542 133.581 3565 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.91 % Allowed : 23.38 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.17), residues: 2700 helix: 1.49 (0.13), residues: 1615 sheet: -0.87 (1.04), residues: 20 loop : -1.44 (0.20), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 710 TYR 0.013 0.001 TYR A 322 PHE 0.023 0.001 PHE B 555 TRP 0.019 0.001 TRP D 416 HIS 0.006 0.001 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (22838) covalent geometry : angle 0.64499 / 0.31 (31088) SS BOND : bond 0.00609 / 0.24 ( 10) SS BOND : angle 2.34873 / 1.34 ( 20) hydrogen bonds : bond 0.05018 / 3.37 ( 1167) hydrogen bonds : angle 3.92204 / 2.79 ( 3438) link_BETA1-4 : bond 0.00533 / 0.32 ( 14) link_BETA1-4 : angle 2.46128 / 1.33 ( 42) link_NAG-ASN : bond 0.00475 / 0.30 ( 16) link_NAG-ASN : angle 3.28294 / 2.09 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 268 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.7779 (mmm) cc_final: 0.7397 (mmm) REVERT: A 235 THR cc_start: 0.7663 (p) cc_final: 0.7417 (p) REVERT: A 240 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7134 (tpt90) REVERT: A 245 LYS cc_start: 0.8165 (tptt) cc_final: 0.7892 (tptp) REVERT: A 398 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8605 (tt) REVERT: B 45 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7770 (mm) REVERT: B 169 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.7614 (mtt90) REVERT: B 207 TYR cc_start: 0.8759 (m-80) cc_final: 0.8259 (m-80) REVERT: B 361 CYS cc_start: 0.6203 (OUTLIER) cc_final: 0.5854 (p) REVERT: B 564 GLU cc_start: 0.7825 (pm20) cc_final: 0.7609 (pm20) REVERT: B 725 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8614 (mp) REVERT: C 45 LEU cc_start: 0.8338 (mm) cc_final: 0.7794 (mm) REVERT: C 556 ASN cc_start: 0.7003 (m110) cc_final: 0.6520 (m110) REVERT: D 37 ASN cc_start: 0.6952 (OUTLIER) cc_final: 0.6747 (p0) REVERT: D 277 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7703 (t80) REVERT: D 308 ILE cc_start: 0.6725 (OUTLIER) cc_final: 0.6304 (tp) REVERT: D 517 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7151 (p0) outliers start: 93 outliers final: 56 residues processed: 339 average time/residue: 0.1388 time to fit residues: 77.9260 Evaluate side-chains 320 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 254 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 530 TRP Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 277 PHE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 507 TYR Chi-restraints excluded: chain D residue 517 ASP Chi-restraints excluded: chain D residue 520 PHE Chi-restraints excluded: chain D residue 548 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 266 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 245 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 190 optimal weight: 0.4980 chunk 176 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 146 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 ASN C 718 ASN D 65 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.200393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.126311 restraints weight = 30183.712| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.20 r_work: 0.3181 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22878 Z= 0.145 Angle : 0.665 11.560 31198 Z= 0.314 Chirality : 0.045 0.457 3484 Planarity : 0.004 0.060 3904 Dihedral : 11.726 127.447 3562 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 4.04 % Allowed : 22.92 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.17), residues: 2700 helix: 1.51 (0.13), residues: 1616 sheet: -0.66 (1.06), residues: 20 loop : -1.41 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 97 TYR 0.013 0.001 TYR A 322 PHE 0.025 0.001 PHE C 390 TRP 0.020 0.001 TRP D 416 HIS 0.007 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (22838) covalent geometry : angle 0.64396 / 0.31 (31088) SS BOND : bond 0.00596 / 0.21 ( 10) SS BOND : angle 2.18358 / 1.27 ( 20) hydrogen bonds : bond 0.04888 / 3.29 ( 1167) hydrogen bonds : angle 3.88809 / 2.77 ( 3438) link_BETA1-4 : bond 0.00463 / 0.28 ( 14) link_BETA1-4 : angle 2.79132 / 1.52 ( 42) link_NAG-ASN : bond 0.00509 / 0.32 ( 16) link_NAG-ASN : angle 3.13318 / 2.00 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 260 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.7818 (mmm) cc_final: 0.7409 (mmm) REVERT: A 146 GLU cc_start: 0.7400 (tp30) cc_final: 0.7189 (tp30) REVERT: A 193 ILE cc_start: 0.7329 (OUTLIER) cc_final: 0.7103 (mp) REVERT: A 235 THR cc_start: 0.7675 (p) cc_final: 0.7431 (p) REVERT: A 245 LYS cc_start: 0.8160 (tptt) cc_final: 0.7760 (tptm) REVERT: A 398 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8620 (tt) REVERT: A 502 MET cc_start: 0.6357 (pmm) cc_final: 0.6152 (pmm) REVERT: B 21 ILE cc_start: 0.7237 (OUTLIER) cc_final: 0.7031 (mp) REVERT: B 45 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7812 (mm) REVERT: B 169 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.7581 (mtt90) REVERT: B 725 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8607 (mp) REVERT: C 45 LEU cc_start: 0.8317 (mm) cc_final: 0.7745 (mm) REVERT: C 401 HIS cc_start: 0.8351 (OUTLIER) cc_final: 0.7495 (t-90) REVERT: C 556 ASN cc_start: 0.6932 (m110) cc_final: 0.6416 (m110) REVERT: D 268 TRP cc_start: 0.7742 (m100) cc_final: 0.6611 (m-10) REVERT: D 277 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7810 (t80) REVERT: D 308 ILE cc_start: 0.6692 (OUTLIER) cc_final: 0.6280 (tp) REVERT: D 517 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7134 (p0) outliers start: 96 outliers final: 65 residues processed: 336 average time/residue: 0.1323 time to fit residues: 73.9203 Evaluate side-chains 332 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 257 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 530 TRP Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 277 PHE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 507 TYR Chi-restraints excluded: chain D residue 517 ASP Chi-restraints excluded: chain D residue 520 PHE Chi-restraints excluded: chain D residue 548 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 11 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 245 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 59 optimal weight: 0.0570 chunk 67 optimal weight: 7.9990 chunk 229 optimal weight: 2.9990 overall best weight: 1.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN D 65 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.199489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.124611 restraints weight = 30354.652| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.85 r_work: 0.3160 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22878 Z= 0.156 Angle : 0.669 10.903 31198 Z= 0.316 Chirality : 0.046 0.423 3484 Planarity : 0.004 0.060 3904 Dihedral : 10.664 112.707 3562 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.63 % Allowed : 22.33 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.17), residues: 2700 helix: 1.53 (0.13), residues: 1612 sheet: -0.73 (1.08), residues: 20 loop : -1.39 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 97 TYR 0.018 0.001 TYR C 50 PHE 0.025 0.001 PHE B 555 TRP 0.023 0.001 TRP D 416 HIS 0.008 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (22838) covalent geometry : angle 0.64757 / 0.31 (31088) SS BOND : bond 0.00713 / 0.27 ( 10) SS BOND : angle 1.32265 / 0.62 ( 20) hydrogen bonds : bond 0.05036 / 3.39 ( 1167) hydrogen bonds : angle 3.88706 / 2.77 ( 3438) link_BETA1-4 : bond 0.00444 / 0.27 ( 14) link_BETA1-4 : angle 3.27745 / 1.86 ( 42) link_NAG-ASN : bond 0.00480 / 0.30 ( 16) link_NAG-ASN : angle 3.01018 / 1.92 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 271 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.7814 (mmm) cc_final: 0.7406 (mmm) REVERT: A 235 THR cc_start: 0.7724 (p) cc_final: 0.7493 (p) REVERT: A 240 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6809 (tpm170) REVERT: A 292 TYR cc_start: 0.7492 (m-80) cc_final: 0.7195 (m-10) REVERT: A 398 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8600 (tt) REVERT: B 21 ILE cc_start: 0.7157 (OUTLIER) cc_final: 0.6951 (mp) REVERT: B 45 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7981 (mm) REVERT: B 169 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.7665 (mtt90) REVERT: B 207 TYR cc_start: 0.8759 (m-80) cc_final: 0.8277 (m-80) REVERT: B 401 HIS cc_start: 0.8537 (OUTLIER) cc_final: 0.7232 (t-90) REVERT: B 564 GLU cc_start: 0.7868 (pm20) cc_final: 0.7648 (pm20) REVERT: B 725 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8666 (mp) REVERT: C 45 LEU cc_start: 0.8368 (mm) cc_final: 0.7811 (mm) REVERT: C 207 TYR cc_start: 0.8886 (m-80) cc_final: 0.8641 (m-80) REVERT: C 401 HIS cc_start: 0.8453 (OUTLIER) cc_final: 0.7483 (t-90) REVERT: C 556 ASN cc_start: 0.6995 (m110) cc_final: 0.6391 (m110) REVERT: C 741 ILE cc_start: 0.7296 (OUTLIER) cc_final: 0.6809 (tt) REVERT: D 146 GLU cc_start: 0.7401 (tp30) cc_final: 0.7105 (tp30) REVERT: D 277 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7882 (t80) REVERT: D 308 ILE cc_start: 0.6699 (OUTLIER) cc_final: 0.6266 (tp) REVERT: D 381 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.6940 (mm-40) REVERT: D 492 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8181 (tt) REVERT: D 517 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7115 (p0) outliers start: 110 outliers final: 75 residues processed: 359 average time/residue: 0.1338 time to fit residues: 80.2448 Evaluate side-chains 351 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 262 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 530 TRP Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 277 PHE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 492 ILE Chi-restraints excluded: chain D residue 517 ASP Chi-restraints excluded: chain D residue 520 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 133 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 260 optimal weight: 0.0670 chunk 69 optimal weight: 0.8980 chunk 134 optimal weight: 8.9990 chunk 200 optimal weight: 0.6980 chunk 114 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN D 65 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.201227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.126677 restraints weight = 30190.129| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.81 r_work: 0.3232 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22878 Z= 0.121 Angle : 0.652 11.052 31198 Z= 0.307 Chirality : 0.044 0.406 3484 Planarity : 0.004 0.059 3904 Dihedral : 9.948 105.837 3562 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.90 % Allowed : 24.22 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.17), residues: 2700 helix: 1.63 (0.13), residues: 1618 sheet: -0.42 (1.12), residues: 20 loop : -1.37 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 97 TYR 0.022 0.001 TYR C 50 PHE 0.027 0.001 PHE C 390 TRP 0.018 0.001 TRP D 268 HIS 0.007 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (22838) covalent geometry : angle 0.62751 / 0.30 (31088) SS BOND : bond 0.00761 / 0.29 ( 10) SS BOND : angle 2.03169 / 1.12 ( 20) hydrogen bonds : bond 0.04264 / 2.87 ( 1167) hydrogen bonds : angle 3.78956 / 2.69 ( 3438) link_BETA1-4 : bond 0.00478 / 0.28 ( 14) link_BETA1-4 : angle 3.24960 / 1.94 ( 42) link_NAG-ASN : bond 0.00535 / 0.34 ( 16) link_NAG-ASN : angle 3.22853 / 2.01 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 282 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7407 (mmm) REVERT: A 146 GLU cc_start: 0.7489 (tp30) cc_final: 0.7075 (tp30) REVERT: A 235 THR cc_start: 0.7694 (p) cc_final: 0.7448 (p) REVERT: A 245 LYS cc_start: 0.7974 (tptt) cc_final: 0.7522 (tptm) REVERT: A 292 TYR cc_start: 0.7413 (m-80) cc_final: 0.7144 (m-10) REVERT: A 436 MET cc_start: 0.7847 (tpp) cc_final: 0.7568 (tpp) REVERT: B 45 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7932 (mm) REVERT: B 169 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.7323 (mtt90) REVERT: B 361 CYS cc_start: 0.6297 (t) cc_final: 0.5846 (p) REVERT: B 471 ASP cc_start: 0.8133 (t0) cc_final: 0.7705 (t0) REVERT: B 503 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8148 (mp) REVERT: C 45 LEU cc_start: 0.8269 (mm) cc_final: 0.7687 (mm) REVERT: C 401 HIS cc_start: 0.8241 (OUTLIER) cc_final: 0.7381 (t-90) REVERT: C 471 ASP cc_start: 0.8252 (t0) cc_final: 0.7901 (t0) REVERT: C 556 ASN cc_start: 0.6865 (m110) cc_final: 0.6316 (m110) REVERT: D 35 TRP cc_start: 0.7338 (m100) cc_final: 0.6880 (m100) REVERT: D 119 MET cc_start: 0.7372 (tpt) cc_final: 0.7116 (tpt) REVERT: D 146 GLU cc_start: 0.7407 (tp30) cc_final: 0.7169 (tp30) REVERT: D 277 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7736 (t80) REVERT: D 391 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6564 (mp0) REVERT: D 449 ILE cc_start: 0.7919 (mm) cc_final: 0.7477 (tp) REVERT: D 492 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8136 (tt) REVERT: D 517 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7129 (p0) outliers start: 69 outliers final: 49 residues processed: 335 average time/residue: 0.1344 time to fit residues: 74.8096 Evaluate side-chains 325 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 268 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 530 TRP Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 277 PHE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 492 ILE Chi-restraints excluded: chain D residue 517 ASP Chi-restraints excluded: chain D residue 520 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 208 optimal weight: 30.0000 chunk 43 optimal weight: 0.0070 chunk 45 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 35 optimal weight: 5.9990 chunk 205 optimal weight: 0.0570 chunk 81 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN D 65 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.201838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.129123 restraints weight = 30340.476| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.68 r_work: 0.3246 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22878 Z= 0.120 Angle : 0.668 13.647 31198 Z= 0.312 Chirality : 0.044 0.390 3484 Planarity : 0.004 0.059 3904 Dihedral : 9.357 102.131 3562 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.20 % Allowed : 24.35 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.17), residues: 2700 helix: 1.74 (0.13), residues: 1595 sheet: -0.55 (1.14), residues: 20 loop : -1.29 (0.20), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 97 TYR 0.024 0.001 TYR C 50 PHE 0.032 0.001 PHE C 28 TRP 0.016 0.001 TRP D 416 HIS 0.009 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (22838) covalent geometry : angle 0.64186 / 0.30 (31088) SS BOND : bond 0.00779 / 0.26 ( 10) SS BOND : angle 3.09105 / 1.70 ( 20) hydrogen bonds : bond 0.04106 / 2.76 ( 1167) hydrogen bonds : angle 3.72778 / 2.65 ( 3438) link_BETA1-4 : bond 0.00490 / 0.30 ( 14) link_BETA1-4 : angle 3.23075 / 1.96 ( 42) link_NAG-ASN : bond 0.00627 / 0.40 ( 16) link_NAG-ASN : angle 3.20220 / 2.02 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 281 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7420 (mmm) REVERT: A 146 GLU cc_start: 0.7498 (tp30) cc_final: 0.7101 (tp30) REVERT: A 235 THR cc_start: 0.7675 (p) cc_final: 0.7452 (p) REVERT: A 240 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.6527 (tpm170) REVERT: A 245 LYS cc_start: 0.8078 (tptt) cc_final: 0.7788 (tptp) REVERT: A 292 TYR cc_start: 0.7446 (m-80) cc_final: 0.7219 (m-10) REVERT: A 436 MET cc_start: 0.7963 (tpp) cc_final: 0.7727 (tpp) REVERT: B 123 MET cc_start: 0.8501 (mtp) cc_final: 0.8292 (mtt) REVERT: B 169 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.7459 (mtt90) REVERT: B 207 TYR cc_start: 0.8622 (m-80) cc_final: 0.8241 (m-80) REVERT: B 350 ASP cc_start: 0.7711 (t0) cc_final: 0.7442 (t0) REVERT: B 361 CYS cc_start: 0.5995 (t) cc_final: 0.5787 (p) REVERT: B 401 HIS cc_start: 0.8439 (OUTLIER) cc_final: 0.7114 (t-90) REVERT: B 471 ASP cc_start: 0.8137 (t0) cc_final: 0.7703 (t0) REVERT: B 503 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8139 (mp) REVERT: B 564 GLU cc_start: 0.7893 (pm20) cc_final: 0.7679 (pm20) REVERT: B 725 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8645 (mp) REVERT: C 45 LEU cc_start: 0.8315 (mm) cc_final: 0.7716 (mm) REVERT: C 137 ASN cc_start: 0.8525 (t0) cc_final: 0.8201 (t0) REVERT: C 340 GLN cc_start: 0.1656 (OUTLIER) cc_final: 0.1388 (tp-100) REVERT: C 347 THR cc_start: 0.7990 (OUTLIER) cc_final: 0.7580 (p) REVERT: C 401 HIS cc_start: 0.8251 (OUTLIER) cc_final: 0.7382 (t-90) REVERT: C 471 ASP cc_start: 0.8219 (t0) cc_final: 0.7864 (t0) REVERT: C 556 ASN cc_start: 0.6839 (m110) cc_final: 0.6276 (m110) REVERT: C 741 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6680 (tt) REVERT: D 35 TRP cc_start: 0.7354 (m100) cc_final: 0.6916 (m100) REVERT: D 119 MET cc_start: 0.7376 (tpt) cc_final: 0.7140 (tpt) REVERT: D 146 GLU cc_start: 0.7405 (tp30) cc_final: 0.7189 (tp30) REVERT: D 277 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7778 (t80) REVERT: D 449 ILE cc_start: 0.7972 (mm) cc_final: 0.7548 (tp) REVERT: D 492 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8086 (tt) REVERT: D 517 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.7023 (p0) outliers start: 76 outliers final: 48 residues processed: 338 average time/residue: 0.1251 time to fit residues: 70.3422 Evaluate side-chains 329 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 268 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 530 TRP Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 277 PHE Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 492 ILE Chi-restraints excluded: chain D residue 517 ASP Chi-restraints excluded: chain D residue 520 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 125 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 199 optimal weight: 0.8980 chunk 226 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 241 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 264 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 222 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN D 65 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.199484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.127449 restraints weight = 30245.732| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.75 r_work: 0.3192 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22878 Z= 0.152 Angle : 0.688 15.255 31198 Z= 0.326 Chirality : 0.045 0.382 3484 Planarity : 0.004 0.059 3904 Dihedral : 8.985 97.862 3562 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.90 % Allowed : 24.64 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.17), residues: 2700 helix: 1.65 (0.13), residues: 1612 sheet: None (None), residues: 0 loop : -1.37 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 240 TYR 0.014 0.001 TYR A 128 PHE 0.035 0.002 PHE A 520 TRP 0.037 0.001 TRP A 416 HIS 0.008 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (22838) covalent geometry : angle 0.66283 / 0.32 (31088) SS BOND : bond 0.00468 / 0.20 ( 10) SS BOND : angle 3.16611 / 1.70 ( 20) hydrogen bonds : bond 0.04817 / 3.25 ( 1167) hydrogen bonds : angle 3.82375 / 2.72 ( 3438) link_BETA1-4 : bond 0.00437 / 0.28 ( 14) link_BETA1-4 : angle 3.18793 / 1.90 ( 42) link_NAG-ASN : bond 0.00580 / 0.37 ( 16) link_NAG-ASN : angle 3.14836 / 2.00 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 276 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.7162 (mm) cc_final: 0.6904 (tp) REVERT: A 119 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7426 (mmm) REVERT: A 146 GLU cc_start: 0.7508 (tp30) cc_final: 0.7124 (tp30) REVERT: A 235 THR cc_start: 0.7737 (p) cc_final: 0.7525 (p) REVERT: A 245 LYS cc_start: 0.8095 (tptt) cc_final: 0.7660 (tptm) REVERT: A 292 TYR cc_start: 0.7390 (m-80) cc_final: 0.7149 (m-10) REVERT: A 436 MET cc_start: 0.7912 (tpp) cc_final: 0.7697 (tpp) REVERT: B 207 TYR cc_start: 0.8687 (m-80) cc_final: 0.8275 (m-80) REVERT: B 350 ASP cc_start: 0.7591 (t0) cc_final: 0.7381 (t0) REVERT: B 361 CYS cc_start: 0.6094 (t) cc_final: 0.5775 (p) REVERT: B 401 HIS cc_start: 0.8472 (OUTLIER) cc_final: 0.7094 (t-90) REVERT: B 471 ASP cc_start: 0.8173 (t0) cc_final: 0.7722 (t0) REVERT: B 564 GLU cc_start: 0.7861 (pm20) cc_final: 0.7645 (pm20) REVERT: B 725 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8684 (mp) REVERT: C 45 LEU cc_start: 0.8357 (mm) cc_final: 0.7791 (mm) REVERT: C 137 ASN cc_start: 0.8652 (t0) cc_final: 0.8335 (t0) REVERT: C 207 TYR cc_start: 0.8678 (m-80) cc_final: 0.8257 (m-80) REVERT: C 340 GLN cc_start: 0.1633 (OUTLIER) cc_final: 0.1375 (tp-100) REVERT: C 347 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7592 (p) REVERT: C 401 HIS cc_start: 0.8346 (OUTLIER) cc_final: 0.7433 (t-90) REVERT: C 471 ASP cc_start: 0.8204 (t0) cc_final: 0.7842 (t0) REVERT: C 556 ASN cc_start: 0.6857 (m110) cc_final: 0.6254 (m110) REVERT: C 741 ILE cc_start: 0.7115 (OUTLIER) cc_final: 0.6650 (tt) REVERT: D 35 TRP cc_start: 0.7437 (m100) cc_final: 0.6876 (m100) REVERT: D 119 MET cc_start: 0.7424 (tpt) cc_final: 0.7193 (tpt) REVERT: D 277 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7766 (t80) REVERT: D 391 GLU cc_start: 0.7529 (mt-10) cc_final: 0.6613 (mp0) REVERT: D 449 ILE cc_start: 0.7989 (mm) cc_final: 0.7568 (tp) REVERT: D 492 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8137 (tp) REVERT: D 517 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.7030 (p0) outliers start: 69 outliers final: 50 residues processed: 331 average time/residue: 0.1330 time to fit residues: 73.3290 Evaluate side-chains 326 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 266 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 530 TRP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 277 PHE Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 492 ILE Chi-restraints excluded: chain D residue 517 ASP Chi-restraints excluded: chain D residue 520 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 31 optimal weight: 0.6980 chunk 243 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 252 optimal weight: 30.0000 chunk 114 optimal weight: 5.9990 chunk 176 optimal weight: 0.6980 chunk 131 optimal weight: 0.0050 chunk 120 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 HIS C 718 ASN D 65 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.200795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.125023 restraints weight = 30364.911| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.79 r_work: 0.3228 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22878 Z= 0.131 Angle : 0.683 13.053 31198 Z= 0.321 Chirality : 0.045 0.378 3484 Planarity : 0.004 0.059 3904 Dihedral : 8.629 97.169 3562 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.69 % Allowed : 24.89 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.17), residues: 2700 helix: 1.67 (0.13), residues: 1616 sheet: None (None), residues: 0 loop : -1.42 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 98 TYR 0.014 0.001 TYR C 50 PHE 0.026 0.001 PHE A 520 TRP 0.022 0.001 TRP D 416 HIS 0.009 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (22838) covalent geometry : angle 0.65831 / 0.31 (31088) SS BOND : bond 0.00615 / 0.22 ( 10) SS BOND : angle 3.06292 / 1.66 ( 20) hydrogen bonds : bond 0.04424 / 2.97 ( 1167) hydrogen bonds : angle 3.78918 / 2.71 ( 3438) link_BETA1-4 : bond 0.00456 / 0.27 ( 14) link_BETA1-4 : angle 3.12719 / 1.84 ( 42) link_NAG-ASN : bond 0.00584 / 0.37 ( 16) link_NAG-ASN : angle 3.12184 / 1.99 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 274 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.6937 (mm) cc_final: 0.6720 (tp) REVERT: A 119 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7407 (mmm) REVERT: A 124 MET cc_start: 0.7002 (mmp) cc_final: 0.6091 (ttt) REVERT: A 146 GLU cc_start: 0.7490 (tp30) cc_final: 0.7088 (tp30) REVERT: A 235 THR cc_start: 0.7721 (p) cc_final: 0.7519 (p) REVERT: A 245 LYS cc_start: 0.8047 (tptt) cc_final: 0.7725 (tptp) REVERT: A 292 TYR cc_start: 0.7363 (m-80) cc_final: 0.7133 (m-10) REVERT: A 436 MET cc_start: 0.7903 (tpp) cc_final: 0.7689 (tpp) REVERT: B 169 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.7458 (mtt90) REVERT: B 207 TYR cc_start: 0.8673 (m-80) cc_final: 0.8252 (m-80) REVERT: B 361 CYS cc_start: 0.6124 (t) cc_final: 0.5786 (p) REVERT: B 401 HIS cc_start: 0.8430 (OUTLIER) cc_final: 0.7127 (t-90) REVERT: B 471 ASP cc_start: 0.8134 (t0) cc_final: 0.7681 (t0) REVERT: B 503 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8149 (mp) REVERT: B 564 GLU cc_start: 0.7875 (pm20) cc_final: 0.7667 (pm20) REVERT: B 725 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8669 (mp) REVERT: C 45 LEU cc_start: 0.8291 (mm) cc_final: 0.7695 (mm) REVERT: C 137 ASN cc_start: 0.8562 (t0) cc_final: 0.8303 (t0) REVERT: C 207 TYR cc_start: 0.8656 (m-80) cc_final: 0.8253 (m-80) REVERT: C 340 GLN cc_start: 0.1599 (OUTLIER) cc_final: 0.1368 (tp-100) REVERT: C 347 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7576 (p) REVERT: C 401 HIS cc_start: 0.8283 (OUTLIER) cc_final: 0.7357 (t-90) REVERT: C 471 ASP cc_start: 0.8167 (t0) cc_final: 0.7812 (t0) REVERT: C 556 ASN cc_start: 0.6876 (m110) cc_final: 0.6251 (m110) REVERT: C 741 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6613 (tt) REVERT: D 35 TRP cc_start: 0.7385 (m100) cc_final: 0.6892 (m100) REVERT: D 119 MET cc_start: 0.7344 (tpt) cc_final: 0.7119 (tpt) REVERT: D 277 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7738 (t80) REVERT: D 391 GLU cc_start: 0.7535 (mt-10) cc_final: 0.6598 (mp0) REVERT: D 449 ILE cc_start: 0.7995 (mm) cc_final: 0.7582 (tp) REVERT: D 492 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.8001 (tp) REVERT: D 517 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7203 (p0) outliers start: 64 outliers final: 47 residues processed: 321 average time/residue: 0.1271 time to fit residues: 68.8755 Evaluate side-chains 329 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 270 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 530 TRP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 200 CYS Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 277 PHE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 492 ILE Chi-restraints excluded: chain D residue 517 ASP Chi-restraints excluded: chain D residue 520 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 0 optimal weight: 30.0000 chunk 134 optimal weight: 10.0000 chunk 254 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 202 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 175 optimal weight: 7.9990 chunk 190 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 HIS C 718 ASN D 65 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.195927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.118406 restraints weight = 30125.776| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.03 r_work: 0.3098 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 22878 Z= 0.219 Angle : 0.741 14.828 31198 Z= 0.356 Chirality : 0.048 0.376 3484 Planarity : 0.005 0.058 3904 Dihedral : 8.497 93.729 3562 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.78 % Allowed : 24.98 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.17), residues: 2700 helix: 1.45 (0.13), residues: 1612 sheet: -0.71 (1.07), residues: 20 loop : -1.46 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 98 TYR 0.018 0.002 TYR A 128 PHE 0.026 0.002 PHE B 555 TRP 0.024 0.002 TRP D 416 HIS 0.008 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.22 (22838) covalent geometry : angle 0.71835 / 0.35 (31088) SS BOND : bond 0.00777 / 0.30 ( 10) SS BOND : angle 3.34256 / 1.80 ( 20) hydrogen bonds : bond 0.05835 / 3.93 ( 1167) hydrogen bonds : angle 4.00836 / 2.87 ( 3438) link_BETA1-4 : bond 0.00452 / 0.24 ( 14) link_BETA1-4 : angle 3.17800 / 1.86 ( 42) link_NAG-ASN : bond 0.00579 / 0.37 ( 16) link_NAG-ASN : angle 3.07757 / 1.97 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7692.47 seconds wall clock time: 131 minutes 41.24 seconds (7901.24 seconds total)