Starting phenix.real_space_refine on Thu Jun 26 00:28:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyz_26200/06_2025/7tyz_26200.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyz_26200/06_2025/7tyz_26200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tyz_26200/06_2025/7tyz_26200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyz_26200/06_2025/7tyz_26200.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyz_26200/06_2025/7tyz_26200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyz_26200/06_2025/7tyz_26200.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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 129 5.16 5 C 18870 2.51 5 N 4899 2.21 5 O 5838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 2.57s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29736 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8463 Classifications: {'peptide': 1082} Link IDs: {'PTRANS': 57, 'TRANS': 1024} Chain breaks: 5 Chain: "B" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1153 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "C" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8463 Classifications: {'peptide': 1082} Link IDs: {'PTRANS': 57, 'TRANS': 1024} Chain breaks: 7 Chain: "D" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1153 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "E" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8463 Classifications: {'peptide': 1082} Link IDs: {'PTRANS': 57, 'TRANS': 1024} Chain breaks: 6 Chain: "F" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1153 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: "J" 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: "O" 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: "U" 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: "V" 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: "W" 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: "X" 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 19.80, per 1000 atoms: 0.67 Number of scatterers: 29736 At special positions: 0 Unit cell: (162.378, 159.759, 222.615, 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 129 16.00 O 5838 8.00 N 4899 7.00 C 18870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.04 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.04 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " 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 ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A1074 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C 234 " " NAG C1306 " - " ASN C 165 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 603 " " NAG E1303 " - " ASN E 616 " " NAG E1304 " - " ASN E1074 " " NAG E1305 " - " ASN E 234 " " NAG E1306 " - " ASN E 165 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 709 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN A 282 " " NAG L 1 " - " ASN A 343 " " NAG M 1 " - " ASN C 709 " " NAG N 1 " - " ASN C 801 " " NAG O 1 " - " ASN C1134 " " NAG P 1 " - " ASN C 282 " " NAG Q 1 " - " ASN C 343 " " NAG R 1 " - " ASN C 331 " " NAG S 1 " - " ASN E 331 " " NAG T 1 " - " ASN E 709 " " NAG U 1 " - " ASN E 801 " " NAG V 1 " - " ASN E1134 " " NAG W 1 " - " ASN E 282 " " NAG X 1 " - " ASN E 343 " Time building additional restraints: 7.47 Conformation dependent library (CDL) restraints added in 3.4 seconds 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 51 sheets defined 28.1% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.588A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.774A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.857A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.622A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 619 through 623 removed outlier: 3.702A pdb=" N ALA A 623 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 782 removed outlier: 4.265A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.821A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.659A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.517A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.547A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.180A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 16 through 24 Processing helix chain 'B' and resid 27 through 37 removed outlier: 3.574A pdb=" N GLY B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 59 through 70 Processing helix chain 'B' and resid 82 through 91 Processing helix chain 'B' and resid 92 through 103 removed outlier: 4.253A pdb=" N VAL B 96 " --> pdb=" O HIS B 92 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 123 Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.599A pdb=" N ASN B 135 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 157 Processing helix chain 'B' and resid 158 through 168 removed outlier: 3.857A pdb=" N SER B 168 " --> pdb=" O ILE B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.514A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.892A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.677A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.755A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.519A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 761 through 783 removed outlier: 3.796A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.521A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.589A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.576A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.590A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.208A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE C 993 " --> pdb=" O ALA C 989 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'D' and resid 16 through 25 Processing helix chain 'D' and resid 26 through 36 removed outlier: 3.533A pdb=" N ASN D 36 " --> pdb=" O ILE D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 82 through 91 Processing helix chain 'D' and resid 92 through 103 removed outlier: 4.094A pdb=" N VAL D 96 " --> pdb=" O HIS D 92 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 124 Processing helix chain 'D' and resid 125 through 136 Processing helix chain 'D' and resid 148 through 157 Processing helix chain 'D' and resid 158 through 168 removed outlier: 3.631A pdb=" N SER D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 301 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 365 through 370 removed outlier: 3.842A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 410 removed outlier: 3.644A pdb=" N GLU E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 506 Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 758 through 783 removed outlier: 4.255A pdb=" N LEU E 763 " --> pdb=" O PHE E 759 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN E 764 " --> pdb=" O CYS E 760 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR E 778 " --> pdb=" O GLN E 774 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN E 779 " --> pdb=" O ASP E 775 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU E 780 " --> pdb=" O LYS E 776 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL E 781 " --> pdb=" O ASN E 777 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA E 783 " --> pdb=" O GLN E 779 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 824 Processing helix chain 'E' and resid 866 through 885 removed outlier: 3.797A pdb=" N GLN E 872 " --> pdb=" O GLU E 868 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR E 883 " --> pdb=" O ALA E 879 " (cutoff:3.500A) Processing helix chain 'E' and resid 886 through 890 Processing helix chain 'E' and resid 897 through 907 Processing helix chain 'E' and resid 913 through 919 removed outlier: 3.608A pdb=" N TYR E 917 " --> pdb=" O GLN E 913 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 removed outlier: 3.542A pdb=" N ILE E 934 " --> pdb=" O ALA E 930 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLN E 935 " --> pdb=" O ILE E 931 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP E 936 " --> pdb=" O GLY E 932 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR E 941 " --> pdb=" O SER E 937 " (cutoff:3.500A) Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.675A pdb=" N GLN E 949 " --> pdb=" O LEU E 945 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL E 952 " --> pdb=" O LEU E 948 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 983 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.247A pdb=" N GLU E 990 " --> pdb=" O PRO E 986 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE E 993 " --> pdb=" O ALA E 989 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU E1017 " --> pdb=" O ILE E1013 " (cutoff:3.500A) Processing helix chain 'E' and resid 1141 through 1146 Processing helix chain 'F' and resid 16 through 25 Processing helix chain 'F' and resid 26 through 36 Processing helix chain 'F' and resid 49 through 57 Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 82 through 91 Processing helix chain 'F' and resid 93 through 103 removed outlier: 3.579A pdb=" N GLU F 97 " --> pdb=" O LEU F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 123 Processing helix chain 'F' and resid 125 through 135 Processing helix chain 'F' and resid 148 through 157 Processing helix chain 'F' and resid 158 through 167 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 9.025A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.853A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.625A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.801A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 141 through 145 removed outlier: 6.259A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 310 through 318 removed outlier: 5.464A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA9, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.772A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.772A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.827A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 659 removed outlier: 6.247A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.564A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.960A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 removed outlier: 6.463A pdb=" N ALA E 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.681A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.197A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.865A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.538A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 141 through 145 removed outlier: 6.580A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.437A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 650 " --> pdb=" O PHE C 643 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AC9, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.503A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.503A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AD3, first strand: chain 'C' and resid 654 through 659 removed outlier: 6.231A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.528A pdb=" N ALA C 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.963A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.943A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AD8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'E' and resid 27 through 30 removed outlier: 8.917A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR E 63 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL E 267 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE E 65 " --> pdb=" O TYR E 265 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR E 265 " --> pdb=" O PHE E 65 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA E 263 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E 264 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL E 227 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 50 through 55 removed outlier: 3.859A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.650A pdb=" N LEU E 84 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL E 126 " --> pdb=" O SER E 172 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 141 through 145 removed outlier: 6.502A pdb=" N GLY E 142 " --> pdb=" O SER E 155 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 310 through 318 removed outlier: 5.440A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E 650 " --> pdb=" O PHE E 643 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 310 through 318 removed outlier: 5.440A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 325 through 326 Processing sheet with id=AE7, first strand: chain 'E' and resid 376 through 378 removed outlier: 3.996A pdb=" N THR E 376 " --> pdb=" O ALA E 435 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA E 435 " --> pdb=" O THR E 376 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG E 509 " --> pdb=" O TRP E 436 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR E 396 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 376 through 378 removed outlier: 3.996A pdb=" N THR E 376 " --> pdb=" O ALA E 435 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA E 435 " --> pdb=" O THR E 376 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG E 509 " --> pdb=" O TRP E 436 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL E 510 " --> pdb=" O PHE E 400 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE E 400 " --> pdb=" O VAL E 510 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 452 through 453 removed outlier: 3.789A pdb=" N GLN E 493 " --> pdb=" O TYR E 453 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 654 through 659 removed outlier: 6.222A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N VAL E 656 " --> pdb=" O THR E 696 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 712 through 715 Processing sheet with id=AF3, first strand: chain 'E' and resid 718 through 728 removed outlier: 6.956A pdb=" N GLY E1059 " --> pdb=" O SER E1055 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N SER E1055 " --> pdb=" O GLY E1059 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL E1061 " --> pdb=" O PRO E1053 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU E1063 " --> pdb=" O SER E1051 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER E1051 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL E1065 " --> pdb=" O LEU E1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 735 through 736 Processing sheet with id=AF5, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 5.054A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 1094 through 1097 1027 hydrogen bonds defined for protein. 2799 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: 13.17 Time building geometry restraints manager: 8.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9527 1.34 - 1.47: 7444 1.47 - 1.59: 13243 1.59 - 1.71: 2 1.71 - 1.83: 165 Bond restraints: 30381 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C1 MAN R 4 " pdb=" C2 MAN R 4 " ideal model delta sigma weight residual 1.526 1.614 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C1 NAG E1301 " pdb=" O5 NAG E1301 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C1 MAN R 4 " pdb=" O5 MAN R 4 " ideal model delta sigma weight residual 1.399 1.479 -0.080 2.00e-02 2.50e+03 1.61e+01 ... (remaining 30376 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 40292 1.81 - 3.61: 864 3.61 - 5.42: 139 5.42 - 7.22: 40 7.22 - 9.03: 5 Bond angle restraints: 41340 Sorted by residual: angle pdb=" CA LYS C 462 " pdb=" CB LYS C 462 " pdb=" CG LYS C 462 " ideal model delta sigma weight residual 114.10 122.95 -8.85 2.00e+00 2.50e-01 1.96e+01 angle pdb=" C GLY C 404 " pdb=" N ASP C 405 " pdb=" CA ASP C 405 " ideal model delta sigma weight residual 120.38 125.06 -4.68 1.46e+00 4.69e-01 1.03e+01 angle pdb=" N GLN F 166 " pdb=" CA GLN F 166 " pdb=" CB GLN F 166 " ideal model delta sigma weight residual 110.39 115.23 -4.84 1.66e+00 3.63e-01 8.51e+00 angle pdb=" C SER E 359 " pdb=" N ASN E 360 " pdb=" CA ASN E 360 " ideal model delta sigma weight residual 121.54 127.03 -5.49 1.91e+00 2.74e-01 8.26e+00 angle pdb=" C CYS A 131 " pdb=" CA CYS A 131 " pdb=" CB CYS A 131 " ideal model delta sigma weight residual 114.41 108.05 6.36 2.30e+00 1.89e-01 7.66e+00 ... (remaining 41335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.34: 17694 24.34 - 48.68: 970 48.68 - 73.02: 161 73.02 - 97.36: 76 97.36 - 121.71: 65 Dihedral angle restraints: 18966 sinusoidal: 8211 harmonic: 10755 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 11.73 81.27 1 1.00e+01 1.00e-02 8.14e+01 dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 14.56 78.44 1 1.00e+01 1.00e-02 7.68e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 15.19 77.81 1 1.00e+01 1.00e-02 7.57e+01 ... (remaining 18963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 4857 0.159 - 0.319: 27 0.319 - 0.478: 6 0.478 - 0.637: 1 0.637 - 0.797: 2 Chirality restraints: 4893 Sorted by residual: chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN E 282 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.50e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.01e+01 ... (remaining 4890 not shown) Planarity restraints: 5313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 282 " 0.036 2.00e-02 2.50e+03 3.26e-02 1.33e+01 pdb=" CG ASN E 282 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN E 282 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN E 282 " -0.036 2.00e-02 2.50e+03 pdb=" C1 NAG W 1 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C1142 " 0.052 5.00e-02 4.00e+02 7.80e-02 9.73e+00 pdb=" N PRO C1143 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO C1143 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C1143 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 616 " 0.027 2.00e-02 2.50e+03 2.62e-02 8.60e+00 pdb=" CG ASN A 616 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 616 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 616 " -0.011 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " 0.020 2.00e-02 2.50e+03 ... (remaining 5310 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 715 2.68 - 3.24: 28527 3.24 - 3.79: 43990 3.79 - 4.35: 56725 4.35 - 4.90: 93907 Nonbonded interactions: 223864 Sorted by model distance: nonbonded pdb=" OG1 THR E 676 " pdb=" O SER E 691 " model vdw 2.126 3.040 nonbonded pdb=" OG1 THR C 676 " pdb=" O SER C 691 " model vdw 2.139 3.040 nonbonded pdb=" OD1 ASN A 616 " pdb=" N2 NAG A1303 " model vdw 2.169 3.120 nonbonded pdb=" OG SER A 803 " pdb=" OE1 GLN A 804 " model vdw 2.196 3.040 nonbonded pdb=" OG SER E 349 " pdb=" O LEU E 452 " model vdw 2.199 3.040 ... (remaining 223859 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'N' selection = chain 'O' selection = chain 'U' selection = chain 'V' } 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 group one per residue 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: 25.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.330 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 69.410 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.210 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: 0.020 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 0.091 30489 Z= 0.183 Angle : 0.687 17.827 41622 Z= 0.316 Chirality : 0.052 0.797 4893 Planarity : 0.004 0.078 5277 Dihedral : 17.212 121.706 11922 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.71 % Favored : 91.26 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.14), residues: 3663 helix: 1.14 (0.18), residues: 948 sheet: -0.60 (0.19), residues: 738 loop : -2.22 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 79 HIS 0.005 0.001 HIS B 52 PHE 0.016 0.001 PHE E 157 TYR 0.020 0.001 TYR A 421 ARG 0.004 0.000 ARG E 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00889 ( 36) link_NAG-ASN : angle 4.29171 ( 108) link_BETA1-4 : bond 0.00924 ( 27) link_BETA1-4 : angle 3.08180 ( 81) link_ALPHA1-3 : bond 0.01396 ( 3) link_ALPHA1-3 : angle 2.60297 ( 9) hydrogen bonds : bond 0.17701 ( 999) hydrogen bonds : angle 7.12215 ( 2799) SS BOND : bond 0.00258 ( 42) SS BOND : angle 1.25243 ( 84) covalent geometry : bond 0.00384 (30381) covalent geometry : angle 0.63535 (41340) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 3.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 147 LYS cc_start: 0.5170 (mmtm) cc_final: 0.4925 (mttm) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.4158 time to fit residues: 131.7201 Evaluate side-chains 127 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 311 optimal weight: 0.9980 chunk 279 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 188 optimal weight: 0.4980 chunk 149 optimal weight: 3.9990 chunk 289 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 175 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 335 optimal weight: 3.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN A 501 ASN B 52 HIS ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN C 52 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.121368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.075784 restraints weight = 83146.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.078981 restraints weight = 42569.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.078870 restraints weight = 25570.020| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 30489 Z= 0.227 Angle : 0.725 17.576 41622 Z= 0.346 Chirality : 0.049 0.359 4893 Planarity : 0.005 0.071 5277 Dihedral : 12.596 104.568 5322 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 0.75 % Allowed : 7.22 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.13), residues: 3663 helix: 0.85 (0.17), residues: 957 sheet: -0.68 (0.18), residues: 729 loop : -2.27 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 152 HIS 0.007 0.001 HIS E 146 PHE 0.024 0.002 PHE C 906 TYR 0.030 0.002 TYR C 351 ARG 0.005 0.000 ARG E 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00618 ( 36) link_NAG-ASN : angle 3.55130 ( 108) link_BETA1-4 : bond 0.01132 ( 27) link_BETA1-4 : angle 3.48541 ( 81) link_ALPHA1-3 : bond 0.02586 ( 3) link_ALPHA1-3 : angle 2.00149 ( 9) hydrogen bonds : bond 0.05359 ( 999) hydrogen bonds : angle 5.54131 ( 2799) SS BOND : bond 0.00484 ( 42) SS BOND : angle 1.62197 ( 84) covalent geometry : bond 0.00532 (30381) covalent geometry : angle 0.68330 (41340) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 3.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 52 HIS cc_start: 0.6288 (t70) cc_final: 0.6078 (t70) REVERT: D 147 LYS cc_start: 0.4402 (mmtm) cc_final: 0.4015 (mttm) REVERT: E 583 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7284 (tm-30) outliers start: 24 outliers final: 18 residues processed: 162 average time/residue: 0.4349 time to fit residues: 121.3763 Evaluate side-chains 137 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 4.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain F residue 60 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 339 optimal weight: 2.9990 chunk 309 optimal weight: 0.8980 chunk 362 optimal weight: 8.9990 chunk 206 optimal weight: 1.9990 chunk 235 optimal weight: 20.0000 chunk 153 optimal weight: 7.9990 chunk 154 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 349 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 268 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.121710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.076276 restraints weight = 83311.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.079514 restraints weight = 42170.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.079353 restraints weight = 25787.503| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30489 Z= 0.166 Angle : 0.662 18.228 41622 Z= 0.314 Chirality : 0.047 0.397 4893 Planarity : 0.004 0.064 5277 Dihedral : 11.054 105.163 5322 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 1.12 % Allowed : 9.97 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.14), residues: 3663 helix: 0.90 (0.17), residues: 954 sheet: -0.74 (0.18), residues: 756 loop : -2.20 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 258 HIS 0.010 0.001 HIS E 146 PHE 0.015 0.001 PHE C 906 TYR 0.021 0.001 TYR A 421 ARG 0.004 0.000 ARG E 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 36) link_NAG-ASN : angle 3.21585 ( 108) link_BETA1-4 : bond 0.00979 ( 27) link_BETA1-4 : angle 3.26706 ( 81) link_ALPHA1-3 : bond 0.02316 ( 3) link_ALPHA1-3 : angle 2.29117 ( 9) hydrogen bonds : bond 0.04690 ( 999) hydrogen bonds : angle 5.19012 ( 2799) SS BOND : bond 0.00344 ( 42) SS BOND : angle 1.31306 ( 84) covalent geometry : bond 0.00383 (30381) covalent geometry : angle 0.62395 (41340) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 5.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8601 (t80) REVERT: C 157 PHE cc_start: 0.6564 (t80) cc_final: 0.5728 (m-10) REVERT: C 160 TYR cc_start: 0.7145 (p90) cc_final: 0.6633 (p90) REVERT: D 52 HIS cc_start: 0.6170 (t70) cc_final: 0.5947 (t70) REVERT: D 147 LYS cc_start: 0.4420 (mmtm) cc_final: 0.3993 (mttm) REVERT: E 583 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7305 (tm-30) outliers start: 36 outliers final: 21 residues processed: 163 average time/residue: 0.4666 time to fit residues: 133.7824 Evaluate side-chains 147 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 3.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain F residue 60 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 207 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 365 optimal weight: 0.9990 chunk 272 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 123 optimal weight: 30.0000 chunk 26 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.118301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.073161 restraints weight = 83798.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.076744 restraints weight = 45507.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.075906 restraints weight = 25708.028| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 30489 Z= 0.312 Angle : 0.778 17.738 41622 Z= 0.377 Chirality : 0.050 0.334 4893 Planarity : 0.005 0.067 5277 Dihedral : 10.412 99.281 5322 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer: Outliers : 1.81 % Allowed : 12.18 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.13), residues: 3663 helix: 0.52 (0.17), residues: 942 sheet: -0.74 (0.19), residues: 708 loop : -2.46 (0.12), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 152 HIS 0.008 0.001 HIS E 146 PHE 0.024 0.002 PHE C 906 TYR 0.025 0.002 TYR A 421 ARG 0.007 0.001 ARG E1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00701 ( 36) link_NAG-ASN : angle 3.29587 ( 108) link_BETA1-4 : bond 0.01062 ( 27) link_BETA1-4 : angle 3.19905 ( 81) link_ALPHA1-3 : bond 0.02200 ( 3) link_ALPHA1-3 : angle 2.15718 ( 9) hydrogen bonds : bond 0.05760 ( 999) hydrogen bonds : angle 5.43625 ( 2799) SS BOND : bond 0.00559 ( 42) SS BOND : angle 1.80476 ( 84) covalent geometry : bond 0.00735 (30381) covalent geometry : angle 0.74432 (41340) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 133 time to evaluate : 3.449 Fit side-chains REVERT: C 1002 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8226 (pp30) REVERT: D 147 LYS cc_start: 0.4376 (mmtm) cc_final: 0.3980 (mttm) REVERT: E 583 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7311 (tm-30) outliers start: 58 outliers final: 42 residues processed: 181 average time/residue: 0.3576 time to fit residues: 113.1898 Evaluate side-chains 163 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 120 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain E residue 882 ILE Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 896 ILE Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 997 ILE Chi-restraints excluded: chain F residue 60 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 107 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 310 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 93 optimal weight: 0.6980 chunk 48 optimal weight: 10.0000 chunk 92 optimal weight: 0.0670 chunk 178 optimal weight: 0.0060 chunk 66 optimal weight: 3.9990 chunk 354 optimal weight: 9.9990 chunk 290 optimal weight: 0.5980 overall best weight: 0.8736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 ASN E 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.121301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.076243 restraints weight = 82827.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.079487 restraints weight = 41763.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.079454 restraints weight = 25668.317| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30489 Z= 0.123 Angle : 0.648 18.022 41622 Z= 0.308 Chirality : 0.045 0.337 4893 Planarity : 0.004 0.074 5277 Dihedral : 9.422 97.347 5322 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.34 % Allowed : 13.71 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.14), residues: 3663 helix: 0.85 (0.17), residues: 954 sheet: -0.85 (0.18), residues: 786 loop : -2.24 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 353 HIS 0.004 0.001 HIS E 146 PHE 0.023 0.001 PHE C 168 TYR 0.021 0.001 TYR C 473 ARG 0.004 0.000 ARG E 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00493 ( 36) link_NAG-ASN : angle 3.05838 ( 108) link_BETA1-4 : bond 0.01009 ( 27) link_BETA1-4 : angle 3.06264 ( 81) link_ALPHA1-3 : bond 0.02427 ( 3) link_ALPHA1-3 : angle 2.48827 ( 9) hydrogen bonds : bond 0.04333 ( 999) hydrogen bonds : angle 4.99934 ( 2799) SS BOND : bond 0.00278 ( 42) SS BOND : angle 1.40656 ( 84) covalent geometry : bond 0.00269 (30381) covalent geometry : angle 0.61191 (41340) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 2.987 Fit side-chains revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8603 (t80) REVERT: D 147 LYS cc_start: 0.4436 (mmtm) cc_final: 0.4029 (mttm) REVERT: E 1029 MET cc_start: 0.9022 (tpp) cc_final: 0.8592 (ttm) outliers start: 43 outliers final: 28 residues processed: 174 average time/residue: 0.3534 time to fit residues: 108.5029 Evaluate side-chains 152 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 4.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain F residue 60 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 292 optimal weight: 4.9990 chunk 350 optimal weight: 2.9990 chunk 232 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 304 optimal weight: 2.9990 chunk 342 optimal weight: 2.9990 chunk 358 optimal weight: 20.0000 chunk 221 optimal weight: 0.7980 chunk 259 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.120530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.075799 restraints weight = 83246.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.078960 restraints weight = 44811.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.078318 restraints weight = 26423.135| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30489 Z= 0.156 Angle : 0.652 17.822 41622 Z= 0.309 Chirality : 0.045 0.344 4893 Planarity : 0.004 0.065 5277 Dihedral : 8.616 94.711 5322 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 1.50 % Allowed : 14.90 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.14), residues: 3663 helix: 0.94 (0.17), residues: 954 sheet: -0.74 (0.19), residues: 759 loop : -2.24 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 152 HIS 0.004 0.001 HIS D 59 PHE 0.017 0.001 PHE C 168 TYR 0.021 0.001 TYR C 473 ARG 0.004 0.000 ARG E 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 36) link_NAG-ASN : angle 3.14334 ( 108) link_BETA1-4 : bond 0.01015 ( 27) link_BETA1-4 : angle 3.04589 ( 81) link_ALPHA1-3 : bond 0.02223 ( 3) link_ALPHA1-3 : angle 2.44952 ( 9) hydrogen bonds : bond 0.04357 ( 999) hydrogen bonds : angle 4.91229 ( 2799) SS BOND : bond 0.00340 ( 42) SS BOND : angle 1.44052 ( 84) covalent geometry : bond 0.00364 (30381) covalent geometry : angle 0.61512 (41340) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 133 time to evaluate : 3.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8604 (t80) REVERT: D 147 LYS cc_start: 0.4426 (mmtm) cc_final: 0.3993 (mttm) REVERT: E 583 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7312 (tm-30) REVERT: E 633 TRP cc_start: 0.5962 (OUTLIER) cc_final: 0.5518 (p90) outliers start: 48 outliers final: 35 residues processed: 176 average time/residue: 0.3575 time to fit residues: 109.2375 Evaluate side-chains 159 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 633 TRP Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1027 THR Chi-restraints excluded: chain F residue 60 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 270 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 291 optimal weight: 0.0000 chunk 364 optimal weight: 0.6980 chunk 126 optimal weight: 7.9990 chunk 236 optimal weight: 0.1980 chunk 178 optimal weight: 0.0770 chunk 64 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 219 optimal weight: 0.9980 overall best weight: 0.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.122868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.078184 restraints weight = 83306.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.081232 restraints weight = 42675.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.080838 restraints weight = 26360.200| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 30489 Z= 0.108 Angle : 0.622 17.984 41622 Z= 0.295 Chirality : 0.045 0.352 4893 Planarity : 0.004 0.072 5277 Dihedral : 7.755 92.219 5322 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.67 % Favored : 92.30 % Rotamer: Outliers : 1.31 % Allowed : 15.43 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.14), residues: 3663 helix: 1.20 (0.17), residues: 954 sheet: -0.59 (0.19), residues: 765 loop : -2.14 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.005 0.001 HIS E 146 PHE 0.019 0.001 PHE C 168 TYR 0.022 0.001 TYR C 473 ARG 0.003 0.000 ARG F 23 Details of bonding type rmsd link_NAG-ASN : bond 0.00446 ( 36) link_NAG-ASN : angle 2.93417 ( 108) link_BETA1-4 : bond 0.01055 ( 27) link_BETA1-4 : angle 3.07919 ( 81) link_ALPHA1-3 : bond 0.02159 ( 3) link_ALPHA1-3 : angle 2.57507 ( 9) hydrogen bonds : bond 0.03587 ( 999) hydrogen bonds : angle 4.66853 ( 2799) SS BOND : bond 0.00297 ( 42) SS BOND : angle 1.22929 ( 84) covalent geometry : bond 0.00232 (30381) covalent geometry : angle 0.58643 (41340) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 3.605 Fit side-chains revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8614 (t80) REVERT: C 84 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8020 (mm) REVERT: C 554 GLU cc_start: 0.7605 (mp0) cc_final: 0.7398 (mp0) REVERT: D 147 LYS cc_start: 0.4405 (mmtm) cc_final: 0.3996 (mttm) REVERT: E 329 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8596 (t80) REVERT: E 583 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7276 (tm-30) outliers start: 42 outliers final: 26 residues processed: 180 average time/residue: 0.3587 time to fit residues: 112.1949 Evaluate side-chains 157 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1144 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain F residue 60 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 356 optimal weight: 30.0000 chunk 122 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 217 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.118173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.073185 restraints weight = 83798.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.076385 restraints weight = 42182.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.076276 restraints weight = 26224.394| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.118 30489 Z= 0.311 Angle : 0.761 17.389 41622 Z= 0.369 Chirality : 0.049 0.345 4893 Planarity : 0.005 0.075 5277 Dihedral : 8.024 90.432 5322 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.25 % Favored : 88.73 % Rotamer: Outliers : 1.62 % Allowed : 15.50 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.13), residues: 3663 helix: 0.70 (0.17), residues: 954 sheet: -0.78 (0.19), residues: 720 loop : -2.37 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 152 HIS 0.007 0.001 HIS E 146 PHE 0.026 0.002 PHE A 486 TYR 0.022 0.002 TYR C1067 ARG 0.006 0.001 ARG E 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00625 ( 36) link_NAG-ASN : angle 3.12049 ( 108) link_BETA1-4 : bond 0.01008 ( 27) link_BETA1-4 : angle 3.08485 ( 81) link_ALPHA1-3 : bond 0.02132 ( 3) link_ALPHA1-3 : angle 2.40904 ( 9) hydrogen bonds : bond 0.05485 ( 999) hydrogen bonds : angle 5.15771 ( 2799) SS BOND : bond 0.00644 ( 42) SS BOND : angle 1.91678 ( 84) covalent geometry : bond 0.00740 (30381) covalent geometry : angle 0.72840 (41340) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 124 time to evaluate : 3.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 HIS cc_start: 0.4178 (OUTLIER) cc_final: 0.3877 (t-170) REVERT: C 84 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8135 (mm) REVERT: D 147 LYS cc_start: 0.4396 (mmtm) cc_final: 0.3978 (mttm) REVERT: E 137 ASN cc_start: 0.6882 (t0) cc_final: 0.6423 (m-40) REVERT: E 633 TRP cc_start: 0.6255 (OUTLIER) cc_final: 0.5899 (p90) outliers start: 52 outliers final: 38 residues processed: 169 average time/residue: 0.3582 time to fit residues: 105.5143 Evaluate side-chains 161 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 120 time to evaluate : 3.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 457 ARG Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 633 TRP Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain F residue 60 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 70 optimal weight: 0.8980 chunk 244 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 295 optimal weight: 0.9990 chunk 368 optimal weight: 4.9990 chunk 219 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.120832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.076218 restraints weight = 82929.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.079501 restraints weight = 41464.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.079378 restraints weight = 25834.964| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30489 Z= 0.127 Angle : 0.647 17.765 41622 Z= 0.310 Chirality : 0.045 0.358 4893 Planarity : 0.004 0.066 5277 Dihedral : 7.546 87.848 5322 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.14 % Favored : 91.84 % Rotamer: Outliers : 1.31 % Allowed : 16.03 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.14), residues: 3663 helix: 0.93 (0.17), residues: 957 sheet: -0.76 (0.19), residues: 753 loop : -2.22 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.004 0.001 HIS E 146 PHE 0.015 0.001 PHE A 157 TYR 0.022 0.001 TYR E 473 ARG 0.004 0.000 ARG E 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 36) link_NAG-ASN : angle 2.87230 ( 108) link_BETA1-4 : bond 0.01011 ( 27) link_BETA1-4 : angle 3.01427 ( 81) link_ALPHA1-3 : bond 0.02098 ( 3) link_ALPHA1-3 : angle 2.53742 ( 9) hydrogen bonds : bond 0.04321 ( 999) hydrogen bonds : angle 4.82049 ( 2799) SS BOND : bond 0.00338 ( 42) SS BOND : angle 1.47814 ( 84) covalent geometry : bond 0.00286 (30381) covalent geometry : angle 0.61295 (41340) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 4.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8075 (mm) REVERT: C 425 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7621 (tp) REVERT: C 554 GLU cc_start: 0.7597 (mp0) cc_final: 0.7396 (mp0) REVERT: C 1002 GLN cc_start: 0.8260 (pp30) cc_final: 0.7987 (pp30) REVERT: D 147 LYS cc_start: 0.4476 (mmtm) cc_final: 0.4085 (mttm) REVERT: E 137 ASN cc_start: 0.6866 (t0) cc_final: 0.6396 (m-40) REVERT: E 329 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8589 (t80) outliers start: 42 outliers final: 34 residues processed: 167 average time/residue: 0.4529 time to fit residues: 135.9186 Evaluate side-chains 166 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 3.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1144 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 457 ARG Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain F residue 60 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 307 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 182 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 292 optimal weight: 20.0000 chunk 223 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 260 optimal weight: 0.8980 chunk 280 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.124080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.080845 restraints weight = 86186.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.082394 restraints weight = 44792.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.083007 restraints weight = 26789.820| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30489 Z= 0.125 Angle : 0.631 17.717 41622 Z= 0.300 Chirality : 0.045 0.356 4893 Planarity : 0.004 0.080 5277 Dihedral : 7.144 85.600 5322 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.23 % Favored : 90.75 % Rotamer: Outliers : 1.19 % Allowed : 16.37 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.14), residues: 3663 helix: 1.11 (0.17), residues: 954 sheet: -0.68 (0.19), residues: 753 loop : -2.16 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.008 0.001 HIS E 146 PHE 0.013 0.001 PHE A 157 TYR 0.022 0.001 TYR A 904 ARG 0.010 0.000 ARG E1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 36) link_NAG-ASN : angle 2.75352 ( 108) link_BETA1-4 : bond 0.01017 ( 27) link_BETA1-4 : angle 3.00584 ( 81) link_ALPHA1-3 : bond 0.02139 ( 3) link_ALPHA1-3 : angle 2.60033 ( 9) hydrogen bonds : bond 0.03980 ( 999) hydrogen bonds : angle 4.68185 ( 2799) SS BOND : bond 0.00323 ( 42) SS BOND : angle 1.41576 ( 84) covalent geometry : bond 0.00284 (30381) covalent geometry : angle 0.59839 (41340) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 2.943 Fit side-chains revert: symmetry clash REVERT: C 84 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8041 (mm) REVERT: C 554 GLU cc_start: 0.7545 (mp0) cc_final: 0.7335 (mp0) REVERT: D 147 LYS cc_start: 0.4394 (mmtm) cc_final: 0.4017 (mttm) REVERT: E 137 ASN cc_start: 0.6830 (t0) cc_final: 0.6350 (m-40) REVERT: E 329 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8651 (t80) REVERT: E 383 SER cc_start: 0.7708 (m) cc_final: 0.7504 (t) outliers start: 38 outliers final: 35 residues processed: 164 average time/residue: 0.3718 time to fit residues: 105.0917 Evaluate side-chains 165 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1144 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain E residue 453 TYR Chi-restraints excluded: chain E residue 457 ARG Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 590 CYS Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 779 GLN Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain F residue 60 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 60 optimal weight: 6.9990 chunk 337 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 221 optimal weight: 0.9980 chunk 317 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 358 optimal weight: 20.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN B 52 HIS F 118 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.119141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.074492 restraints weight = 83508.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.077419 restraints weight = 41699.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.077721 restraints weight = 26895.957| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 30489 Z= 0.229 Angle : 0.697 17.527 41622 Z= 0.336 Chirality : 0.047 0.354 4893 Planarity : 0.005 0.076 5277 Dihedral : 7.333 84.937 5322 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.21 % Favored : 89.76 % Rotamer: Outliers : 1.31 % Allowed : 16.24 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.13), residues: 3663 helix: 0.86 (0.17), residues: 957 sheet: -0.72 (0.19), residues: 729 loop : -2.27 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 152 HIS 0.009 0.001 HIS B 52 PHE 0.015 0.002 PHE C 565 TYR 0.025 0.001 TYR A 904 ARG 0.005 0.000 ARG E 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 36) link_NAG-ASN : angle 2.93109 ( 108) link_BETA1-4 : bond 0.00997 ( 27) link_BETA1-4 : angle 2.96816 ( 81) link_ALPHA1-3 : bond 0.02042 ( 3) link_ALPHA1-3 : angle 2.57638 ( 9) hydrogen bonds : bond 0.04893 ( 999) hydrogen bonds : angle 4.92989 ( 2799) SS BOND : bond 0.00440 ( 42) SS BOND : angle 1.72360 ( 84) covalent geometry : bond 0.00541 (30381) covalent geometry : angle 0.66531 (41340) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10756.90 seconds wall clock time: 196 minutes 58.58 seconds (11818.58 seconds total)