Starting phenix.real_space_refine on Mon Aug 25 11:43:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jmo_61608/08_2025/9jmo_61608.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jmo_61608/08_2025/9jmo_61608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jmo_61608/08_2025/9jmo_61608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jmo_61608/08_2025/9jmo_61608.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jmo_61608/08_2025/9jmo_61608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jmo_61608/08_2025/9jmo_61608.map" } resolution = 2.8 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 147 5.16 5 C 17542 2.51 5 N 4523 2.21 5 O 5482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27694 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 8886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 8886 Classifications: {'peptide': 1140} Link IDs: {'PTRANS': 57, 'TRANS': 1082} Chain breaks: 7 Chain: "B" Number of atoms: 8886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 8886 Classifications: {'peptide': 1140} Link IDs: {'PTRANS': 57, 'TRANS': 1082} Chain breaks: 7 Chain: "C" Number of atoms: 8886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 8886 Classifications: {'peptide': 1140} Link IDs: {'PTRANS': 57, 'TRANS': 1082} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 160 Unusual residues: {'EIC': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 160 Unusual residues: {'EIC': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 174 Unusual residues: {'EIC': 1, 'NAG': 11} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.93, per 1000 atoms: 0.21 Number of scatterers: 27694 At special positions: 0 Unit cell: (139.92, 151.36, 163.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 147 16.00 O 5482 8.00 N 4523 7.00 C 17542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 201 " distance=2.04 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 483 " distance=2.03 Simple disulfide: pdb=" SG CYS A 442 " - pdb=" SG CYS A 580 " distance=2.03 Simple disulfide: pdb=" SG CYS A 507 " - pdb=" SG CYS A 526 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 645 " distance=2.04 Simple disulfide: pdb=" SG CYS A 674 " - pdb=" SG CYS A 709 " distance=2.03 Simple disulfide: pdb=" SG CYS A 723 " - pdb=" SG CYS A 732 " distance=2.03 Simple disulfide: pdb=" SG CYS A 798 " - pdb=" SG CYS A 820 " distance=2.03 Simple disulfide: pdb=" SG CYS A 803 " - pdb=" SG CYS A 809 " distance=2.03 Simple disulfide: pdb=" SG CYS A 904 " - pdb=" SG CYS A 917 " distance=2.03 Simple disulfide: pdb=" SG CYS A1098 " - pdb=" SG CYS A1109 " distance=2.03 Simple disulfide: pdb=" SG CYS A1148 " - pdb=" SG CYS A1156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 354 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 483 " distance=2.03 Simple disulfide: pdb=" SG CYS B 442 " - pdb=" SG CYS B 580 " distance=2.03 Simple disulfide: pdb=" SG CYS B 507 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 645 " distance=2.03 Simple disulfide: pdb=" SG CYS B 674 " - pdb=" SG CYS B 709 " distance=2.03 Simple disulfide: pdb=" SG CYS B 723 " - pdb=" SG CYS B 732 " distance=2.03 Simple disulfide: pdb=" SG CYS B 798 " - pdb=" SG CYS B 820 " distance=2.03 Simple disulfide: pdb=" SG CYS B 803 " - pdb=" SG CYS B 809 " distance=2.03 Simple disulfide: pdb=" SG CYS B 904 " - pdb=" SG CYS B 917 " distance=2.03 Simple disulfide: pdb=" SG CYS B1098 " - pdb=" SG CYS B1109 " distance=2.03 Simple disulfide: pdb=" SG CYS B1148 " - pdb=" SG CYS B1156 " distance=2.04 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 191 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 354 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 430 " - pdb=" SG CYS C 483 " distance=2.03 Simple disulfide: pdb=" SG CYS C 442 " - pdb=" SG CYS C 580 " distance=2.03 Simple disulfide: pdb=" SG CYS C 507 " - pdb=" SG CYS C 526 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 645 " distance=2.03 Simple disulfide: pdb=" SG CYS C 674 " - pdb=" SG CYS C 709 " distance=2.04 Simple disulfide: pdb=" SG CYS C 723 " - pdb=" SG CYS C 732 " distance=2.03 Simple disulfide: pdb=" SG CYS C 798 " - pdb=" SG CYS C 820 " distance=2.03 Simple disulfide: pdb=" SG CYS C 803 " - pdb=" SG CYS C 809 " distance=2.04 Simple disulfide: pdb=" SG CYS C 904 " - pdb=" SG CYS C 917 " distance=2.03 Simple disulfide: pdb=" SG CYS C1098 " - pdb=" SG CYS C1109 " distance=2.03 Simple disulfide: pdb=" SG CYS C1148 " - pdb=" SG CYS C1156 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " 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 K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1401 " - " ASN A 110 " " NAG A1402 " - " ASN A 249 " " NAG A1403 " - " ASN A 715 " " NAG A1404 " - " ASN A 755 " " NAG A1405 " - " ASN A 777 " " NAG A1406 " - " ASN A 197 " " NAG A1407 " - " ASN A 614 " " NAG A1408 " - " ASN A 862 " " NAG A1409 " - " ASN A 492 " " NAG A1410 " - " ASN A 587 " " NAG B1401 " - " ASN B 249 " " NAG B1402 " - " ASN B 715 " " NAG B1403 " - " ASN B 755 " " NAG B1404 " - " ASN B 777 " " NAG B1405 " - " ASN B 197 " " NAG B1406 " - " ASN B 614 " " NAG B1407 " - " ASN B 862 " " NAG B1408 " - " ASN B 110 " " NAG B1409 " - " ASN B 492 " " NAG B1410 " - " ASN B 587 " " NAG C1402 " - " ASN C 66 " " NAG C1403 " - " ASN C 110 " " NAG C1404 " - " ASN C 249 " " NAG C1405 " - " ASN C 715 " " NAG C1406 " - " ASN C 755 " " NAG C1407 " - " ASN C 777 " " NAG C1408 " - " ASN C 197 " " NAG C1409 " - " ASN C 614 " " NAG C1410 " - " ASN C 862 " " NAG C1411 " - " ASN C 492 " " NAG C1412 " - " ASN C 587 " " NAG D 1 " - " ASN A 66 " " NAG E 1 " - " ASN A 131 " " NAG F 1 " - " ASN A 172 " " NAG G 1 " - " ASN A 227 " " NAG H 1 " - " ASN A 403 " " NAG I 1 " - " ASN A 415 " " NAG J 1 " - " ASN B 66 " " NAG K 1 " - " ASN B 131 " " NAG L 1 " - " ASN B 172 " " NAG M 1 " - " ASN B 227 " " NAG N 1 " - " ASN B 403 " " NAG O 1 " - " ASN B 415 " " NAG P 1 " - " ASN C 131 " " NAG R 1 " - " ASN C 403 " " NAG S 1 " - " ASN C 415 " " NAG T 1 " - " ASN C 227 " Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 984.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 6744 Ramachandran restraints generated. 3372 Oldfield, 0 Emsley, 3372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6402 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 59 sheets defined 27.0% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 227 through 236 removed outlier: 3.884A pdb=" N SER A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 390 through 396 removed outlier: 3.785A pdb=" N PHE A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.649A pdb=" N PHE A 404 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 422 removed outlier: 3.605A pdb=" N LEU A 422 " --> pdb=" O ARG A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 441 Processing helix chain 'A' and resid 454 through 462 removed outlier: 5.170A pdb=" N SER A 459 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 462 " --> pdb=" O SER A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 473 Processing helix chain 'A' and resid 511 through 515 removed outlier: 3.508A pdb=" N SER A 515 " --> pdb=" O PRO A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 531 Processing helix chain 'A' and resid 583 through 585 No H-bonds generated for 'chain 'A' and resid 583 through 585' Processing helix chain 'A' and resid 673 through 678 removed outlier: 3.684A pdb=" N VAL A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 804 Processing helix chain 'A' and resid 806 through 813 Processing helix chain 'A' and resid 816 through 845 Processing helix chain 'A' and resid 863 through 867 Processing helix chain 'A' and resid 880 through 889 removed outlier: 3.535A pdb=" N LYS A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 907 Processing helix chain 'A' and resid 918 through 923 Processing helix chain 'A' and resid 932 through 943 removed outlier: 3.686A pdb=" N LEU A 943 " --> pdb=" O TYR A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 974 Processing helix chain 'A' and resid 978 through 985 Processing helix chain 'A' and resid 985 through 1002 Processing helix chain 'A' and resid 1008 through 1031 Processing helix chain 'A' and resid 1032 through 1034 No H-bonds generated for 'chain 'A' and resid 1032 through 1034' Processing helix chain 'A' and resid 1042 through 1050 removed outlier: 3.588A pdb=" N ILE A1046 " --> pdb=" O SER A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1099 Processing helix chain 'B' and resid 37 through 41 removed outlier: 3.735A pdb=" N GLN B 41 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 227 through 236 removed outlier: 4.017A pdb=" N SER B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 390 through 396 removed outlier: 3.802A pdb=" N PHE B 394 " --> pdb=" O PHE B 390 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER B 396 " --> pdb=" O ALA B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 404 removed outlier: 3.651A pdb=" N PHE B 404 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 422 Processing helix chain 'B' and resid 434 through 441 Processing helix chain 'B' and resid 454 through 462 removed outlier: 3.524A pdb=" N ALA B 458 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N SER B 459 " --> pdb=" O SER B 456 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 462 " --> pdb=" O SER B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 473 Processing helix chain 'B' and resid 511 through 515 removed outlier: 3.518A pdb=" N SER B 515 " --> pdb=" O PRO B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 620 through 623 removed outlier: 3.564A pdb=" N GLN B 623 " --> pdb=" O LEU B 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 620 through 623' Processing helix chain 'B' and resid 673 through 678 removed outlier: 3.559A pdb=" N VAL B 677 " --> pdb=" O ALA B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 804 Processing helix chain 'B' and resid 806 through 814 Processing helix chain 'B' and resid 816 through 845 Processing helix chain 'B' and resid 863 through 867 Processing helix chain 'B' and resid 880 through 889 removed outlier: 3.519A pdb=" N LYS B 889 " --> pdb=" O LEU B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 907 removed outlier: 3.532A pdb=" N GLN B 907 " --> pdb=" O GLU B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 923 Processing helix chain 'B' and resid 932 through 943 removed outlier: 3.660A pdb=" N LEU B 943 " --> pdb=" O TYR B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 974 Processing helix chain 'B' and resid 978 through 985 Processing helix chain 'B' and resid 985 through 1002 removed outlier: 3.792A pdb=" N THR B1002 " --> pdb=" O GLY B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1031 removed outlier: 3.571A pdb=" N ALA B1012 " --> pdb=" O ASN B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1032 through 1034 No H-bonds generated for 'chain 'B' and resid 1032 through 1034' Processing helix chain 'B' and resid 1042 through 1050 removed outlier: 3.628A pdb=" N ILE B1046 " --> pdb=" O SER B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1099 Processing helix chain 'B' and resid 1213 through 1218 Processing helix chain 'C' and resid 37 through 41 removed outlier: 3.813A pdb=" N GLN C 41 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 181 through 183 No H-bonds generated for 'chain 'C' and resid 181 through 183' Processing helix chain 'C' and resid 227 through 236 removed outlier: 3.808A pdb=" N SER C 236 " --> pdb=" O SER C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 312 removed outlier: 3.889A pdb=" N ARG C 312 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 357 Processing helix chain 'C' and resid 390 through 396 removed outlier: 3.828A pdb=" N PHE C 394 " --> pdb=" O PHE C 390 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER C 396 " --> pdb=" O ALA C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 404 removed outlier: 3.652A pdb=" N PHE C 404 " --> pdb=" O VAL C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 422 removed outlier: 3.707A pdb=" N LEU C 422 " --> pdb=" O ARG C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 441 Processing helix chain 'C' and resid 454 through 462 removed outlier: 3.515A pdb=" N ALA C 458 " --> pdb=" O LEU C 455 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N SER C 459 " --> pdb=" O SER C 456 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG C 462 " --> pdb=" O SER C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 473 Processing helix chain 'C' and resid 526 through 531 Processing helix chain 'C' and resid 673 through 678 Processing helix chain 'C' and resid 797 through 804 Processing helix chain 'C' and resid 806 through 814 Processing helix chain 'C' and resid 816 through 844 Processing helix chain 'C' and resid 863 through 867 Processing helix chain 'C' and resid 880 through 889 Processing helix chain 'C' and resid 899 through 907 Processing helix chain 'C' and resid 915 through 923 removed outlier: 4.704A pdb=" N PHE C 920 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL C 921 " --> pdb=" O CYS C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 932 through 944 removed outlier: 3.546A pdb=" N GLU C 936 " --> pdb=" O ASP C 932 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR C 944 " --> pdb=" O THR C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 974 Processing helix chain 'C' and resid 978 through 985 Processing helix chain 'C' and resid 985 through 1002 Processing helix chain 'C' and resid 1008 through 1031 removed outlier: 3.502A pdb=" N ALA C1012 " --> pdb=" O ASN C1008 " (cutoff:3.500A) Processing helix chain 'C' and resid 1032 through 1034 No H-bonds generated for 'chain 'C' and resid 1032 through 1034' Processing helix chain 'C' and resid 1042 through 1050 removed outlier: 3.635A pdb=" N ILE C1046 " --> pdb=" O SER C1042 " (cutoff:3.500A) Processing helix chain 'C' and resid 1051 through 1099 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 removed outlier: 6.267A pdb=" N SER A 63 " --> pdb=" O TYR C 627 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL C 626 " --> pdb=" O VAL C 634 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL C 634 " --> pdb=" O VAL C 646 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR C 643 " --> pdb=" O CYS C 615 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE C 379 " --> pdb=" O SER C 602 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 75 removed outlier: 4.191A pdb=" N ARG A 340 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.828A pdb=" N ASP A 287 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N SER A 272 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU A 285 " --> pdb=" O SER A 272 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA7, first strand: chain 'A' and resid 133 through 134 removed outlier: 4.396A pdb=" N ALA A 314 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.627A pdb=" N ALA A 158 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 212 through 214 removed outlier: 6.514A pdb=" N ILE A 212 " --> pdb=" O SER A 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 364 through 371 removed outlier: 4.732A pdb=" N VAL A 654 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N SER A 370 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL A 652 " --> pdb=" O SER A 370 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 708 " --> pdb=" O THR A 705 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 378 through 381 removed outlier: 6.737A pdb=" N PHE A 379 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL A 634 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 626 " --> pdb=" O VAL A 634 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 405 through 409 removed outlier: 3.661A pdb=" N SER A 445 " --> pdb=" O GLN A 571 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 562 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA A 488 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N VAL A 425 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 413 through 414 Processing sheet with id=AB5, first strand: chain 'A' and resid 502 through 508 removed outlier: 6.792A pdb=" N THR A 551 " --> pdb=" O THR A 505 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N CYS A 507 " --> pdb=" O THR A 549 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR A 549 " --> pdb=" O CYS A 507 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 714 through 720 removed outlier: 8.192A pdb=" N LEU A 751 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU A 718 " --> pdb=" O LEU A 751 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU A 731 " --> pdb=" O LEU A 727 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 760 through 761 removed outlier: 6.044A pdb=" N HIS A 760 " --> pdb=" O THR B 850 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1113 through 1121 removed outlier: 6.290A pdb=" N HIS A1114 " --> pdb=" O TYR A1133 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR A1133 " --> pdb=" O HIS A1114 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR A1142 " --> pdb=" O THR A1166 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE A1164 " --> pdb=" O ALA A1144 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1113 through 1121 removed outlier: 6.290A pdb=" N HIS A1114 " --> pdb=" O TYR A1133 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR A1133 " --> pdb=" O HIS A1114 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN A 777 " --> pdb=" O THR A1136 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N HIS A1138 " --> pdb=" O PRO A 775 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASN A1140 " --> pdb=" O GLU A 773 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLU A 773 " --> pdb=" O ASN A1140 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR A1142 " --> pdb=" O ILE A 771 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE A 771 " --> pdb=" O THR A1142 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA A1144 " --> pdb=" O ARG A 769 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ARG A 769 " --> pdb=" O ALA A1144 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 793 through 796 removed outlier: 4.544A pdb=" N LYS A 793 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AC3, first strand: chain 'A' and resid 959 through 961 removed outlier: 4.332A pdb=" N ILE C 771 " --> pdb=" O ALA A 961 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ARG C 769 " --> pdb=" O ALA C1144 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA C1144 " --> pdb=" O ARG C 769 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE C 771 " --> pdb=" O THR C1142 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR C1142 " --> pdb=" O ILE C 771 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLU C 773 " --> pdb=" O ASN C1140 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN C1140 " --> pdb=" O GLU C 773 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS C1138 " --> pdb=" O PRO C 775 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASN C 777 " --> pdb=" O THR C1136 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TYR C1133 " --> pdb=" O HIS C1114 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N HIS C1114 " --> pdb=" O TYR C1133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 959 through 961 removed outlier: 4.332A pdb=" N ILE C 771 " --> pdb=" O ALA A 961 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ARG C 769 " --> pdb=" O ALA C1144 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA C1144 " --> pdb=" O ARG C 769 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE C 771 " --> pdb=" O THR C1142 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR C1142 " --> pdb=" O ILE C 771 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLU C 773 " --> pdb=" O ASN C1140 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN C1140 " --> pdb=" O GLU C 773 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS C1138 " --> pdb=" O PRO C 775 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASN C 777 " --> pdb=" O THR C1136 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR C1142 " --> pdb=" O THR C1166 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE C1164 " --> pdb=" O ALA C1144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1196 through 1199 removed outlier: 3.561A pdb=" N CYS A1156 " --> pdb=" O VAL A1199 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 34 through 35 removed outlier: 5.972A pdb=" N VAL B 34 " --> pdb=" O ILE B 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 68 through 75 removed outlier: 4.432A pdb=" N ARG B 340 " --> pdb=" O ASP B 331 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.822A pdb=" N ASP B 287 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER B 272 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU B 285 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 116 through 117 Processing sheet with id=AD1, first strand: chain 'B' and resid 116 through 117 Processing sheet with id=AD2, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AD3, first strand: chain 'B' and resid 158 through 161 removed outlier: 4.652A pdb=" N ALA B 158 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 212 through 214 removed outlier: 6.369A pdb=" N ILE B 212 " --> pdb=" O SER B 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 364 through 372 removed outlier: 4.656A pdb=" N VAL B 654 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N SER B 370 " --> pdb=" O VAL B 652 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL B 652 " --> pdb=" O SER B 370 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY B 670 " --> pdb=" O PRO B 653 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 708 " --> pdb=" O THR B 705 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 378 through 381 removed outlier: 6.688A pdb=" N PHE B 379 " --> pdb=" O SER B 602 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYR B 643 " --> pdb=" O CYS B 615 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL B 634 " --> pdb=" O VAL B 646 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 626 " --> pdb=" O VAL B 634 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 386 through 387 removed outlier: 6.299A pdb=" N SER B 386 " --> pdb=" O ASN B 413 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N CYS B 412 " --> pdb=" O CYS B 580 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 405 through 409 removed outlier: 3.592A pdb=" N SER B 445 " --> pdb=" O GLN B 571 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU B 562 " --> pdb=" O VAL B 489 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR B 482 " --> pdb=" O CYS B 430 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N CYS B 430 " --> pdb=" O THR B 482 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG B 484 " --> pdb=" O PHE B 428 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE B 428 " --> pdb=" O ARG B 484 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU B 486 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 500 through 508 removed outlier: 6.557A pdb=" N THR B 551 " --> pdb=" O THR B 505 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N CYS B 507 " --> pdb=" O THR B 549 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR B 549 " --> pdb=" O CYS B 507 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 713 through 720 removed outlier: 6.942A pdb=" N LEU B 749 " --> pdb=" O VAL B 714 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N THR B 716 " --> pdb=" O LEU B 749 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N LEU B 751 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU B 718 " --> pdb=" O LEU B 751 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU B 731 " --> pdb=" O LEU B 727 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 760 through 761 removed outlier: 6.069A pdb=" N HIS B 760 " --> pdb=" O THR C 850 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'B' and resid 1113 through 1122 removed outlier: 6.337A pdb=" N HIS B1114 " --> pdb=" O TYR B1133 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N TYR B1133 " --> pdb=" O HIS B1114 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N THR B1142 " --> pdb=" O THR B1166 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE B1164 " --> pdb=" O ALA B1144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1113 through 1122 removed outlier: 6.337A pdb=" N HIS B1114 " --> pdb=" O TYR B1133 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N TYR B1133 " --> pdb=" O HIS B1114 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLY B1125 " --> pdb=" O GLN B 788 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLN B 788 " --> pdb=" O GLY B1125 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR B1127 " --> pdb=" O PHE B 786 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE B 786 " --> pdb=" O TYR B1127 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE B1129 " --> pdb=" O GLN B 784 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN B 784 " --> pdb=" O PHE B1129 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B1131 " --> pdb=" O VAL B 782 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL B 782 " --> pdb=" O VAL B1131 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR B1133 " --> pdb=" O PHE B 780 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N PHE B 780 " --> pdb=" O TYR B1133 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHE B 778 " --> pdb=" O PRO B1135 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA B1137 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE B 771 " --> pdb=" O ALA C 961 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 793 through 796 removed outlier: 4.551A pdb=" N LYS B 793 " --> pdb=" O LEU B 927 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 1147 through 1149 Processing sheet with id=AE7, first strand: chain 'B' and resid 1156 through 1159 Processing sheet with id=AE8, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AE9, first strand: chain 'C' and resid 67 through 75 removed outlier: 4.236A pdb=" N ARG C 340 " --> pdb=" O ASP C 331 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.813A pdb=" N ASP C 287 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N SER C 272 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU C 285 " --> pdb=" O SER C 272 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 116 through 117 Processing sheet with id=AF3, first strand: chain 'C' and resid 116 through 117 Processing sheet with id=AF4, first strand: chain 'C' and resid 133 through 134 removed outlier: 3.848A pdb=" N ALA C 314 " --> pdb=" O VAL C 145 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 159 through 161 Processing sheet with id=AF6, first strand: chain 'C' and resid 212 through 214 removed outlier: 6.166A pdb=" N ILE C 212 " --> pdb=" O SER C 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'C' and resid 364 through 367 removed outlier: 3.917A pdb=" N GLY C 708 " --> pdb=" O THR C 705 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 371 through 372 Processing sheet with id=AF9, first strand: chain 'C' and resid 386 through 387 removed outlier: 6.127A pdb=" N SER C 386 " --> pdb=" O ASN C 413 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'C' and resid 405 through 409 removed outlier: 3.627A pdb=" N SER C 445 " --> pdb=" O GLN C 571 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU C 562 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR C 482 " --> pdb=" O CYS C 430 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N CYS C 430 " --> pdb=" O THR C 482 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ARG C 484 " --> pdb=" O PHE C 428 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE C 428 " --> pdb=" O ARG C 484 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU C 486 " --> pdb=" O SER C 426 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 500 through 509 removed outlier: 6.520A pdb=" N THR C 551 " --> pdb=" O THR C 505 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N CYS C 507 " --> pdb=" O THR C 549 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR C 549 " --> pdb=" O CYS C 507 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 714 through 720 removed outlier: 7.011A pdb=" N LEU C 749 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N THR C 716 " --> pdb=" O LEU C 749 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N LEU C 751 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU C 718 " --> pdb=" O LEU C 751 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU C 731 " --> pdb=" O LEU C 727 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 793 through 796 removed outlier: 4.656A pdb=" N LYS C 793 " --> pdb=" O LEU C 927 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 1196 through 1199 removed outlier: 3.813A pdb=" N CYS C1156 " --> pdb=" O VAL C1199 " (cutoff:3.500A) 1159 hydrogen bonds defined for protein. 3150 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: 5.67 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5069 1.33 - 1.45: 8326 1.45 - 1.58: 14743 1.58 - 1.71: 0 1.71 - 1.84: 195 Bond restraints: 28333 Sorted by residual: bond pdb=" CA ASP A 206 " pdb=" C ASP A 206 " ideal model delta sigma weight residual 1.530 1.475 0.055 1.10e-02 8.26e+03 2.46e+01 bond pdb=" N PHE B1004 " pdb=" CA PHE B1004 " ideal model delta sigma weight residual 1.464 1.418 0.046 1.30e-02 5.92e+03 1.23e+01 bond pdb=" CA GLY C 701 " pdb=" C GLY C 701 " ideal model delta sigma weight residual 1.515 1.469 0.046 1.43e-02 4.89e+03 1.01e+01 bond pdb=" C MET C 703 " pdb=" O MET C 703 " ideal model delta sigma weight residual 1.234 1.199 0.035 1.22e-02 6.72e+03 8.35e+00 bond pdb=" CA PHE B1004 " pdb=" CB PHE B1004 " ideal model delta sigma weight residual 1.523 1.487 0.037 1.27e-02 6.20e+03 8.30e+00 ... (remaining 28328 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 37350 1.52 - 3.05: 1012 3.05 - 4.57: 133 4.57 - 6.09: 32 6.09 - 7.62: 10 Bond angle restraints: 38537 Sorted by residual: angle pdb=" C LEU C1152 " pdb=" N PRO C1153 " pdb=" CA PRO C1153 " ideal model delta sigma weight residual 120.38 115.63 4.75 1.03e+00 9.43e-01 2.13e+01 angle pdb=" N PRO C 702 " pdb=" CA PRO C 702 " pdb=" CB PRO C 702 " ideal model delta sigma weight residual 103.27 100.01 3.26 9.00e-01 1.23e+00 1.31e+01 angle pdb=" N THR B1002 " pdb=" CA THR B1002 " pdb=" C THR B1002 " ideal model delta sigma weight residual 110.80 118.42 -7.62 2.13e+00 2.20e-01 1.28e+01 angle pdb=" CA LEU C1152 " pdb=" C LEU C1152 " pdb=" N PRO C1153 " ideal model delta sigma weight residual 120.93 117.46 3.47 1.06e+00 8.90e-01 1.07e+01 angle pdb=" C PRO C 702 " pdb=" CA PRO C 702 " pdb=" CB PRO C 702 " ideal model delta sigma weight residual 111.64 107.78 3.86 1.26e+00 6.30e-01 9.41e+00 ... (remaining 38532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.70: 16378 22.70 - 45.40: 1086 45.40 - 68.11: 220 68.11 - 90.81: 76 90.81 - 113.51: 24 Dihedral angle restraints: 17784 sinusoidal: 7788 harmonic: 9996 Sorted by residual: dihedral pdb=" CB CYS A 615 " pdb=" SG CYS A 615 " pdb=" SG CYS A 645 " pdb=" CB CYS A 645 " ideal model delta sinusoidal sigma weight residual 93.00 40.33 52.67 1 1.00e+01 1.00e-02 3.78e+01 dihedral pdb=" CB CYS C 615 " pdb=" SG CYS C 615 " pdb=" SG CYS C 645 " pdb=" CB CYS C 645 " ideal model delta sinusoidal sigma weight residual -86.00 -137.76 51.76 1 1.00e+01 1.00e-02 3.66e+01 dihedral pdb=" CB CYS C 723 " pdb=" SG CYS C 723 " pdb=" SG CYS C 732 " pdb=" CB CYS C 732 " ideal model delta sinusoidal sigma weight residual -86.00 -41.95 -44.05 1 1.00e+01 1.00e-02 2.70e+01 ... (remaining 17781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3616 0.055 - 0.111: 740 0.111 - 0.166: 123 0.166 - 0.222: 2 0.222 - 0.277: 7 Chirality restraints: 4488 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 4485 not shown) Planarity restraints: 4960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C1152 " 0.046 5.00e-02 4.00e+02 6.91e-02 7.64e+00 pdb=" N PRO C1153 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO C1153 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C1153 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 701 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.11e+00 pdb=" N PRO C 702 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 702 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 702 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 875 " -0.013 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C GLN B 875 " 0.044 2.00e-02 2.50e+03 pdb=" O GLN B 875 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR B 876 " -0.015 2.00e-02 2.50e+03 ... (remaining 4957 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6378 2.79 - 3.32: 23159 3.32 - 3.84: 46917 3.84 - 4.37: 55431 4.37 - 4.90: 96118 Nonbonded interactions: 228003 Sorted by model distance: nonbonded pdb=" O TYR C 378 " pdb=" OG1 THR C 589 " model vdw 2.259 3.040 nonbonded pdb=" OG1 THR B 790 " pdb=" OE1 GLN B 834 " model vdw 2.271 3.040 nonbonded pdb=" O TYR A 378 " pdb=" OG1 THR A 589 " model vdw 2.292 3.040 nonbonded pdb=" OH TYR B 414 " pdb=" OH TYR B 443 " model vdw 2.294 3.040 nonbonded pdb=" O TYR B 378 " pdb=" OG1 THR B 589 " model vdw 2.297 3.040 ... (remaining 227998 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 1218 or resid 1402 through 1410)) selection = (chain 'B' and (resid 18 through 1218 or resid 1402 through 1410)) selection = (chain 'C' and (resid 18 through 1218 or resid 1402 through 1410)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'K' selection = chain 'L' selection = chain 'P' selection = chain 'Q' } 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=0.00 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: 3.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.510 Find NCS groups from input model: 0.570 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:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28451 Z= 0.198 Angle : 0.603 7.615 38843 Z= 0.301 Chirality : 0.047 0.277 4488 Planarity : 0.005 0.069 4913 Dihedral : 16.372 113.512 11238 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.28 % Favored : 97.69 % Rotamer: Outliers : 0.74 % Allowed : 15.13 % Favored : 84.13 % 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 aren not related in a simple way. whole: -0.05 (0.14), residues: 3372 helix: 0.97 (0.19), residues: 729 sheet: 0.86 (0.19), residues: 777 loop : -0.84 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 814 TYR 0.016 0.001 TYR B 901 PHE 0.022 0.001 PHE C 537 TRP 0.008 0.001 TRP A 44 HIS 0.007 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00398 (28333) covalent geometry : angle 0.59119 (38537) SS BOND : bond 0.00278 ( 48) SS BOND : angle 1.07182 ( 96) hydrogen bonds : bond 0.17983 ( 1077) hydrogen bonds : angle 7.33789 ( 3150) link_BETA1-4 : bond 0.00519 ( 23) link_BETA1-4 : angle 1.50649 ( 69) link_NAG-ASN : bond 0.00172 ( 47) link_NAG-ASN : angle 1.64613 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6744 Ramachandran restraints generated. 3372 Oldfield, 0 Emsley, 3372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6744 Ramachandran restraints generated. 3372 Oldfield, 0 Emsley, 3372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.703 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 16 residues processed: 173 average time/residue: 0.5035 time to fit residues: 104.3129 Evaluate side-chains 170 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 1082 GLU Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1148 CYS Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain C residue 443 TYR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 702 PRO Chi-restraints excluded: chain C residue 709 CYS Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 1192 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 0.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 HIS A 205 GLN A 985 ASN B 986 GLN C 205 GLN C 256 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 ASN C 750 GLN C1167 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.105372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.082283 restraints weight = 42316.294| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.01 r_work: 0.2897 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 28451 Z= 0.269 Angle : 0.637 7.278 38843 Z= 0.325 Chirality : 0.048 0.271 4488 Planarity : 0.005 0.080 4913 Dihedral : 10.091 83.356 5263 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.05 % Allowed : 14.04 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.14), residues: 3372 helix: 1.17 (0.19), residues: 723 sheet: 0.98 (0.19), residues: 750 loop : -0.90 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 814 TYR 0.016 0.002 TYR A 170 PHE 0.021 0.002 PHE A 286 TRP 0.005 0.001 TRP C 503 HIS 0.005 0.002 HIS A1114 Details of bonding type rmsd covalent geometry : bond 0.00642 (28333) covalent geometry : angle 0.61948 (38537) SS BOND : bond 0.00417 ( 48) SS BOND : angle 1.27191 ( 96) hydrogen bonds : bond 0.06268 ( 1077) hydrogen bonds : angle 5.71284 ( 3150) link_BETA1-4 : bond 0.00369 ( 23) link_BETA1-4 : angle 2.36209 ( 69) link_NAG-ASN : bond 0.00319 ( 47) link_NAG-ASN : angle 1.70153 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6744 Ramachandran restraints generated. 3372 Oldfield, 0 Emsley, 3372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6744 Ramachandran restraints generated. 3372 Oldfield, 0 Emsley, 3372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 161 time to evaluate : 0.941 Fit side-chains REVERT: A 313 GLN cc_start: 0.5721 (OUTLIER) cc_final: 0.5393 (mt0) REVERT: A 443 TYR cc_start: 0.9288 (OUTLIER) cc_final: 0.8530 (p90) REVERT: A 600 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7899 (mm-30) REVERT: A 807 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7293 (mm-30) REVERT: B 771 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8792 (mp) REVERT: B 1167 ASN cc_start: 0.6394 (t0) cc_final: 0.5988 (m110) REVERT: C 475 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8835 (tttm) REVERT: C 1154 PRO cc_start: 0.6374 (Cg_exo) cc_final: 0.6084 (Cg_endo) outliers start: 90 outliers final: 32 residues processed: 224 average time/residue: 0.5607 time to fit residues: 149.9013 Evaluate side-chains 192 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 848 GLN Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 443 TYR Chi-restraints excluded: chain C residue 475 LYS Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 558 SER Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 783 THR Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 1000 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 339 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 257 optimal weight: 0.9980 chunk 280 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 299 optimal weight: 7.9990 chunk 102 optimal weight: 0.2980 chunk 238 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 205 GLN A 238 ASN A 834 GLN B 256 GLN ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS B 760 HIS B 986 GLN C 205 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1167 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.108532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.085665 restraints weight = 42129.330| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.01 r_work: 0.2953 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28451 Z= 0.104 Angle : 0.495 7.081 38843 Z= 0.251 Chirality : 0.043 0.223 4488 Planarity : 0.004 0.072 4913 Dihedral : 8.049 67.658 5252 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.86 % Allowed : 15.33 % Favored : 82.81 % 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 aren not related in a simple way. whole: 0.20 (0.14), residues: 3372 helix: 1.58 (0.19), residues: 726 sheet: 0.80 (0.19), residues: 762 loop : -0.75 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 814 TYR 0.010 0.001 TYR C 901 PHE 0.015 0.001 PHE A 286 TRP 0.005 0.001 TRP C 503 HIS 0.004 0.001 HIS C1130 Details of bonding type rmsd covalent geometry : bond 0.00224 (28333) covalent geometry : angle 0.48120 (38537) SS BOND : bond 0.00208 ( 48) SS BOND : angle 0.73515 ( 96) hydrogen bonds : bond 0.04768 ( 1077) hydrogen bonds : angle 5.21989 ( 3150) link_BETA1-4 : bond 0.00362 ( 23) link_BETA1-4 : angle 2.06598 ( 69) link_NAG-ASN : bond 0.00170 ( 47) link_NAG-ASN : angle 1.34339 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6744 Ramachandran restraints generated. 3372 Oldfield, 0 Emsley, 3372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6744 Ramachandran restraints generated. 3372 Oldfield, 0 Emsley, 3372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 159 time to evaluate : 1.116 Fit side-chains REVERT: A 313 GLN cc_start: 0.5683 (OUTLIER) cc_final: 0.5340 (mt0) REVERT: A 600 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7808 (mm-30) REVERT: B 443 TYR cc_start: 0.9208 (OUTLIER) cc_final: 0.8049 (p90) REVERT: B 676 HIS cc_start: 0.8007 (OUTLIER) cc_final: 0.7657 (m90) REVERT: B 771 ILE cc_start: 0.9073 (pt) cc_final: 0.8785 (mp) REVERT: B 1147 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8271 (mt) REVERT: B 1167 ASN cc_start: 0.6386 (t0) cc_final: 0.6007 (m110) REVERT: C 1154 PRO cc_start: 0.6440 (Cg_exo) cc_final: 0.6203 (Cg_endo) outliers start: 55 outliers final: 16 residues processed: 197 average time/residue: 0.5988 time to fit residues: 140.2733 Evaluate side-chains 174 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 676 HIS Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 1147 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 443 TYR Chi-restraints excluded: chain C residue 676 HIS Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 872 VAL Chi-restraints excluded: chain C residue 875 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 303 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 314 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 327 optimal weight: 0.9990 chunk 257 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 804 ASN C 205 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1167 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.106851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.083870 restraints weight = 42089.223| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.00 r_work: 0.2925 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28451 Z= 0.163 Angle : 0.535 6.768 38843 Z= 0.270 Chirality : 0.044 0.234 4488 Planarity : 0.004 0.055 4913 Dihedral : 7.254 68.366 5247 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.74 % Allowed : 14.69 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.14), residues: 3372 helix: 1.59 (0.19), residues: 723 sheet: 0.65 (0.18), residues: 783 loop : -0.76 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 814 TYR 0.012 0.001 TYR C 901 PHE 0.017 0.001 PHE A 286 TRP 0.005 0.001 TRP C 503 HIS 0.024 0.001 HIS B 676 Details of bonding type rmsd covalent geometry : bond 0.00383 (28333) covalent geometry : angle 0.51904 (38537) SS BOND : bond 0.00430 ( 48) SS BOND : angle 1.01692 ( 96) hydrogen bonds : bond 0.05145 ( 1077) hydrogen bonds : angle 5.19869 ( 3150) link_BETA1-4 : bond 0.00337 ( 23) link_BETA1-4 : angle 2.19767 ( 69) link_NAG-ASN : bond 0.00211 ( 47) link_NAG-ASN : angle 1.46940 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6744 Ramachandran restraints generated. 3372 Oldfield, 0 Emsley, 3372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6744 Ramachandran restraints generated. 3372 Oldfield, 0 Emsley, 3372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 159 time to evaluate : 0.686 Fit side-chains REVERT: A 254 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.5791 (mp0) REVERT: A 313 GLN cc_start: 0.5667 (OUTLIER) cc_final: 0.5349 (mt0) REVERT: A 600 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7864 (mm-30) REVERT: B 443 TYR cc_start: 0.9288 (OUTLIER) cc_final: 0.8198 (p90) REVERT: B 771 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8820 (mp) REVERT: B 1082 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7914 (mp0) REVERT: B 1147 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8231 (mt) REVERT: B 1167 ASN cc_start: 0.6363 (t0) cc_final: 0.5982 (m110) outliers start: 81 outliers final: 33 residues processed: 216 average time/residue: 0.5216 time to fit residues: 135.8429 Evaluate side-chains 189 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 860 ASP Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1147 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 443 TYR Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 558 SER Chi-restraints excluded: chain C residue 676 HIS Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 783 THR Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 872 VAL Chi-restraints excluded: chain C residue 875 GLN Chi-restraints excluded: chain C residue 1000 MET Chi-restraints excluded: chain C residue 1111 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 287 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 314 optimal weight: 0.7980 chunk 197 optimal weight: 5.9990 chunk 249 optimal weight: 4.9990 chunk 220 optimal weight: 10.0000 chunk 336 optimal weight: 1.9990 chunk 131 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A 476 GLN A 622 GLN ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 ASN B 840 ASN C 205 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 ASN C1167 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.107646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.084698 restraints weight = 42000.980| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.01 r_work: 0.2940 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28451 Z= 0.122 Angle : 0.497 6.853 38843 Z= 0.252 Chirality : 0.043 0.225 4488 Planarity : 0.004 0.052 4913 Dihedral : 6.410 67.907 5244 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.47 % Allowed : 15.40 % Favored : 82.13 % 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 aren not related in a simple way. whole: 0.23 (0.14), residues: 3372 helix: 1.71 (0.19), residues: 723 sheet: 0.81 (0.19), residues: 753 loop : -0.76 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 814 TYR 0.013 0.001 TYR A 279 PHE 0.016 0.001 PHE A 286 TRP 0.005 0.001 TRP A 952 HIS 0.002 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00277 (28333) covalent geometry : angle 0.48239 (38537) SS BOND : bond 0.00262 ( 48) SS BOND : angle 0.81215 ( 96) hydrogen bonds : bond 0.04715 ( 1077) hydrogen bonds : angle 5.04489 ( 3150) link_BETA1-4 : bond 0.00374 ( 23) link_BETA1-4 : angle 2.00520 ( 69) link_NAG-ASN : bond 0.00173 ( 47) link_NAG-ASN : angle 1.40177 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6744 Ramachandran restraints generated. 3372 Oldfield, 0 Emsley, 3372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6744 Ramachandran restraints generated. 3372 Oldfield, 0 Emsley, 3372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 161 time to evaluate : 1.213 Fit side-chains REVERT: A 254 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.5721 (mp0) REVERT: A 600 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7859 (mm-30) REVERT: A 724 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8327 (mp10) REVERT: B 443 TYR cc_start: 0.9283 (OUTLIER) cc_final: 0.8119 (p90) REVERT: B 676 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.7107 (m90) REVERT: B 771 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8815 (mp) REVERT: B 1000 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7429 (ttt) REVERT: B 1082 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7968 (mp0) REVERT: B 1147 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8208 (mt) REVERT: B 1167 ASN cc_start: 0.6406 (t0) cc_final: 0.6016 (m110) REVERT: C 519 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7674 (mt-10) outliers start: 73 outliers final: 29 residues processed: 217 average time/residue: 0.6061 time to fit residues: 156.9210 Evaluate side-chains 191 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 676 HIS Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 1000 MET Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1147 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 443 TYR Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 676 HIS Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 872 VAL Chi-restraints excluded: chain C residue 875 GLN Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 1000 MET Chi-restraints excluded: chain C residue 1111 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 206 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 240 optimal weight: 0.0670 chunk 40 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 291 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN B 255 ASN ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 ASN C1167 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.104916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.082190 restraints weight = 42284.483| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.98 r_work: 0.2898 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 28451 Z= 0.252 Angle : 0.609 8.012 38843 Z= 0.307 Chirality : 0.047 0.262 4488 Planarity : 0.005 0.054 4913 Dihedral : 6.764 68.986 5244 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.40 % Favored : 97.57 % Rotamer: Outliers : 2.88 % Allowed : 15.13 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.14), residues: 3372 helix: 1.32 (0.19), residues: 723 sheet: 0.57 (0.18), residues: 786 loop : -0.90 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 814 TYR 0.015 0.002 TYR A 170 PHE 0.020 0.002 PHE A 286 TRP 0.006 0.001 TRP A 952 HIS 0.006 0.001 HIS B1130 Details of bonding type rmsd covalent geometry : bond 0.00600 (28333) covalent geometry : angle 0.59121 (38537) SS BOND : bond 0.00404 ( 48) SS BOND : angle 1.24761 ( 96) hydrogen bonds : bond 0.05894 ( 1077) hydrogen bonds : angle 5.33158 ( 3150) link_BETA1-4 : bond 0.00397 ( 23) link_BETA1-4 : angle 2.34222 ( 69) link_NAG-ASN : bond 0.00345 ( 47) link_NAG-ASN : angle 1.72341 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6744 Ramachandran restraints generated. 3372 Oldfield, 0 Emsley, 3372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6744 Ramachandran restraints generated. 3372 Oldfield, 0 Emsley, 3372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 151 time to evaluate : 1.076 Fit side-chains REVERT: A 254 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.5859 (mp0) REVERT: A 600 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7955 (mm-30) REVERT: B 443 TYR cc_start: 0.9327 (OUTLIER) cc_final: 0.8232 (p90) REVERT: B 676 HIS cc_start: 0.7863 (OUTLIER) cc_final: 0.6910 (m90) REVERT: B 1167 ASN cc_start: 0.6455 (t0) cc_final: 0.6036 (m110) REVERT: C 519 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7700 (mt-10) outliers start: 85 outliers final: 46 residues processed: 216 average time/residue: 0.5888 time to fit residues: 152.7356 Evaluate side-chains 200 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 149 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 676 HIS Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 443 TYR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 558 SER Chi-restraints excluded: chain C residue 676 HIS Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 783 THR Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 875 GLN Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 1000 MET Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain C residue 1111 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 125 optimal weight: 0.0570 chunk 212 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 253 optimal weight: 1.9990 chunk 266 optimal weight: 0.2980 chunk 178 optimal weight: 0.2980 chunk 76 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN B 351 GLN B 760 HIS C 205 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1167 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.108055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.085223 restraints weight = 41908.410| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.01 r_work: 0.2950 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 28451 Z= 0.104 Angle : 0.484 7.246 38843 Z= 0.247 Chirality : 0.042 0.218 4488 Planarity : 0.004 0.052 4913 Dihedral : 5.965 67.715 5244 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.96 % Allowed : 16.07 % 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 aren not related in a simple way. whole: 0.21 (0.14), residues: 3372 helix: 1.70 (0.19), residues: 723 sheet: 0.77 (0.19), residues: 735 loop : -0.75 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 814 TYR 0.013 0.001 TYR A 279 PHE 0.016 0.001 PHE C 189 TRP 0.005 0.001 TRP C 44 HIS 0.005 0.001 HIS B 760 Details of bonding type rmsd covalent geometry : bond 0.00229 (28333) covalent geometry : angle 0.47066 (38537) SS BOND : bond 0.00218 ( 48) SS BOND : angle 0.72381 ( 96) hydrogen bonds : bond 0.04465 ( 1077) hydrogen bonds : angle 4.98196 ( 3150) link_BETA1-4 : bond 0.00394 ( 23) link_BETA1-4 : angle 1.83170 ( 69) link_NAG-ASN : bond 0.00176 ( 47) link_NAG-ASN : angle 1.40401 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6744 Ramachandran restraints generated. 3372 Oldfield, 0 Emsley, 3372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6744 Ramachandran restraints generated. 3372 Oldfield, 0 Emsley, 3372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 157 time to evaluate : 1.127 Fit side-chains REVERT: A 254 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.5663 (mp0) REVERT: A 560 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7844 (pm20) REVERT: A 600 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7870 (mm-30) REVERT: B 443 TYR cc_start: 0.9270 (OUTLIER) cc_final: 0.7954 (p90) REVERT: B 676 HIS cc_start: 0.8011 (OUTLIER) cc_final: 0.7299 (m90) REVERT: B 1147 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8296 (mt) REVERT: B 1167 ASN cc_start: 0.6348 (t0) cc_final: 0.5930 (m110) outliers start: 58 outliers final: 25 residues processed: 203 average time/residue: 0.6034 time to fit residues: 146.7009 Evaluate side-chains 182 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 560 GLU Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 676 HIS Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1147 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 443 TYR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 676 HIS Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 875 GLN Chi-restraints excluded: chain C residue 1111 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 142 optimal weight: 5.9990 chunk 268 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 334 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 266 optimal weight: 0.7980 chunk 262 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 338 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN B 760 HIS C 205 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1167 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.107575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.084800 restraints weight = 42141.515| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.00 r_work: 0.2942 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28451 Z= 0.119 Angle : 0.493 6.914 38843 Z= 0.251 Chirality : 0.043 0.219 4488 Planarity : 0.004 0.052 4913 Dihedral : 5.851 68.045 5244 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.86 % Allowed : 16.48 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.14), residues: 3372 helix: 1.75 (0.19), residues: 723 sheet: 0.77 (0.19), residues: 735 loop : -0.72 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 814 TYR 0.013 0.001 TYR A 279 PHE 0.015 0.001 PHE A 286 TRP 0.005 0.001 TRP A 44 HIS 0.005 0.001 HIS B 760 Details of bonding type rmsd covalent geometry : bond 0.00271 (28333) covalent geometry : angle 0.47932 (38537) SS BOND : bond 0.00230 ( 48) SS BOND : angle 0.79042 ( 96) hydrogen bonds : bond 0.04591 ( 1077) hydrogen bonds : angle 4.93324 ( 3150) link_BETA1-4 : bond 0.00385 ( 23) link_BETA1-4 : angle 1.90982 ( 69) link_NAG-ASN : bond 0.00173 ( 47) link_NAG-ASN : angle 1.41657 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6744 Ramachandran restraints generated. 3372 Oldfield, 0 Emsley, 3372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6744 Ramachandran restraints generated. 3372 Oldfield, 0 Emsley, 3372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 156 time to evaluate : 1.129 Fit side-chains REVERT: A 254 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.5700 (mp0) REVERT: A 600 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7868 (mm-30) REVERT: B 443 TYR cc_start: 0.9278 (OUTLIER) cc_final: 0.7957 (p90) REVERT: B 676 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7341 (m90) REVERT: B 722 ASN cc_start: 0.7591 (p0) cc_final: 0.6849 (t0) REVERT: B 1000 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7248 (ttt) REVERT: B 1167 ASN cc_start: 0.6363 (t0) cc_final: 0.5936 (m110) outliers start: 55 outliers final: 30 residues processed: 199 average time/residue: 0.5895 time to fit residues: 141.0073 Evaluate side-chains 185 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 676 HIS Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 1000 MET Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 443 TYR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 558 SER Chi-restraints excluded: chain C residue 676 HIS Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 875 GLN Chi-restraints excluded: chain C residue 1000 MET Chi-restraints excluded: chain C residue 1111 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 198 optimal weight: 7.9990 chunk 313 optimal weight: 0.5980 chunk 142 optimal weight: 5.9990 chunk 242 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 271 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A1209 ASN B 760 HIS B1121 ASN C 205 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1167 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.105660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.082957 restraints weight = 42295.818| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.98 r_work: 0.2910 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 28451 Z= 0.201 Angle : 0.568 7.683 38843 Z= 0.288 Chirality : 0.045 0.245 4488 Planarity : 0.004 0.051 4913 Dihedral : 6.264 68.754 5244 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.03 % Allowed : 16.51 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.14), residues: 3372 helix: 1.53 (0.19), residues: 723 sheet: 0.54 (0.19), residues: 765 loop : -0.80 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 814 TYR 0.013 0.001 TYR A 924 PHE 0.019 0.002 PHE A 286 TRP 0.007 0.001 TRP C 258 HIS 0.005 0.001 HIS B 760 Details of bonding type rmsd covalent geometry : bond 0.00475 (28333) covalent geometry : angle 0.55130 (38537) SS BOND : bond 0.00379 ( 48) SS BOND : angle 1.17880 ( 96) hydrogen bonds : bond 0.05443 ( 1077) hydrogen bonds : angle 5.14541 ( 3150) link_BETA1-4 : bond 0.00404 ( 23) link_BETA1-4 : angle 2.14881 ( 69) link_NAG-ASN : bond 0.00273 ( 47) link_NAG-ASN : angle 1.61189 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6744 Ramachandran restraints generated. 3372 Oldfield, 0 Emsley, 3372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6744 Ramachandran restraints generated. 3372 Oldfield, 0 Emsley, 3372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 149 time to evaluate : 1.075 Fit side-chains REVERT: A 254 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.5830 (mp0) REVERT: A 600 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7918 (mm-30) REVERT: B 443 TYR cc_start: 0.9322 (OUTLIER) cc_final: 0.8138 (p90) REVERT: B 676 HIS cc_start: 0.7920 (OUTLIER) cc_final: 0.7020 (m90) REVERT: B 722 ASN cc_start: 0.7627 (p0) cc_final: 0.6842 (t0) REVERT: B 1000 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7275 (ttt) REVERT: B 1082 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7918 (mp0) REVERT: B 1167 ASN cc_start: 0.6473 (t0) cc_final: 0.6019 (m110) outliers start: 60 outliers final: 38 residues processed: 196 average time/residue: 0.5067 time to fit residues: 119.8055 Evaluate side-chains 188 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 676 HIS Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 1000 MET Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 443 TYR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 558 SER Chi-restraints excluded: chain C residue 676 HIS Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 783 THR Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 875 GLN Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 943 LEU Chi-restraints excluded: chain C residue 1000 MET Chi-restraints excluded: chain C residue 1111 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 3.9990 chunk 264 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 330 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN B 760 HIS B 804 ASN C 205 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1167 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.107168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.084371 restraints weight = 42020.173| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.00 r_work: 0.2934 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28451 Z= 0.122 Angle : 0.502 6.888 38843 Z= 0.257 Chirality : 0.043 0.223 4488 Planarity : 0.004 0.052 4913 Dihedral : 5.941 68.126 5244 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.73 % Allowed : 16.85 % Favored : 81.42 % 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 aren not related in a simple way. whole: 0.17 (0.14), residues: 3372 helix: 1.68 (0.19), residues: 723 sheet: 0.73 (0.19), residues: 735 loop : -0.77 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 814 TYR 0.014 0.001 TYR A 279 PHE 0.016 0.001 PHE C 286 TRP 0.007 0.001 TRP C 258 HIS 0.006 0.001 HIS B 760 Details of bonding type rmsd covalent geometry : bond 0.00279 (28333) covalent geometry : angle 0.48796 (38537) SS BOND : bond 0.00285 ( 48) SS BOND : angle 0.87928 ( 96) hydrogen bonds : bond 0.04732 ( 1077) hydrogen bonds : angle 4.99044 ( 3150) link_BETA1-4 : bond 0.00398 ( 23) link_BETA1-4 : angle 1.88624 ( 69) link_NAG-ASN : bond 0.00172 ( 47) link_NAG-ASN : angle 1.46158 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6744 Ramachandran restraints generated. 3372 Oldfield, 0 Emsley, 3372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6744 Ramachandran restraints generated. 3372 Oldfield, 0 Emsley, 3372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 147 time to evaluate : 1.266 Fit side-chains REVERT: A 254 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.5682 (mp0) REVERT: A 443 TYR cc_start: 0.9314 (OUTLIER) cc_final: 0.8618 (p90) REVERT: A 600 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: B 443 TYR cc_start: 0.9298 (OUTLIER) cc_final: 0.7989 (p90) REVERT: B 676 HIS cc_start: 0.8037 (OUTLIER) cc_final: 0.7282 (m90) REVERT: B 722 ASN cc_start: 0.7582 (p0) cc_final: 0.6810 (t0) REVERT: B 1000 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7288 (ttt) REVERT: B 1167 ASN cc_start: 0.6434 (t0) cc_final: 0.5987 (m110) REVERT: C 283 MET cc_start: 0.8924 (mmm) cc_final: 0.8506 (mtt) REVERT: C 551 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8740 (m) outliers start: 51 outliers final: 31 residues processed: 191 average time/residue: 0.5418 time to fit residues: 125.9878 Evaluate side-chains 184 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 443 TYR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 676 HIS Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 1000 MET Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 443 TYR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 558 SER Chi-restraints excluded: chain C residue 676 HIS Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 875 GLN Chi-restraints excluded: chain C residue 1000 MET Chi-restraints excluded: chain C residue 1111 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 118 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 279 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 258 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 283 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A 811 GLN B 760 HIS C 205 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1167 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.105595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.083736 restraints weight = 42859.427| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.91 r_work: 0.2918 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 28451 Z= 0.196 Angle : 0.563 7.361 38843 Z= 0.285 Chirality : 0.045 0.242 4488 Planarity : 0.004 0.052 4913 Dihedral : 6.218 68.677 5244 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.90 % Allowed : 16.68 % Favored : 81.42 % 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 aren not related in a simple way. whole: 0.03 (0.14), residues: 3372 helix: 1.53 (0.19), residues: 723 sheet: 0.70 (0.19), residues: 747 loop : -0.88 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 814 TYR 0.013 0.001 TYR A 924 PHE 0.019 0.002 PHE A 286 TRP 0.006 0.001 TRP A 952 HIS 0.006 0.001 HIS B 760 Details of bonding type rmsd covalent geometry : bond 0.00465 (28333) covalent geometry : angle 0.54595 (38537) SS BOND : bond 0.00359 ( 48) SS BOND : angle 1.12093 ( 96) hydrogen bonds : bond 0.05399 ( 1077) hydrogen bonds : angle 5.12953 ( 3150) link_BETA1-4 : bond 0.00406 ( 23) link_BETA1-4 : angle 2.13268 ( 69) link_NAG-ASN : bond 0.00265 ( 47) link_NAG-ASN : angle 1.61832 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7778.31 seconds wall clock time: 133 minutes 57.28 seconds (8037.28 seconds total)