Starting phenix.real_space_refine on Sun Sep 13 10:36:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6m18_30040/09_2026/6m18_30040.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m18_30040/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6m18_30040/09_2026/6m18_30040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m18_30040/09_2026/6m18_30040.map" model { file = "/net/cci-nas-00/data/ceres_data/6m18_30040/09_2026/6m18_30040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m18_30040/09_2026/6m18_30040.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6m18_30040/09_2026/6m18_30040.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6m18_30040/09_2026/6m18_30040.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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: 5.07, per 1000 atoms: 0.22 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: 1.96 Conformation dependent library (CDL) restraints added in 857.0 milliseconds 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: 0.42 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: 3.17 Time building geometry restraints manager: 2.46 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: 11826 17.97 - 35.93: 1088 35.93 - 53.90: 264 53.90 - 71.86: 60 71.86 - 89.83: 22 Dihedral angle restraints: 13260 sinusoidal: 5358 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 13257 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: 0.05 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: 1.870 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: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.360 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 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:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 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 : 15.354 89.829 8150 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/Z covalent geometry : bond 0.00723 / 0.37 (23104) covalent geometry : angle 1.03831 / 0.60 (31402) SS BOND : bond 0.08266 / 5.91 ( 10) SS BOND : angle 11.63258 / 7.32 ( 20) hydrogen bonds : bond 0.30804 / 20.17 ( 982) hydrogen bonds : angle 9.79052 / 6.71 ( 2904) link_BETA1-4 : bond 0.01999 / 1.11 ( 14) link_BETA1-4 : angle 11.35693 / 9.45 ( 42) link_NAG-ASN : bond 0.04509 / 2.94 ( 24) link_NAG-ASN : angle 4.77320 / 3.06 ( 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 : 0.759 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: 0.5633 time to fit residues: 263.1816 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 : 1.090 ------------------------------------------------------------------------------- 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... 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 94 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: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.145256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.084454 restraints weight = 38492.522| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.12 r_work: 0.2927 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23152 Z= 0.166 Angle : 0.740 13.259 31536 Z= 0.372 Chirality : 0.047 0.433 3528 Planarity : 0.006 0.070 3916 Dihedral : 8.519 59.430 3070 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.89 % Favored : 92.96 % Rotamer: Outliers : 1.85 % Allowed : 13.54 % Favored : 84.61 % 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: -3.33 (0.14), residues: 2700 helix: -1.84 (0.11), residues: 1642 sheet: 0.36 (1.21), residues: 20 loop : -2.72 (0.17), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 678 TYR 0.016 0.002 TYR C 209 PHE 0.026 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/Z covalent geometry : bond 0.00359 / 0.16 (23104) covalent geometry : angle 0.71367 / 0.37 (31402) SS BOND : bond 0.02631 / 1.35 ( 10) SS BOND : angle 2.33781 / 1.28 ( 20) hydrogen bonds : bond 0.06563 / 4.33 ( 982) hydrogen bonds : angle 4.77721 / 3.25 ( 2904) link_BETA1-4 : bond 0.00205 / 0.13 ( 14) link_BETA1-4 : angle 1.98173 / 1.31 ( 42) link_NAG-ASN : bond 0.00775 / 0.39 ( 24) link_NAG-ASN : angle 3.73166 / 2.51 ( 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 242 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 HIS cc_start: 0.7676 (t70) cc_final: 0.7402 (t70) REVERT: A 210 MET cc_start: 0.7086 (tmm) cc_final: 0.6153 (ttt) REVERT: A 524 HIS cc_start: 0.5777 (OUTLIER) cc_final: 0.4462 (p-80) REVERT: B 34 HIS cc_start: 0.8774 (t-170) cc_final: 0.8482 (t70) REVERT: B 152 MET cc_start: 0.9525 (mmm) cc_final: 0.9273 (mmm) REVERT: B 383 MET cc_start: 0.9352 (mtp) cc_final: 0.9134 (mtm) REVERT: C 108 HIS cc_start: 0.7680 (t70) cc_final: 0.7405 (t70) REVERT: C 210 MET cc_start: 0.7081 (tmm) cc_final: 0.6151 (ttt) REVERT: C 524 HIS cc_start: 0.5774 (OUTLIER) cc_final: 0.4461 (p-80) REVERT: D 34 HIS cc_start: 0.8773 (t-170) cc_final: 0.8476 (t70) REVERT: D 152 MET cc_start: 0.9526 (mmm) cc_final: 0.9272 (mmm) REVERT: D 383 MET cc_start: 0.9354 (mtp) cc_final: 0.9138 (mtm) outliers start: 44 outliers final: 14 residues processed: 232 average time/residue: 0.5547 time to fit residues: 150.1366 Evaluate side-chains 167 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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: 0.9990 chunk 175 optimal weight: 2.9990 chunk 160 optimal weight: 0.0980 chunk 202 optimal weight: 0.6980 chunk 157 optimal weight: 10.0000 chunk 69 optimal weight: 0.4980 chunk 131 optimal weight: 10.0000 chunk 195 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN A 574 GLN B 718 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 GLN 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 = 0.4061 r_free = 0.4061 target = 0.145349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.085365 restraints weight = 38359.512| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.11 r_work: 0.2938 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23152 Z= 0.137 Angle : 0.662 11.338 31536 Z= 0.329 Chirality : 0.045 0.419 3528 Planarity : 0.005 0.057 3916 Dihedral : 7.809 58.048 3060 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.74 % Favored : 93.11 % Rotamer: Outliers : 1.60 % Allowed : 14.38 % Favored : 84.02 % 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: -1.96 (0.15), residues: 2700 helix: -0.59 (0.13), residues: 1628 sheet: -0.11 (0.72), residues: 42 loop : -2.46 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 644 TYR 0.016 0.001 TYR A 578 PHE 0.017 0.001 PHE C 529 TRP 0.015 0.001 TRP C 196 HIS 0.004 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (23104) covalent geometry : angle 0.64128 / 0.32 (31402) SS BOND : bond 0.00998 / 0.51 ( 10) SS BOND : angle 1.90047 / 0.87 ( 20) hydrogen bonds : bond 0.05281 / 3.48 ( 982) hydrogen bonds : angle 4.20610 / 2.87 ( 2904) link_BETA1-4 : bond 0.00231 / 0.11 ( 14) link_BETA1-4 : angle 1.75562 / 1.16 ( 42) link_NAG-ASN : bond 0.00629 / 0.31 ( 24) link_NAG-ASN : angle 3.10452 / 2.07 ( 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 209 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7806 (ttp-110) REVERT: A 108 HIS cc_start: 0.7725 (t70) cc_final: 0.7427 (t70) REVERT: A 124 MET cc_start: 0.7898 (mpt) cc_final: 0.7666 (mpt) REVERT: A 524 HIS cc_start: 0.5759 (OUTLIER) cc_final: 0.4464 (p-80) REVERT: B 152 MET cc_start: 0.9494 (mmm) cc_final: 0.9218 (mmm) REVERT: B 332 MET cc_start: 0.8605 (tpt) cc_final: 0.8299 (tpt) REVERT: B 625 LYS cc_start: 0.9074 (mtpm) cc_final: 0.8780 (mttt) REVERT: C 57 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7806 (ttp-110) REVERT: C 108 HIS cc_start: 0.7721 (t70) cc_final: 0.7423 (t70) REVERT: C 124 MET cc_start: 0.7900 (mpt) cc_final: 0.7666 (mpt) REVERT: C 524 HIS cc_start: 0.5761 (OUTLIER) cc_final: 0.4463 (p-80) REVERT: D 152 MET cc_start: 0.9495 (mmm) cc_final: 0.9218 (mmm) REVERT: D 332 MET cc_start: 0.8606 (tpt) cc_final: 0.8302 (tpt) REVERT: D 625 LYS cc_start: 0.9078 (mtpm) cc_final: 0.8786 (mttt) outliers start: 38 outliers final: 12 residues processed: 203 average time/residue: 0.5898 time to fit residues: 139.1011 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 : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ARG 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 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 57 ARG 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 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: 5.9990 chunk 16 optimal weight: 2.9990 chunk 221 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 230 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 chunk 211 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 ASN A 365 GLN A 527 ASN A 574 GLN B 718 ASN C 340 ASN C 365 GLN C 527 ASN C 574 GLN D 718 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.141602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.081317 restraints weight = 38403.912| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.45 r_work: 0.2825 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 23152 Z= 0.281 Angle : 0.730 10.486 31536 Z= 0.368 Chirality : 0.050 0.394 3528 Planarity : 0.005 0.050 3916 Dihedral : 7.877 59.908 3060 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.22 % Favored : 92.63 % Rotamer: Outliers : 2.10 % Allowed : 15.48 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.16), residues: 2700 helix: -0.23 (0.13), residues: 1638 sheet: -0.40 (0.71), residues: 42 loop : -2.23 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 710 TYR 0.034 0.002 TYR B 381 PHE 0.025 0.002 PHE A 546 TRP 0.015 0.002 TRP C 196 HIS 0.007 0.002 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.28 (23104) covalent geometry : angle 0.71223 / 0.36 (31402) SS BOND : bond 0.00402 / 0.24 ( 10) SS BOND : angle 2.14886 / 1.01 ( 20) hydrogen bonds : bond 0.06193 / 4.06 ( 982) hydrogen bonds : angle 4.24803 / 2.92 ( 2904) link_BETA1-4 : bond 0.00371 / 0.16 ( 14) link_BETA1-4 : angle 1.85795 / 1.17 ( 42) link_NAG-ASN : bond 0.00674 / 0.35 ( 24) link_NAG-ASN : angle 2.98455 / 1.98 ( 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 213 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 163 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 522 ILE cc_start: 0.6409 (pt) cc_final: 0.6078 (pt) REVERT: A 524 HIS cc_start: 0.5750 (OUTLIER) cc_final: 0.4333 (p-80) REVERT: B 60 GLN cc_start: 0.8517 (pm20) cc_final: 0.8243 (pm20) REVERT: B 152 MET cc_start: 0.9546 (mmm) cc_final: 0.9292 (mmm) REVERT: B 332 MET cc_start: 0.8657 (tpt) cc_final: 0.8325 (tpt) REVERT: B 334 THR cc_start: 0.9097 (t) cc_final: 0.8846 (t) REVERT: B 345 HIS cc_start: 0.8287 (t70) cc_final: 0.7930 (t70) REVERT: B 625 LYS cc_start: 0.9141 (mtpm) cc_final: 0.8846 (mttt) REVERT: C 522 ILE cc_start: 0.6405 (pt) cc_final: 0.6077 (pt) REVERT: C 524 HIS cc_start: 0.5751 (OUTLIER) cc_final: 0.4333 (p-80) REVERT: D 60 GLN cc_start: 0.8522 (pm20) cc_final: 0.8247 (pm20) REVERT: D 152 MET cc_start: 0.9549 (mmm) cc_final: 0.9292 (mmm) REVERT: D 332 MET cc_start: 0.8652 (tpt) cc_final: 0.8323 (tpt) REVERT: D 334 THR cc_start: 0.9100 (t) cc_final: 0.8850 (t) REVERT: D 345 HIS cc_start: 0.8290 (t70) cc_final: 0.7934 (t70) REVERT: D 625 LYS cc_start: 0.9138 (mtpm) cc_final: 0.8845 (mttt) outliers start: 50 outliers final: 16 residues processed: 207 average time/residue: 0.5762 time to fit residues: 138.9489 Evaluate side-chains 170 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS 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 689 LYS Chi-restraints excluded: chain C residue 211 CYS 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 689 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 85 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 221 optimal weight: 8.9990 chunk 207 optimal weight: 0.8980 chunk 219 optimal weight: 0.6980 chunk 157 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4042 r_free = 0.4042 target = 0.144031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.084342 restraints weight = 38223.251| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.35 r_work: 0.2898 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23152 Z= 0.121 Angle : 0.608 10.192 31536 Z= 0.304 Chirality : 0.044 0.395 3528 Planarity : 0.004 0.045 3916 Dihedral : 7.543 59.727 3060 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.37 % Favored : 93.48 % Rotamer: Outliers : 1.85 % Allowed : 16.19 % Favored : 81.96 % 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: -0.98 (0.16), residues: 2700 helix: 0.24 (0.13), residues: 1630 sheet: -0.32 (0.71), residues: 42 loop : -2.10 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 169 TYR 0.015 0.001 TYR A 578 PHE 0.024 0.001 PHE C 312 TRP 0.013 0.001 TRP C 196 HIS 0.003 0.001 HIS B 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (23104) covalent geometry : angle 0.59012 / 0.30 (31402) SS BOND : bond 0.00583 / 0.30 ( 10) SS BOND : angle 1.55934 / 0.74 ( 20) hydrogen bonds : bond 0.04660 / 3.05 ( 982) hydrogen bonds : angle 3.99295 / 2.74 ( 2904) link_BETA1-4 : bond 0.00340 / 0.19 ( 14) link_BETA1-4 : angle 1.70960 / 1.12 ( 42) link_NAG-ASN : bond 0.00554 / 0.28 ( 24) link_NAG-ASN : angle 2.72614 / 1.82 ( 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 205 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7582 (mpt) REVERT: A 524 HIS cc_start: 0.5717 (OUTLIER) cc_final: 0.4380 (p-80) REVERT: B 60 GLN cc_start: 0.8499 (pm20) cc_final: 0.8204 (pm20) REVERT: B 332 MET cc_start: 0.8592 (tpt) cc_final: 0.8238 (tpt) REVERT: B 345 HIS cc_start: 0.8284 (t70) cc_final: 0.7929 (t70) REVERT: C 124 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7578 (mpt) REVERT: C 524 HIS cc_start: 0.5714 (OUTLIER) cc_final: 0.4380 (p-80) REVERT: D 60 GLN cc_start: 0.8506 (pm20) cc_final: 0.8209 (pm20) REVERT: D 332 MET cc_start: 0.8592 (tpt) cc_final: 0.8238 (tpt) REVERT: D 345 HIS cc_start: 0.8288 (t70) cc_final: 0.7934 (t70) outliers start: 44 outliers final: 10 residues processed: 201 average time/residue: 0.6152 time to fit residues: 143.0340 Evaluate side-chains 162 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 211 CYS 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 330 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 211 CYS 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 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: 7.9990 chunk 152 optimal weight: 8.9990 chunk 115 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 91 optimal weight: 0.2980 chunk 156 optimal weight: 0.9980 chunk 9 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4049 r_free = 0.4049 target = 0.144531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.085383 restraints weight = 38635.931| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.25 r_work: 0.2916 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23152 Z= 0.117 Angle : 0.605 9.916 31536 Z= 0.301 Chirality : 0.043 0.387 3528 Planarity : 0.004 0.037 3916 Dihedral : 7.389 59.672 3060 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.48 % Favored : 93.37 % Rotamer: Outliers : 1.51 % Allowed : 16.82 % Favored : 81.67 % 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: -0.61 (0.16), residues: 2700 helix: 0.57 (0.13), residues: 1618 sheet: -0.18 (0.73), residues: 42 loop : -2.00 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 460 TYR 0.012 0.001 TYR A 578 PHE 0.026 0.001 PHE A 312 TRP 0.010 0.001 TRP C 196 HIS 0.003 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (23104) covalent geometry : angle 0.58898 / 0.30 (31402) SS BOND : bond 0.00847 / 0.43 ( 10) SS BOND : angle 1.79856 / 0.76 ( 20) hydrogen bonds : bond 0.04300 / 2.81 ( 982) hydrogen bonds : angle 3.87072 / 2.65 ( 2904) link_BETA1-4 : bond 0.00315 / 0.18 ( 14) link_BETA1-4 : angle 1.64595 / 1.07 ( 42) link_NAG-ASN : bond 0.00542 / 0.27 ( 24) link_NAG-ASN : angle 2.59825 / 1.73 ( 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 198 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7555 (mpt) REVERT: A 524 HIS cc_start: 0.5684 (OUTLIER) cc_final: 0.4308 (p-80) REVERT: B 60 GLN cc_start: 0.8490 (pm20) cc_final: 0.8212 (pm20) REVERT: B 62 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7858 (ptm) REVERT: B 332 MET cc_start: 0.8695 (tpt) cc_final: 0.8288 (tpt) REVERT: B 345 HIS cc_start: 0.8311 (t70) cc_final: 0.7966 (t70) REVERT: C 124 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7559 (mpt) REVERT: C 524 HIS cc_start: 0.5670 (OUTLIER) cc_final: 0.4307 (p-80) REVERT: D 60 GLN cc_start: 0.8496 (pm20) cc_final: 0.8215 (pm20) REVERT: D 62 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7853 (ptm) REVERT: D 332 MET cc_start: 0.8691 (tpt) cc_final: 0.8286 (tpt) REVERT: D 345 HIS cc_start: 0.8314 (t70) cc_final: 0.7970 (t70) outliers start: 36 outliers final: 11 residues processed: 190 average time/residue: 0.6301 time to fit residues: 137.6229 Evaluate side-chains 169 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 211 CYS 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 62 MET Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 211 CYS 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 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: 0.0870 chunk 89 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 250 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 217 optimal weight: 0.1980 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4039 r_free = 0.4039 target = 0.143919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.083988 restraints weight = 38450.290| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.10 r_work: 0.2918 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23152 Z= 0.133 Angle : 0.621 11.156 31536 Z= 0.306 Chirality : 0.044 0.380 3528 Planarity : 0.004 0.034 3916 Dihedral : 7.354 59.883 3060 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.63 % Favored : 93.30 % Rotamer: Outliers : 1.60 % Allowed : 16.99 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.17), residues: 2700 helix: 0.70 (0.13), residues: 1614 sheet: 0.01 (0.75), residues: 42 loop : -1.96 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 710 TYR 0.019 0.001 TYR B 381 PHE 0.022 0.001 PHE A 312 TRP 0.011 0.001 TRP B 478 HIS 0.004 0.001 HIS B 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (23104) covalent geometry : angle 0.60565 / 0.30 (31402) SS BOND : bond 0.00785 / 0.40 ( 10) SS BOND : angle 1.77510 / 0.77 ( 20) hydrogen bonds : bond 0.04510 / 2.95 ( 982) hydrogen bonds : angle 3.84227 / 2.63 ( 2904) link_BETA1-4 : bond 0.00284 / 0.17 ( 14) link_BETA1-4 : angle 1.61394 / 1.05 ( 42) link_NAG-ASN : bond 0.00519 / 0.26 ( 24) link_NAG-ASN : angle 2.55428 / 1.69 ( 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 195 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7624 (mpt) REVERT: A 354 ASN cc_start: 0.7749 (OUTLIER) cc_final: 0.7534 (m-40) REVERT: A 524 HIS cc_start: 0.5634 (OUTLIER) cc_final: 0.4244 (p-80) REVERT: B 61 ASN cc_start: 0.8878 (t0) cc_final: 0.8551 (t0) REVERT: B 62 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7707 (ptm) REVERT: B 332 MET cc_start: 0.8677 (tpt) cc_final: 0.8320 (tpt) REVERT: B 345 HIS cc_start: 0.8368 (t70) cc_final: 0.8030 (t70) REVERT: C 124 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7625 (mpt) REVERT: C 354 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7547 (m-40) REVERT: C 524 HIS cc_start: 0.5632 (OUTLIER) cc_final: 0.4239 (p-80) REVERT: D 61 ASN cc_start: 0.8887 (t0) cc_final: 0.8561 (t0) REVERT: D 62 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7702 (ptm) REVERT: D 332 MET cc_start: 0.8679 (tpt) cc_final: 0.8322 (tpt) REVERT: D 345 HIS cc_start: 0.8367 (t70) cc_final: 0.8032 (t70) outliers start: 38 outliers final: 14 residues processed: 189 average time/residue: 0.5626 time to fit residues: 123.5461 Evaluate side-chains 173 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 443 LEU 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 62 MET Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 443 LEU 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 62 MET Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 365 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 231 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 165 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 262 optimal weight: 0.9980 chunk 254 optimal weight: 4.9990 chunk 244 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 574 GLN C 574 GLN D 277 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.144458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.084964 restraints weight = 38210.663| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.10 r_work: 0.2938 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.3664 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= 0.119 Angle : 0.606 10.114 31536 Z= 0.299 Chirality : 0.043 0.377 3528 Planarity : 0.004 0.034 3916 Dihedral : 7.227 59.913 3060 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.19 % Favored : 93.74 % Rotamer: Outliers : 1.51 % Allowed : 17.28 % Favored : 81.20 % 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: 0.84 (0.13), residues: 1614 sheet: -0.14 (0.72), residues: 42 loop : -1.89 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 460 TYR 0.015 0.001 TYR A 578 PHE 0.024 0.001 PHE C 546 TRP 0.021 0.001 TRP C 104 HIS 0.004 0.001 HIS B 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (23104) covalent geometry : angle 0.59133 / 0.30 (31402) SS BOND : bond 0.00639 / 0.33 ( 10) SS BOND : angle 1.43545 / 0.65 ( 20) hydrogen bonds : bond 0.04207 / 2.75 ( 982) hydrogen bonds : angle 3.79881 / 2.59 ( 2904) link_BETA1-4 : bond 0.00300 / 0.17 ( 14) link_BETA1-4 : angle 1.56355 / 1.02 ( 42) link_NAG-ASN : bond 0.00513 / 0.26 ( 24) link_NAG-ASN : angle 2.49045 / 1.65 ( 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 192 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7611 (mpt) REVERT: A 354 ASN cc_start: 0.7723 (OUTLIER) cc_final: 0.7505 (m-40) REVERT: A 502 MET cc_start: 0.6572 (OUTLIER) cc_final: 0.6314 (tmm) REVERT: A 524 HIS cc_start: 0.5639 (OUTLIER) cc_final: 0.4139 (p-80) REVERT: B 61 ASN cc_start: 0.8908 (t0) cc_final: 0.8573 (t0) REVERT: B 332 MET cc_start: 0.8695 (tpt) cc_final: 0.8334 (tpt) REVERT: B 345 HIS cc_start: 0.8341 (t70) cc_final: 0.8017 (t70) REVERT: C 124 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7612 (mpt) REVERT: C 354 ASN cc_start: 0.7725 (OUTLIER) cc_final: 0.7512 (m-40) REVERT: C 502 MET cc_start: 0.6569 (OUTLIER) cc_final: 0.6319 (tmm) REVERT: C 524 HIS cc_start: 0.5633 (OUTLIER) cc_final: 0.4164 (p-80) REVERT: D 61 ASN cc_start: 0.8913 (t0) cc_final: 0.8580 (t0) REVERT: D 332 MET cc_start: 0.8695 (tpt) cc_final: 0.8331 (tpt) REVERT: D 345 HIS cc_start: 0.8350 (t70) cc_final: 0.8028 (t70) outliers start: 36 outliers final: 11 residues processed: 184 average time/residue: 0.5757 time to fit residues: 122.9159 Evaluate side-chains 171 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 502 MET 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 365 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 502 MET 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 365 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 110 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 244 optimal weight: 0.9980 chunk 249 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 149 optimal weight: 9.9990 chunk 259 optimal weight: 3.9990 chunk 154 optimal weight: 0.3980 chunk 131 optimal weight: 9.9990 chunk 134 optimal weight: 20.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 574 GLN B 34 HIS C 574 GLN D 34 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.144399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.084721 restraints weight = 38533.932| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.13 r_work: 0.2932 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3783 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= 0.123 Angle : 0.605 10.412 31536 Z= 0.300 Chirality : 0.043 0.373 3528 Planarity : 0.004 0.033 3916 Dihedral : 7.141 59.966 3060 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.22 % Favored : 93.70 % Rotamer: Outliers : 1.14 % Allowed : 17.75 % Favored : 81.12 % 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: -0.14 (0.17), residues: 2700 helix: 0.97 (0.14), residues: 1610 sheet: -0.08 (0.72), residues: 42 loop : -1.81 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 460 TYR 0.015 0.001 TYR C 578 PHE 0.020 0.001 PHE A 312 TRP 0.027 0.001 TRP A 104 HIS 0.012 0.001 HIS D 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (23104) covalent geometry : angle 0.59042 / 0.30 (31402) SS BOND : bond 0.00629 / 0.32 ( 10) SS BOND : angle 1.52819 / 0.69 ( 20) hydrogen bonds : bond 0.04222 / 2.77 ( 982) hydrogen bonds : angle 3.78012 / 2.59 ( 2904) link_BETA1-4 : bond 0.00300 / 0.17 ( 14) link_BETA1-4 : angle 1.54150 / 1.00 ( 42) link_NAG-ASN : bond 0.00504 / 0.25 ( 24) link_NAG-ASN : angle 2.45327 / 1.62 ( 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 184 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.785 Fit side-chains REVERT: A 124 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7655 (mpt) REVERT: A 494 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7575 (mm) REVERT: A 502 MET cc_start: 0.6656 (tmm) cc_final: 0.6310 (tmm) REVERT: A 521 MET cc_start: 0.5599 (mmt) cc_final: 0.5368 (mmt) REVERT: A 524 HIS cc_start: 0.5903 (OUTLIER) cc_final: 0.4611 (p-80) REVERT: B 61 ASN cc_start: 0.8843 (t0) cc_final: 0.8443 (t0) REVERT: B 332 MET cc_start: 0.8696 (tpt) cc_final: 0.8350 (tpt) REVERT: B 345 HIS cc_start: 0.8381 (t70) cc_final: 0.8063 (t70) REVERT: C 124 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7656 (mpt) REVERT: C 494 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7576 (mm) REVERT: C 502 MET cc_start: 0.6654 (tmm) cc_final: 0.6311 (tmm) REVERT: C 524 HIS cc_start: 0.5786 (OUTLIER) cc_final: 0.4194 (p-80) REVERT: D 61 ASN cc_start: 0.8848 (t0) cc_final: 0.8448 (t0) REVERT: D 332 MET cc_start: 0.8692 (tpt) cc_final: 0.8345 (tpt) REVERT: D 345 HIS cc_start: 0.8391 (t70) cc_final: 0.8076 (t70) outliers start: 27 outliers final: 12 residues processed: 179 average time/residue: 0.5884 time to fit residues: 121.6440 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 : 0.840 ------------------------------------------------------------------------------- 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 124 MET Chi-restraints excluded: chain A residue 211 CYS 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 365 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 211 CYS 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 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: 2.9990 chunk 144 optimal weight: 20.0000 chunk 163 optimal weight: 20.0000 chunk 182 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 83 optimal weight: 0.0170 chunk 205 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4024 r_free = 0.4024 target = 0.142865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.088343 restraints weight = 38442.094| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.30 r_work: 0.2877 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23152 Z= 0.180 Angle : 0.672 12.578 31536 Z= 0.330 Chirality : 0.048 0.513 3528 Planarity : 0.004 0.044 3916 Dihedral : 7.137 59.617 3056 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.67 % Favored : 93.26 % Rotamer: Outliers : 1.09 % Allowed : 18.08 % 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: -0.22 (0.17), residues: 2700 helix: 0.89 (0.13), residues: 1612 sheet: -0.05 (0.71), residues: 42 loop : -1.83 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 710 TYR 0.026 0.001 TYR B 381 PHE 0.021 0.001 PHE A 312 TRP 0.030 0.001 TRP C 104 HIS 0.011 0.001 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (23104) covalent geometry : angle 0.64948 / 0.33 (31402) SS BOND : bond 0.01202 / 0.61 ( 10) SS BOND : angle 1.84113 / 0.83 ( 20) hydrogen bonds : bond 0.04891 / 3.21 ( 982) hydrogen bonds : angle 3.86909 / 2.65 ( 2904) link_BETA1-4 : bond 0.00345 / 0.20 ( 14) link_BETA1-4 : angle 1.58334 / 1.02 ( 42) link_NAG-ASN : bond 0.00504 / 0.26 ( 24) link_NAG-ASN : angle 3.37453 / 2.05 ( 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 176 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.734 Fit side-chains REVERT: A 124 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7617 (mpt) REVERT: A 502 MET cc_start: 0.6607 (tmm) cc_final: 0.6369 (tmm) REVERT: A 521 MET cc_start: 0.5524 (mmt) cc_final: 0.5286 (mmt) REVERT: A 524 HIS cc_start: 0.5892 (OUTLIER) cc_final: 0.4670 (p-80) REVERT: B 330 ASN cc_start: 0.7952 (m110) cc_final: 0.7453 (p0) REVERT: B 332 MET cc_start: 0.8682 (tpt) cc_final: 0.8357 (tpt) REVERT: B 345 HIS cc_start: 0.8459 (t70) cc_final: 0.8136 (t70) REVERT: C 124 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7624 (mpt) REVERT: C 502 MET cc_start: 0.6608 (tmm) cc_final: 0.6376 (tmm) REVERT: C 524 HIS cc_start: 0.5837 (OUTLIER) cc_final: 0.4580 (p-80) REVERT: D 330 ASN cc_start: 0.7950 (m110) cc_final: 0.7446 (p0) REVERT: D 332 MET cc_start: 0.8682 (tpt) cc_final: 0.8359 (tpt) REVERT: D 345 HIS cc_start: 0.8465 (t70) cc_final: 0.8145 (t70) outliers start: 26 outliers final: 8 residues processed: 170 average time/residue: 0.6162 time to fit residues: 120.5321 Evaluate side-chains 158 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 124 MET 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 365 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 124 MET 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 365 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 178 optimal weight: 0.2980 chunk 78 optimal weight: 0.8980 chunk 134 optimal weight: 20.0000 chunk 152 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 25 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 574 GLN B 34 HIS B 61 ASN B 718 ASN C 574 GLN D 34 HIS D 61 ASN D 718 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.142498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.082448 restraints weight = 38496.199| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.17 r_work: 0.2882 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23152 Z= 0.182 Angle : 0.678 14.775 31536 Z= 0.333 Chirality : 0.048 0.638 3528 Planarity : 0.004 0.038 3916 Dihedral : 7.147 58.978 3056 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.74 % Favored : 93.19 % Rotamer: Outliers : 1.05 % Allowed : 18.50 % Favored : 80.45 % 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: -0.22 (0.16), residues: 2700 helix: 0.91 (0.13), residues: 1608 sheet: -0.13 (0.71), residues: 42 loop : -1.87 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 710 TYR 0.026 0.002 TYR B 381 PHE 0.024 0.001 PHE C 546 TRP 0.027 0.001 TRP A 104 HIS 0.011 0.001 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (23104) covalent geometry : angle 0.65003 / 0.33 (31402) SS BOND : bond 0.00905 / 0.46 ( 10) SS BOND : angle 2.05455 / 0.91 ( 20) hydrogen bonds : bond 0.04938 / 3.24 ( 982) hydrogen bonds : angle 3.90207 / 2.68 ( 2904) link_BETA1-4 : bond 0.00316 / 0.17 ( 14) link_BETA1-4 : angle 1.58699 / 1.02 ( 42) link_NAG-ASN : bond 0.00673 / 0.39 ( 24) link_NAG-ASN : angle 3.78350 / 2.24 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9724.75 seconds wall clock time: 165 minutes 57.66 seconds (9957.66 seconds total)