Starting phenix.real_space_refine on Thu Mar 5 13:35:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m18_30040/03_2026/6m18_30040.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m18_30040/03_2026/6m18_30040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6m18_30040/03_2026/6m18_30040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m18_30040/03_2026/6m18_30040.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6m18_30040/03_2026/6m18_30040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m18_30040/03_2026/6m18_30040.map" } resolution = 2.9 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= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4 5.49 5 S 128 5.16 5 C 14618 2.51 5 N 3562 2.21 5 O 4220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22534 Number of models: 1 Model: "" Number of chains: 26 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: 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: "D" 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: "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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: "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: "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: "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: "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: "Q" 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: "R" 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: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 152 Unusual residues: {'3PH': 2, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 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: "C" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 152 Unusual residues: {'3PH': 2, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 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: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 5.86, per 1000 atoms: 0.26 Number of scatterers: 22534 At special positions: 0 Unit cell: (111.961, 138.049, 184.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 128 16.00 P 4 15.00 O 4220 8.00 N 3562 7.00 C 14618 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=2.05 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=1.85 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.02 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 383 " distance=2.05 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.05 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=1.85 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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 Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A 701 " - " ASN A 158 " " NAG A 702 " - " ASN A 182 " " NAG A 703 " - " ASN A 354 " " NAG A 704 " - " ASN A 368 " " NAG B 901 " - " ASN B 322 " " NAG C 701 " - " ASN C 158 " " NAG C 702 " - " ASN C 182 " " NAG C 703 " - " ASN C 354 " " NAG C 704 " - " ASN C 368 " " NAG D 901 " - " ASN D 322 " " NAG E 1 " - " ASN A 258 " " NAG F 1 " - " ASN B 53 " " NAG G 1 " - " ASN B 90 " " NAG H 1 " - " ASN B 103 " " NAG I 1 " - " ASN B 432 " " NAG J 1 " - " ASN B 546 " " NAG K 1 " - " ASN B 690 " " NAG L 1 " - " ASN C 258 " " NAG M 1 " - " ASN D 53 " " NAG N 1 " - " ASN D 90 " " NAG O 1 " - " ASN D 103 " " NAG P 1 " - " ASN D 432 " " NAG Q 1 " - " ASN D 546 " " NAG R 1 " - " ASN D 690 " Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 1.1 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: 134 helices and 10 sheets defined 65.7% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 4.160A pdb=" N GLU A 25 " --> pdb=" O LEU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 50 removed outlier: 3.683A pdb=" N THR A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.561A pdb=" N GLN A 63 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 79 Processing helix chain 'A' and resid 81 through 97 removed outlier: 3.548A pdb=" N ILE A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 removed outlier: 3.682A pdb=" N TRP A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 142 removed outlier: 3.667A pdb=" N LEU A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR A 128 " --> pdb=" O MET A 124 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 169 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.514A pdb=" N TRP A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.767A pdb=" N CYS A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 242 Proline residue: A 230 - end of helix removed outlier: 3.621A pdb=" N ILE A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.536A pdb=" N LEU A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 266 through 279 removed outlier: 3.697A pdb=" N ASP A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 299 through 349 removed outlier: 3.600A pdb=" N SER A 303 " --> pdb=" O CYS A 299 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR A 339 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 349 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 371 removed outlier: 3.775A pdb=" N CYS A 367 " --> pdb=" O MET A 363 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.553A pdb=" N ALA A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 441 removed outlier: 4.224A pdb=" N VAL A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 454 through 470 removed outlier: 3.740A pdb=" N LEU A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR A 459 " --> pdb=" O LYS A 455 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 475 Processing helix chain 'A' and resid 477 through 507 removed outlier: 3.540A pdb=" N TRP A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 485 " --> pdb=" O TRP A 481 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER A 487 " --> pdb=" O SER A 483 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Proline residue: A 493 - end of helix removed outlier: 3.643A pdb=" N CYS A 500 " --> pdb=" O ILE A 496 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 523 removed outlier: 3.520A pdb=" N LYS A 516 " --> pdb=" O ASP A 512 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 536 Processing helix chain 'A' and resid 536 through 553 removed outlier: 3.564A pdb=" N LEU A 543 " --> pdb=" O PRO A 539 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE A 550 " --> pdb=" O PHE A 546 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 608 removed outlier: 4.117A pdb=" N VAL A 585 " --> pdb=" O TRP A 581 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Proline residue: A 593 - end of helix removed outlier: 4.671A pdb=" N ILE A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) Proline residue: A 598 - end of helix removed outlier: 3.951A pdb=" N ALA A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN A 608 " --> pdb=" O LYS A 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 53 removed outlier: 3.526A pdb=" N THR B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU B 37 " --> pdb=" O ASN B 33 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 80 removed outlier: 3.821A pdb=" N MET B 62 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 72 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.525A pdb=" N GLN B 96 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 97 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN B 102 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.939A pdb=" N VAL B 107 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 108 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 130 removed outlier: 3.570A pdb=" N ASN B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 155 removed outlier: 3.585A pdb=" N ILE B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 193 removed outlier: 3.625A pdb=" N ARG B 169 " --> pdb=" O TRP B 165 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL B 172 " --> pdb=" O TRP B 168 " (cutoff:3.500A) Proline residue: B 178 - end of helix removed outlier: 3.674A pdb=" N GLU B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 204 Processing helix chain 'B' and resid 205 through 208 removed outlier: 3.595A pdb=" N GLU B 208 " --> pdb=" O GLY B 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 205 through 208' Processing helix chain 'B' and resid 220 through 249 removed outlier: 3.833A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU B 232 " --> pdb=" O HIS B 228 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 233 " --> pdb=" O THR B 229 " (cutoff:3.500A) Proline residue: B 235 - end of helix removed outlier: 3.580A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (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 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 278 through 283 Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 305 through 318 removed outlier: 3.591A pdb=" N PHE B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 365 through 383 removed outlier: 3.647A pdb=" N HIS B 373 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS B 378 " --> pdb=" O HIS B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 393 removed outlier: 3.696A pdb=" N ARG B 393 " --> pdb=" O PHE B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 412 removed outlier: 3.924A pdb=" N GLY B 405 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 422 removed outlier: 4.105A pdb=" N SER B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 446 removed outlier: 3.530A pdb=" N LYS B 441 " --> pdb=" O ASN B 437 " (cutoff:3.500A) removed outlier: 3.808A 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 469 through 471 No H-bonds generated for 'chain 'B' and resid 469 through 471' Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.570A pdb=" N TRP B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 502 removed outlier: 3.533A pdb=" N SER B 502 " --> pdb=" O ASP B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 removed outlier: 3.593A pdb=" N SER B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 533 removed outlier: 3.940A pdb=" N THR B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 removed outlier: 3.576A pdb=" N LYS B 541 " --> pdb=" O PRO B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 559 removed outlier: 3.923A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 572 removed outlier: 3.715A pdb=" N GLU B 571 " --> pdb=" O THR B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 588 Processing helix chain 'B' and resid 588 through 599 removed outlier: 3.706A pdb=" N TRP B 594 " --> pdb=" O PRO B 590 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP B 597 " --> pdb=" O THR B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 628 removed outlier: 3.508A pdb=" N ALA B 627 " --> pdb=" O SER B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 658 removed outlier: 3.634A pdb=" N MET B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 696 through 707 removed outlier: 3.621A pdb=" N LYS B 702 " --> pdb=" O THR B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 715 removed outlier: 3.542A pdb=" N ALA B 714 " --> pdb=" O ARG B 710 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 715 " --> pdb=" O ILE B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 762 removed outlier: 3.631A pdb=" N VAL B 745 " --> pdb=" O ILE B 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 25 removed outlier: 4.160A pdb=" N GLU C 25 " --> pdb=" O LEU C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 50 removed outlier: 3.683A pdb=" N THR C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 removed outlier: 3.561A pdb=" N GLN C 63 " --> pdb=" O PRO C 59 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 79 Processing helix chain 'C' and resid 81 through 97 removed outlier: 3.548A pdb=" N ILE C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY C 93 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN C 94 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 105 removed outlier: 3.682A pdb=" N TRP C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 142 removed outlier: 3.667A pdb=" N LEU C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR C 128 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN C 130 " --> pdb=" O GLY C 126 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 133 " --> pdb=" O TYR C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 169 Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.514A pdb=" N TRP C 176 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 212 removed outlier: 3.767A pdb=" N CYS C 211 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 242 Proline residue: C 230 - end of helix removed outlier: 3.621A pdb=" N ILE C 239 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.536A pdb=" N LEU C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 266 through 279 removed outlier: 3.697A pdb=" N ASP C 270 " --> pdb=" O ASP C 266 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL C 275 " --> pdb=" O ALA C 271 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 291 Processing helix chain 'C' and resid 299 through 349 removed outlier: 3.600A pdb=" N SER C 303 " --> pdb=" O CYS C 299 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 314 " --> pdb=" O ASN C 310 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL C 315 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C 318 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR C 339 " --> pdb=" O ASP C 335 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU C 344 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP C 349 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 371 removed outlier: 3.775A pdb=" N CYS C 367 " --> pdb=" O MET C 363 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN C 368 " --> pdb=" O GLN C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.553A pdb=" N ALA C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 441 removed outlier: 4.224A pdb=" N VAL C 418 " --> pdb=" O PRO C 414 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET C 423 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL C 441 " --> pdb=" O GLU C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 Processing helix chain 'C' and resid 454 through 470 removed outlier: 3.740A pdb=" N LEU C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR C 459 " --> pdb=" O LYS C 455 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 468 " --> pdb=" O LEU C 464 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 475 Processing helix chain 'C' and resid 477 through 507 removed outlier: 3.540A pdb=" N TRP C 481 " --> pdb=" O SER C 477 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 485 " --> pdb=" O TRP C 481 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP C 486 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER C 487 " --> pdb=" O SER C 483 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) Proline residue: C 493 - end of helix removed outlier: 3.643A pdb=" N CYS C 500 " --> pdb=" O ILE C 496 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 506 " --> pdb=" O MET C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 523 removed outlier: 3.520A pdb=" N LYS C 516 " --> pdb=" O ASP C 512 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET C 521 " --> pdb=" O ASP C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 536 Processing helix chain 'C' and resid 536 through 553 removed outlier: 3.564A pdb=" N LEU C 543 " --> pdb=" O PRO C 539 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 544 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 545 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE C 546 " --> pdb=" O MET C 542 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE C 550 " --> pdb=" O PHE C 546 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 608 removed outlier: 4.117A pdb=" N VAL C 585 " --> pdb=" O TRP C 581 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) Proline residue: C 593 - end of helix removed outlier: 4.671A pdb=" N ILE C 597 " --> pdb=" O PRO C 593 " (cutoff:3.500A) Proline residue: C 598 - end of helix removed outlier: 3.951A pdb=" N ALA C 601 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 605 " --> pdb=" O ALA C 601 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN C 608 " --> pdb=" O LYS C 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 53 removed outlier: 3.526A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 80 removed outlier: 3.821A pdb=" N MET D 62 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.525A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 97 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.939A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 130 removed outlier: 3.570A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER D 128 " --> pdb=" O SER D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.585A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 193 removed outlier: 3.625A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU D 171 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.674A pdb=" N GLU D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA D 191 " --> pdb=" O LYS D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 205 through 208 removed outlier: 3.595A pdb=" N GLU D 208 " --> pdb=" O GLY D 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 205 through 208' Processing helix chain 'D' and resid 220 through 249 removed outlier: 3.833A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.580A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 295 through 300 Processing helix chain 'D' and resid 305 through 318 removed outlier: 3.591A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL D 316 " --> pdb=" O GLU D 312 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 330 Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.647A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.696A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 412 removed outlier: 3.924A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 4.105A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 446 removed outlier: 3.530A pdb=" N LYS D 441 " --> pdb=" O ASN D 437 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.570A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 removed outlier: 3.533A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 removed outlier: 3.593A pdb=" N SER D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.940A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.576A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 559 removed outlier: 3.923A pdb=" N LYS D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.715A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.706A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 628 removed outlier: 3.508A pdb=" N ALA D 627 " --> pdb=" O SER D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 658 removed outlier: 3.634A pdb=" N MET D 640 " --> pdb=" O ASN D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 668 No H-bonds generated for 'chain 'D' and resid 666 through 668' Processing helix chain 'D' and resid 696 through 707 removed outlier: 3.621A pdb=" N LYS D 702 " --> pdb=" O THR D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 715 removed outlier: 3.542A pdb=" N ALA D 714 " --> pdb=" O ARG D 710 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE D 715 " --> pdb=" O ILE D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.631A pdb=" N VAL D 745 " --> pdb=" O ILE D 741 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'B' and resid 262 through 263 removed outlier: 6.035A 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 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 670 through 673 removed outlier: 6.503A pdb=" N ASP B 693 " --> pdb=" O ALA B 687 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 670 through 673 Processing sheet with id=AA6, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AA7, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.035A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AA9, first strand: chain 'D' and resid 670 through 673 removed outlier: 6.503A pdb=" N ASP D 693 " --> pdb=" O ALA D 687 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 670 through 673 990 hydrogen bonds defined for protein. 2904 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.86 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 6602 1.34 - 1.47: 6442 1.47 - 1.61: 9848 1.61 - 1.74: 2 1.74 - 1.88: 210 Bond restraints: 23104 Sorted by residual: bond pdb=" C31 3PH C 705 " pdb=" O31 3PH C 705 " ideal model delta sigma weight residual 1.325 1.456 -0.131 2.00e-02 2.50e+03 4.26e+01 bond pdb=" C31 3PH A 705 " pdb=" O31 3PH A 705 " ideal model delta sigma weight residual 1.325 1.456 -0.131 2.00e-02 2.50e+03 4.26e+01 bond pdb=" C21 3PH C 705 " pdb=" O21 3PH C 705 " ideal model delta sigma weight residual 1.328 1.454 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C21 3PH A 705 " pdb=" O21 3PH A 705 " ideal model delta sigma weight residual 1.328 1.454 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C21 3PH C 706 " pdb=" O21 3PH C 706 " ideal model delta sigma weight residual 1.328 1.453 -0.125 2.00e-02 2.50e+03 3.92e+01 ... (remaining 23099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 30502 2.67 - 5.35: 770 5.35 - 8.02: 92 8.02 - 10.70: 26 10.70 - 13.37: 12 Bond angle restraints: 31402 Sorted by residual: angle pdb=" N LEU A 485 " pdb=" CA LEU A 485 " pdb=" C LEU A 485 " ideal model delta sigma weight residual 111.28 121.05 -9.77 1.09e+00 8.42e-01 8.03e+01 angle pdb=" N LEU C 485 " pdb=" CA LEU C 485 " pdb=" C LEU C 485 " ideal model delta sigma weight residual 111.28 121.05 -9.77 1.09e+00 8.42e-01 8.03e+01 angle pdb=" C CYS D 133 " pdb=" N ASN D 134 " pdb=" CA ASN D 134 " ideal model delta sigma weight residual 120.49 132.77 -12.28 1.42e+00 4.96e-01 7.48e+01 angle pdb=" C CYS B 133 " pdb=" N ASN B 134 " pdb=" CA ASN B 134 " ideal model delta sigma weight residual 120.49 132.77 -12.28 1.42e+00 4.96e-01 7.48e+01 angle pdb=" C ILE C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.24 112.45 6.79 1.04e+00 9.25e-01 4.27e+01 ... (remaining 31397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 12536 17.97 - 35.93: 1160 35.93 - 53.90: 310 53.90 - 71.86: 66 71.86 - 89.83: 22 Dihedral angle restraints: 14094 sinusoidal: 6192 harmonic: 7902 Sorted by residual: dihedral pdb=" CB CYS B 344 " pdb=" SG CYS B 344 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -5.98 -80.02 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" CB CYS D 344 " pdb=" SG CYS D 344 " pdb=" SG CYS D 361 " pdb=" CB CYS D 361 " ideal model delta sinusoidal sigma weight residual -86.00 -5.98 -80.02 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" CA GLU B 145 " pdb=" C GLU B 145 " pdb=" N PRO B 146 " pdb=" CA PRO B 146 " ideal model delta harmonic sigma weight residual 180.00 152.58 27.42 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 14091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 3480 0.189 - 0.378: 38 0.378 - 0.567: 8 0.567 - 0.756: 0 0.756 - 0.945: 2 Chirality restraints: 3528 Sorted by residual: chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-02 2.50e+03 2.23e+03 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-02 2.50e+03 2.23e+03 chirality pdb=" CA TRP A 195 " pdb=" N TRP A 195 " pdb=" C TRP A 195 " pdb=" CB TRP A 195 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.71e+00 ... (remaining 3525 not shown) Planarity restraints: 3940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 492 " -0.069 5.00e-02 4.00e+02 9.99e-02 1.60e+01 pdb=" N PRO A 493 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO A 493 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 493 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 492 " 0.069 5.00e-02 4.00e+02 9.99e-02 1.60e+01 pdb=" N PRO C 493 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO C 493 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 493 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 217 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C GLU C 217 " 0.047 2.00e-02 2.50e+03 pdb=" O GLU C 217 " -0.017 2.00e-02 2.50e+03 pdb=" N THR C 218 " -0.016 2.00e-02 2.50e+03 ... (remaining 3937 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 256 2.63 - 3.20: 18988 3.20 - 3.76: 33375 3.76 - 4.33: 48993 4.33 - 4.90: 78899 Nonbonded interactions: 180511 Sorted by model distance: nonbonded pdb=" N GLU D 171 " pdb=" OE1 GLU D 171 " model vdw 2.060 3.120 nonbonded pdb=" N GLU B 171 " pdb=" OE1 GLU B 171 " model vdw 2.060 3.120 nonbonded pdb=" O ASN D 330 " pdb=" OG SER D 331 " model vdw 2.150 3.040 nonbonded pdb=" O ASN B 330 " pdb=" OG SER B 331 " model vdw 2.150 3.040 nonbonded pdb=" O CYS C 62 " pdb=" CA GLY C 67 " model vdw 2.257 3.440 ... (remaining 180506 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 'Q' selection = chain 'R' } 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.620 Find NCS groups from input model: 0.500 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:7.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 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 : 0.008 0.183 23152 Z= 0.392 Angle : 1.176 47.858 31536 Z= 0.635 Chirality : 0.069 0.945 3528 Planarity : 0.007 0.100 3916 Dihedral : 15.273 89.829 8984 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 1.11 % Allowed : 7.70 % Favored : 91.19 % Rotamer: Outliers : 3.28 % Allowed : 6.73 % Favored : 89.99 % Cbeta Deviations : 0.08 % 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: -5.88 (0.11), residues: 2700 helix: -4.22 (0.06), residues: 1608 sheet: 0.33 (0.67), residues: 44 loop : -3.27 (0.16), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 366 TYR 0.022 0.002 TYR C 560 PHE 0.036 0.002 PHE B 400 TRP 0.023 0.002 TRP A 56 HIS 0.007 0.001 HIS B 241 Details of bonding type rmsd covalent geometry : bond 0.00723 (23104) covalent geometry : angle 1.03831 (31402) SS BOND : bond 0.08266 ( 10) SS BOND : angle 11.63258 ( 20) hydrogen bonds : bond 0.30804 ( 982) hydrogen bonds : angle 9.79052 ( 2904) link_BETA1-4 : bond 0.01999 ( 14) link_BETA1-4 : angle 11.35693 ( 42) link_NAG-ASN : bond 0.04509 ( 24) link_NAG-ASN : angle 4.77320 ( 72) *********************** 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 420 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 342 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7770 (mm) REVERT: B 62 MET cc_start: 0.7843 (ptt) cc_final: 0.7553 (ptp) REVERT: B 152 MET cc_start: 0.9242 (mmm) cc_final: 0.8931 (mmm) REVERT: B 249 MET cc_start: 0.8905 (mtm) cc_final: 0.8564 (mtp) REVERT: B 334 THR cc_start: 0.8933 (t) cc_final: 0.8661 (m) REVERT: B 383 MET cc_start: 0.8954 (mtp) cc_final: 0.8738 (mtm) REVERT: B 474 MET cc_start: 0.9146 (mmm) cc_final: 0.8876 (mmp) REVERT: B 625 LYS cc_start: 0.8905 (mtpt) cc_final: 0.8639 (mtpt) REVERT: C 494 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7771 (mm) REVERT: D 62 MET cc_start: 0.7845 (ptt) cc_final: 0.7554 (ptp) REVERT: D 152 MET cc_start: 0.9244 (mmm) cc_final: 0.8934 (mmm) REVERT: D 249 MET cc_start: 0.8904 (mtm) cc_final: 0.8564 (mtp) REVERT: D 334 THR cc_start: 0.8932 (t) cc_final: 0.8661 (m) REVERT: D 383 MET cc_start: 0.8958 (mtp) cc_final: 0.8741 (mtm) REVERT: D 474 MET cc_start: 0.9148 (mmm) cc_final: 0.8877 (mmp) REVERT: D 625 LYS cc_start: 0.8905 (mtpt) cc_final: 0.8640 (mtpt) outliers start: 78 outliers final: 6 residues processed: 404 average time/residue: 0.6261 time to fit residues: 291.1612 Evaluate side-chains 188 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 180 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 680 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 293 ASN A 297 ASN A 310 ASN A 365 GLN A 574 GLN B 33 ASN B 42 GLN B 58 ASN B 64 ASN B 98 GLN B 101 GLN B 149 ASN B 194 ASN B 340 GLN B 373 HIS B 493 HIS B 505 HIS B 586 ASN B 599 ASN B 718 ASN C 40 GLN C 293 ASN C 297 ASN C 310 ASN C 365 GLN C 574 GLN D 33 ASN D 42 GLN D 58 ASN D 64 ASN D 98 GLN D 101 GLN D 149 ASN D 194 ASN D 340 GLN D 373 HIS D 493 HIS D 505 HIS D 586 ASN D 599 ASN D 718 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.145280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.084469 restraints weight = 38483.170| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.12 r_work: 0.2928 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23152 Z= 0.164 Angle : 0.739 14.117 31536 Z= 0.372 Chirality : 0.047 0.467 3528 Planarity : 0.006 0.070 3916 Dihedral : 9.578 59.995 3904 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.74 % Favored : 93.11 % Rotamer: Outliers : 1.77 % Allowed : 13.37 % Favored : 84.86 % 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: -3.37 (0.14), residues: 2700 helix: -1.86 (0.11), residues: 1632 sheet: 0.40 (1.22), residues: 20 loop : -2.76 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 678 TYR 0.015 0.002 TYR A 578 PHE 0.027 0.001 PHE A 546 TRP 0.016 0.001 TRP C 196 HIS 0.005 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00356 (23104) covalent geometry : angle 0.71085 (31402) SS BOND : bond 0.01053 ( 10) SS BOND : angle 2.29327 ( 20) hydrogen bonds : bond 0.06738 ( 982) hydrogen bonds : angle 4.80956 ( 2904) link_BETA1-4 : bond 0.00437 ( 14) link_BETA1-4 : angle 2.13815 ( 42) link_NAG-ASN : bond 0.00646 ( 24) link_NAG-ASN : angle 3.83931 ( 72) *********************** 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 240 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 198 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 HIS cc_start: 0.7649 (t70) cc_final: 0.7373 (t70) REVERT: A 210 MET cc_start: 0.7003 (tmm) cc_final: 0.6115 (ttt) REVERT: A 524 HIS cc_start: 0.5741 (OUTLIER) cc_final: 0.4421 (p-80) REVERT: B 34 HIS cc_start: 0.8761 (t-170) cc_final: 0.8465 (t70) REVERT: B 152 MET cc_start: 0.9526 (mmm) cc_final: 0.9272 (mmm) REVERT: B 383 MET cc_start: 0.9357 (mtp) cc_final: 0.9142 (mtm) REVERT: C 108 HIS cc_start: 0.7651 (t70) cc_final: 0.7375 (t70) REVERT: C 210 MET cc_start: 0.7001 (tmm) cc_final: 0.6113 (ttt) REVERT: C 524 HIS cc_start: 0.5739 (OUTLIER) cc_final: 0.4418 (p-80) REVERT: D 34 HIS cc_start: 0.8765 (t-170) cc_final: 0.8465 (t70) REVERT: D 152 MET cc_start: 0.9524 (mmm) cc_final: 0.9268 (mmm) REVERT: D 383 MET cc_start: 0.9360 (mtp) cc_final: 0.9145 (mtm) outliers start: 42 outliers final: 14 residues processed: 232 average time/residue: 0.6072 time to fit residues: 163.4608 Evaluate side-chains 164 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 689 LYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 559 ARG Chi-restraints excluded: chain D residue 689 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 231 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 202 optimal weight: 0.4980 chunk 157 optimal weight: 9.9990 chunk 69 optimal weight: 0.5980 chunk 131 optimal weight: 10.0000 chunk 195 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 GLN B 718 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 574 GLN D 718 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.142972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.082329 restraints weight = 38306.559| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.10 r_work: 0.2879 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 23152 Z= 0.204 Angle : 0.710 11.146 31536 Z= 0.356 Chirality : 0.048 0.419 3528 Planarity : 0.005 0.060 3916 Dihedral : 8.732 59.486 3894 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.89 % Favored : 92.96 % Rotamer: Outliers : 2.10 % Allowed : 14.55 % Favored : 83.35 % 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: -2.01 (0.15), residues: 2700 helix: -0.62 (0.13), residues: 1622 sheet: -0.15 (0.74), residues: 42 loop : -2.48 (0.17), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 710 TYR 0.019 0.002 TYR B 381 PHE 0.017 0.002 PHE B 400 TRP 0.016 0.001 TRP C 196 HIS 0.006 0.001 HIS B 241 Details of bonding type rmsd covalent geometry : bond 0.00484 (23104) covalent geometry : angle 0.68854 (31402) SS BOND : bond 0.01087 ( 10) SS BOND : angle 2.42325 ( 20) hydrogen bonds : bond 0.06047 ( 982) hydrogen bonds : angle 4.29856 ( 2904) link_BETA1-4 : bond 0.00363 ( 14) link_BETA1-4 : angle 2.01832 ( 42) link_NAG-ASN : bond 0.00668 ( 24) link_NAG-ASN : angle 3.12403 ( 72) *********************** 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 220 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 170 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 HIS cc_start: 0.7755 (t70) cc_final: 0.7464 (t70) REVERT: A 124 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7666 (mpt) REVERT: A 522 ILE cc_start: 0.6521 (pt) cc_final: 0.6273 (pt) REVERT: A 524 HIS cc_start: 0.5887 (OUTLIER) cc_final: 0.4542 (p-80) REVERT: B 60 GLN cc_start: 0.8603 (pm20) cc_final: 0.8335 (pm20) REVERT: B 152 MET cc_start: 0.9506 (mmm) cc_final: 0.9265 (mmm) REVERT: B 332 MET cc_start: 0.8608 (tpt) cc_final: 0.8320 (tpt) REVERT: B 334 THR cc_start: 0.9043 (t) cc_final: 0.8786 (t) REVERT: B 625 LYS cc_start: 0.9096 (mtpm) cc_final: 0.8784 (mttt) REVERT: C 108 HIS cc_start: 0.7758 (t70) cc_final: 0.7464 (t70) REVERT: C 124 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7665 (mpt) REVERT: C 522 ILE cc_start: 0.6523 (pt) cc_final: 0.6274 (pt) REVERT: C 524 HIS cc_start: 0.5889 (OUTLIER) cc_final: 0.4545 (p-80) REVERT: D 60 GLN cc_start: 0.8602 (pm20) cc_final: 0.8333 (pm20) REVERT: D 152 MET cc_start: 0.9510 (mmm) cc_final: 0.9267 (mmm) REVERT: D 332 MET cc_start: 0.8610 (tpt) cc_final: 0.8324 (tpt) REVERT: D 334 THR cc_start: 0.9045 (t) cc_final: 0.8788 (t) REVERT: D 625 LYS cc_start: 0.9097 (mtpm) cc_final: 0.8788 (mttt) outliers start: 50 outliers final: 16 residues processed: 210 average time/residue: 0.6197 time to fit residues: 150.7142 Evaluate side-chains 176 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 689 LYS Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 559 ARG Chi-restraints excluded: chain D residue 689 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 48 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 221 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 230 optimal weight: 0.7980 chunk 179 optimal weight: 9.9990 chunk 211 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN A 574 GLN B 718 ASN C 340 ASN C 574 GLN D 718 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.142615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.081875 restraints weight = 38292.982| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.06 r_work: 0.2875 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23152 Z= 0.189 Angle : 0.665 10.524 31536 Z= 0.335 Chirality : 0.047 0.402 3528 Planarity : 0.005 0.050 3916 Dihedral : 8.323 59.329 3894 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.11 % Favored : 92.74 % Rotamer: Outliers : 2.19 % Allowed : 15.22 % Favored : 82.59 % 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: -1.34 (0.16), residues: 2700 helix: -0.08 (0.13), residues: 1630 sheet: -0.42 (0.71), residues: 42 loop : -2.21 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 710 TYR 0.027 0.002 TYR B 381 PHE 0.022 0.001 PHE C 546 TRP 0.014 0.001 TRP C 196 HIS 0.006 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00450 (23104) covalent geometry : angle 0.64528 (31402) SS BOND : bond 0.01160 ( 10) SS BOND : angle 2.29513 ( 20) hydrogen bonds : bond 0.05459 ( 982) hydrogen bonds : angle 4.14729 ( 2904) link_BETA1-4 : bond 0.00184 ( 14) link_BETA1-4 : angle 1.94661 ( 42) link_NAG-ASN : bond 0.00605 ( 24) link_NAG-ASN : angle 2.94432 ( 72) *********************** 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 222 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 170 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 524 HIS cc_start: 0.5707 (OUTLIER) cc_final: 0.4288 (p-80) REVERT: B 60 GLN cc_start: 0.8484 (pm20) cc_final: 0.8212 (pm20) REVERT: B 152 MET cc_start: 0.9516 (mmm) cc_final: 0.9254 (mmm) REVERT: B 332 MET cc_start: 0.8607 (tpt) cc_final: 0.8274 (tpt) REVERT: B 334 THR cc_start: 0.9112 (t) cc_final: 0.8860 (t) REVERT: B 345 HIS cc_start: 0.8278 (t70) cc_final: 0.7924 (t70) REVERT: B 625 LYS cc_start: 0.9082 (mtpm) cc_final: 0.8848 (mttt) REVERT: C 124 MET cc_start: 0.7783 (mpt) cc_final: 0.7581 (mpt) REVERT: C 524 HIS cc_start: 0.5710 (OUTLIER) cc_final: 0.4293 (p-80) REVERT: D 60 GLN cc_start: 0.8487 (pm20) cc_final: 0.8216 (pm20) REVERT: D 152 MET cc_start: 0.9515 (mmm) cc_final: 0.9245 (mmm) REVERT: D 332 MET cc_start: 0.8606 (tpt) cc_final: 0.8275 (tpt) REVERT: D 334 THR cc_start: 0.9114 (t) cc_final: 0.8863 (t) REVERT: D 345 HIS cc_start: 0.8281 (t70) cc_final: 0.7929 (t70) REVERT: D 625 LYS cc_start: 0.9080 (mtpm) cc_final: 0.8849 (mttt) outliers start: 52 outliers final: 12 residues processed: 216 average time/residue: 0.5877 time to fit residues: 148.2641 Evaluate side-chains 174 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 365 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 85 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 221 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 chunk 219 optimal weight: 0.8980 chunk 157 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 GLN B 718 ASN C 574 GLN D 718 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.143010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.082984 restraints weight = 38245.897| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.10 r_work: 0.2897 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23152 Z= 0.146 Angle : 0.624 9.972 31536 Z= 0.312 Chirality : 0.045 0.392 3528 Planarity : 0.004 0.044 3916 Dihedral : 7.983 59.960 3894 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.44 % Favored : 93.41 % Rotamer: Outliers : 1.72 % Allowed : 16.44 % Favored : 81.83 % 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: -0.89 (0.16), residues: 2700 helix: 0.30 (0.13), residues: 1628 sheet: -0.36 (0.71), residues: 42 loop : -2.04 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 460 TYR 0.020 0.001 TYR B 381 PHE 0.024 0.001 PHE A 312 TRP 0.012 0.001 TRP C 196 HIS 0.004 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00339 (23104) covalent geometry : angle 0.60585 (31402) SS BOND : bond 0.00620 ( 10) SS BOND : angle 1.66383 ( 20) hydrogen bonds : bond 0.04865 ( 982) hydrogen bonds : angle 3.98917 ( 2904) link_BETA1-4 : bond 0.00295 ( 14) link_BETA1-4 : angle 1.83802 ( 42) link_NAG-ASN : bond 0.00557 ( 24) link_NAG-ASN : angle 2.75039 ( 72) *********************** 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 201 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 524 HIS cc_start: 0.5528 (OUTLIER) cc_final: 0.4213 (p-80) REVERT: A 542 MET cc_start: 0.7827 (ptm) cc_final: 0.7247 (ptp) REVERT: B 332 MET cc_start: 0.8607 (tpt) cc_final: 0.8296 (tpt) REVERT: B 334 THR cc_start: 0.9119 (t) cc_final: 0.8843 (t) REVERT: B 345 HIS cc_start: 0.8367 (t70) cc_final: 0.8014 (t70) REVERT: C 124 MET cc_start: 0.7922 (mpt) cc_final: 0.7668 (mpt) REVERT: C 524 HIS cc_start: 0.5522 (OUTLIER) cc_final: 0.4208 (p-80) REVERT: C 542 MET cc_start: 0.7829 (ptm) cc_final: 0.7252 (ptp) REVERT: D 332 MET cc_start: 0.8610 (tpt) cc_final: 0.8301 (tpt) REVERT: D 334 THR cc_start: 0.9118 (t) cc_final: 0.8841 (t) REVERT: D 345 HIS cc_start: 0.8377 (t70) cc_final: 0.8028 (t70) outliers start: 41 outliers final: 12 residues processed: 194 average time/residue: 0.6330 time to fit residues: 141.7697 Evaluate side-chains 166 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 365 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 200 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 chunk 115 optimal weight: 0.0070 chunk 103 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 91 optimal weight: 0.3980 chunk 156 optimal weight: 0.0870 chunk 9 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.0778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 GLN B 718 ASN C 574 GLN D 718 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.143754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.084138 restraints weight = 38461.135| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.37 r_work: 0.2894 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23152 Z= 0.125 Angle : 0.610 10.716 31536 Z= 0.303 Chirality : 0.044 0.384 3528 Planarity : 0.004 0.036 3916 Dihedral : 7.689 59.940 3894 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.67 % Favored : 93.19 % Rotamer: Outliers : 2.02 % Allowed : 16.48 % Favored : 81.50 % 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 (0.16), residues: 2700 helix: 0.58 (0.13), residues: 1614 sheet: -0.13 (0.73), residues: 42 loop : -1.99 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 460 TYR 0.016 0.001 TYR B 381 PHE 0.024 0.001 PHE A 546 TRP 0.011 0.001 TRP D 478 HIS 0.009 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00284 (23104) covalent geometry : angle 0.59275 (31402) SS BOND : bond 0.00914 ( 10) SS BOND : angle 1.50375 ( 20) hydrogen bonds : bond 0.04466 ( 982) hydrogen bonds : angle 3.90011 ( 2904) link_BETA1-4 : bond 0.00280 ( 14) link_BETA1-4 : angle 1.75295 ( 42) link_NAG-ASN : bond 0.00535 ( 24) link_NAG-ASN : angle 2.67179 ( 72) *********************** 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 210 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.6577 (tmt) cc_final: 0.6237 (tmt) REVERT: A 524 HIS cc_start: 0.5622 (OUTLIER) cc_final: 0.4274 (p-80) REVERT: B 62 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7675 (ptm) REVERT: B 332 MET cc_start: 0.8653 (tpt) cc_final: 0.8283 (tpt) REVERT: B 345 HIS cc_start: 0.8384 (t70) cc_final: 0.8046 (t70) REVERT: C 210 MET cc_start: 0.6573 (tmt) cc_final: 0.6232 (tmt) REVERT: C 524 HIS cc_start: 0.5620 (OUTLIER) cc_final: 0.4277 (p-80) REVERT: D 62 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7673 (ptm) REVERT: D 332 MET cc_start: 0.8659 (tpt) cc_final: 0.8291 (tpt) REVERT: D 345 HIS cc_start: 0.8389 (t70) cc_final: 0.8053 (t70) outliers start: 48 outliers final: 14 residues processed: 200 average time/residue: 0.6284 time to fit residues: 145.1835 Evaluate side-chains 166 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 365 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 250 optimal weight: 0.0670 chunk 259 optimal weight: 2.9990 chunk 78 optimal weight: 0.0970 chunk 49 optimal weight: 5.9990 chunk 217 optimal weight: 0.8980 overall best weight: 1.2120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 GLN B 34 HIS B 718 ASN C 574 GLN D 34 HIS D 718 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.144325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.088947 restraints weight = 38354.018| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.49 r_work: 0.2882 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23152 Z= 0.132 Angle : 0.623 10.978 31536 Z= 0.307 Chirality : 0.044 0.379 3528 Planarity : 0.004 0.035 3916 Dihedral : 7.539 59.884 3894 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.59 % Favored : 93.33 % Rotamer: Outliers : 1.93 % Allowed : 17.24 % Favored : 80.82 % 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: -0.40 (0.17), residues: 2700 helix: 0.74 (0.13), residues: 1614 sheet: 0.05 (0.76), residues: 42 loop : -1.91 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 460 TYR 0.016 0.001 TYR D 381 PHE 0.020 0.001 PHE A 312 TRP 0.019 0.001 TRP C 104 HIS 0.009 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00305 (23104) covalent geometry : angle 0.60648 (31402) SS BOND : bond 0.00775 ( 10) SS BOND : angle 1.71662 ( 20) hydrogen bonds : bond 0.04459 ( 982) hydrogen bonds : angle 3.86161 ( 2904) link_BETA1-4 : bond 0.00308 ( 14) link_BETA1-4 : angle 1.71687 ( 42) link_NAG-ASN : bond 0.00526 ( 24) link_NAG-ASN : angle 2.62449 ( 72) *********************** 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 200 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 0.873 Fit side-chains REVERT: A 210 MET cc_start: 0.6630 (tmt) cc_final: 0.6313 (tmt) REVERT: A 524 HIS cc_start: 0.5661 (OUTLIER) cc_final: 0.4269 (p-80) REVERT: B 332 MET cc_start: 0.8748 (tpt) cc_final: 0.8376 (tpt) REVERT: B 345 HIS cc_start: 0.8431 (t70) cc_final: 0.8097 (t70) REVERT: C 210 MET cc_start: 0.6622 (tmt) cc_final: 0.6304 (tmt) REVERT: C 524 HIS cc_start: 0.5658 (OUTLIER) cc_final: 0.4267 (p-80) REVERT: D 332 MET cc_start: 0.8753 (tpt) cc_final: 0.8379 (tpt) REVERT: D 345 HIS cc_start: 0.8438 (t70) cc_final: 0.8109 (t70) outliers start: 46 outliers final: 14 residues processed: 193 average time/residue: 0.6541 time to fit residues: 145.6012 Evaluate side-chains 168 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 558 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 231 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 262 optimal weight: 0.9990 chunk 254 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 GLN B 34 HIS B 718 ASN C 574 GLN D 34 HIS D 718 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.143498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.083558 restraints weight = 38169.346| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.09 r_work: 0.2909 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23152 Z= 0.139 Angle : 0.631 10.679 31536 Z= 0.311 Chirality : 0.045 0.467 3528 Planarity : 0.004 0.036 3916 Dihedral : 7.350 59.710 3890 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.52 % Favored : 93.41 % Rotamer: Outliers : 1.56 % Allowed : 17.45 % Favored : 80.99 % 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: -0.30 (0.17), residues: 2700 helix: 0.83 (0.13), residues: 1610 sheet: -0.02 (0.73), residues: 42 loop : -1.88 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 460 TYR 0.017 0.001 TYR B 381 PHE 0.024 0.001 PHE C 546 TRP 0.024 0.001 TRP C 104 HIS 0.011 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00323 (23104) covalent geometry : angle 0.60838 (31402) SS BOND : bond 0.00691 ( 10) SS BOND : angle 1.57244 ( 20) hydrogen bonds : bond 0.04500 ( 982) hydrogen bonds : angle 3.84968 ( 2904) link_BETA1-4 : bond 0.00299 ( 14) link_BETA1-4 : angle 1.70028 ( 42) link_NAG-ASN : bond 0.00527 ( 24) link_NAG-ASN : angle 3.25639 ( 72) *********************** 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 189 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.5565 (OUTLIER) cc_final: 0.5083 (tm) REVERT: A 210 MET cc_start: 0.6651 (tmt) cc_final: 0.6310 (tmt) REVERT: A 524 HIS cc_start: 0.5573 (OUTLIER) cc_final: 0.4151 (p-80) REVERT: B 332 MET cc_start: 0.8703 (tpt) cc_final: 0.8367 (tpt) REVERT: B 345 HIS cc_start: 0.8416 (t70) cc_final: 0.8094 (t70) REVERT: C 18 LEU cc_start: 0.5568 (OUTLIER) cc_final: 0.5087 (tm) REVERT: C 210 MET cc_start: 0.6650 (tmt) cc_final: 0.6308 (tmt) REVERT: C 524 HIS cc_start: 0.5573 (OUTLIER) cc_final: 0.4153 (p-80) REVERT: D 332 MET cc_start: 0.8708 (tpt) cc_final: 0.8373 (tpt) REVERT: D 345 HIS cc_start: 0.8427 (t70) cc_final: 0.8108 (t70) outliers start: 37 outliers final: 16 residues processed: 183 average time/residue: 0.6278 time to fit residues: 132.9112 Evaluate side-chains 164 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 558 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 110 optimal weight: 0.5980 chunk 41 optimal weight: 8.9990 chunk 244 optimal weight: 0.8980 chunk 249 optimal weight: 0.0980 chunk 107 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 259 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 131 optimal weight: 0.0010 chunk 134 optimal weight: 20.0000 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 GLN B 34 HIS B 718 ASN C 574 GLN D 34 HIS D 277 ASN D 718 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.144195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.084630 restraints weight = 38588.718| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.11 r_work: 0.2929 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23152 Z= 0.122 Angle : 0.631 12.876 31536 Z= 0.307 Chirality : 0.046 0.618 3528 Planarity : 0.004 0.034 3916 Dihedral : 7.191 59.647 3890 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.44 % Favored : 93.48 % Rotamer: Outliers : 1.35 % Allowed : 18.08 % Favored : 80.57 % 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: -0.18 (0.17), residues: 2700 helix: 0.93 (0.13), residues: 1608 sheet: -0.08 (0.72), residues: 42 loop : -1.82 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 678 TYR 0.014 0.001 TYR A 578 PHE 0.018 0.001 PHE A 312 TRP 0.025 0.001 TRP C 104 HIS 0.011 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00277 (23104) covalent geometry : angle 0.60523 (31402) SS BOND : bond 0.00626 ( 10) SS BOND : angle 1.46202 ( 20) hydrogen bonds : bond 0.04202 ( 982) hydrogen bonds : angle 3.81588 ( 2904) link_BETA1-4 : bond 0.00323 ( 14) link_BETA1-4 : angle 1.65245 ( 42) link_NAG-ASN : bond 0.00613 ( 24) link_NAG-ASN : angle 3.51638 ( 72) *********************** 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 183 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.868 Fit side-chains REVERT: A 18 LEU cc_start: 0.5683 (OUTLIER) cc_final: 0.5087 (tm) REVERT: A 210 MET cc_start: 0.6632 (tmt) cc_final: 0.6287 (tmt) REVERT: A 494 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7444 (mm) REVERT: A 524 HIS cc_start: 0.5839 (OUTLIER) cc_final: 0.4287 (p-80) REVERT: B 332 MET cc_start: 0.8700 (tpt) cc_final: 0.8363 (tpt) REVERT: B 345 HIS cc_start: 0.8433 (t70) cc_final: 0.8121 (t70) REVERT: C 18 LEU cc_start: 0.5685 (OUTLIER) cc_final: 0.5091 (tm) REVERT: C 210 MET cc_start: 0.6627 (tmt) cc_final: 0.6282 (tmt) REVERT: C 494 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7449 (mm) REVERT: C 524 HIS cc_start: 0.5840 (OUTLIER) cc_final: 0.4293 (p-80) REVERT: D 332 MET cc_start: 0.8701 (tpt) cc_final: 0.8361 (tpt) REVERT: D 345 HIS cc_start: 0.8440 (t70) cc_final: 0.8129 (t70) outliers start: 32 outliers final: 14 residues processed: 179 average time/residue: 0.6253 time to fit residues: 129.3803 Evaluate side-chains 166 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 365 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 262 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 163 optimal weight: 20.0000 chunk 182 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 83 optimal weight: 0.0870 chunk 205 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 GLN B 34 HIS B 718 ASN C 574 GLN D 34 HIS D 718 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.142631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.082436 restraints weight = 38487.637| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.11 r_work: 0.2890 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23152 Z= 0.169 Angle : 0.658 11.730 31536 Z= 0.325 Chirality : 0.046 0.431 3528 Planarity : 0.004 0.043 3916 Dihedral : 7.191 59.924 3890 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.81 % Favored : 93.11 % Rotamer: Outliers : 1.26 % Allowed : 18.38 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.16), residues: 2700 helix: 0.84 (0.13), residues: 1614 sheet: -0.15 (0.71), residues: 42 loop : -1.80 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 710 TYR 0.028 0.001 TYR B 381 PHE 0.019 0.001 PHE A 312 TRP 0.026 0.001 TRP C 104 HIS 0.011 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00403 (23104) covalent geometry : angle 0.63804 (31402) SS BOND : bond 0.00722 ( 10) SS BOND : angle 1.75558 ( 20) hydrogen bonds : bond 0.04894 ( 982) hydrogen bonds : angle 3.88495 ( 2904) link_BETA1-4 : bond 0.00301 ( 14) link_BETA1-4 : angle 1.69655 ( 42) link_NAG-ASN : bond 0.00538 ( 24) link_NAG-ASN : angle 3.13344 ( 72) ********************** 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 183 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.884 Fit side-chains REVERT: A 210 MET cc_start: 0.6711 (tmt) cc_final: 0.6348 (tmt) REVERT: A 437 GLU cc_start: 0.6747 (tm-30) cc_final: 0.6546 (tm-30) REVERT: A 494 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7512 (mm) REVERT: A 502 MET cc_start: 0.6637 (ttm) cc_final: 0.6426 (tmm) REVERT: A 524 HIS cc_start: 0.5923 (OUTLIER) cc_final: 0.4753 (p-80) REVERT: B 332 MET cc_start: 0.8648 (tpt) cc_final: 0.8332 (tpt) REVERT: B 345 HIS cc_start: 0.8455 (t70) cc_final: 0.8144 (t70) REVERT: C 210 MET cc_start: 0.6705 (tmt) cc_final: 0.6341 (tmt) REVERT: C 437 GLU cc_start: 0.6770 (tm-30) cc_final: 0.6564 (tm-30) REVERT: C 494 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7509 (mm) REVERT: C 502 MET cc_start: 0.6635 (ttm) cc_final: 0.6424 (tmm) REVERT: C 524 HIS cc_start: 0.5926 (OUTLIER) cc_final: 0.4758 (p-80) REVERT: D 332 MET cc_start: 0.8640 (tpt) cc_final: 0.8330 (tpt) REVERT: D 345 HIS cc_start: 0.8460 (t70) cc_final: 0.8153 (t70) outliers start: 30 outliers final: 12 residues processed: 177 average time/residue: 0.6468 time to fit residues: 131.5641 Evaluate side-chains 160 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 524 HIS Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 365 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 178 optimal weight: 0.0470 chunk 78 optimal weight: 0.4980 chunk 134 optimal weight: 20.0000 chunk 152 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 25 optimal weight: 0.0040 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.6492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 GLN B 34 HIS B 718 ASN C 574 GLN D 34 HIS D 718 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.144235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.084894 restraints weight = 38549.537| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.10 r_work: 0.2937 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23152 Z= 0.116 Angle : 0.615 11.617 31536 Z= 0.303 Chirality : 0.044 0.367 3528 Planarity : 0.004 0.032 3916 Dihedral : 6.977 59.770 3890 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.09 % Allowed : 18.59 % Favored : 80.32 % 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: -0.03 (0.17), residues: 2700 helix: 1.01 (0.13), residues: 1614 sheet: -0.06 (0.71), residues: 42 loop : -1.70 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 678 TYR 0.015 0.001 TYR A 578 PHE 0.023 0.001 PHE C 546 TRP 0.021 0.001 TRP C 104 HIS 0.012 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00260 (23104) covalent geometry : angle 0.59657 (31402) SS BOND : bond 0.01095 ( 10) SS BOND : angle 1.80351 ( 20) hydrogen bonds : bond 0.04115 ( 982) hydrogen bonds : angle 3.80831 ( 2904) link_BETA1-4 : bond 0.00268 ( 14) link_BETA1-4 : angle 1.61236 ( 42) link_NAG-ASN : bond 0.00544 ( 24) link_NAG-ASN : angle 2.87094 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10612.73 seconds wall clock time: 180 minutes 46.58 seconds (10846.58 seconds total)