Starting phenix.real_space_refine on Mon Jul 6 16:37:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wgb_32482/07_2026/7wgb_32482.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wgb_32482/07_2026/7wgb_32482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wgb_32482/07_2026/7wgb_32482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wgb_32482/07_2026/7wgb_32482.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wgb_32482/07_2026/7wgb_32482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wgb_32482/07_2026/7wgb_32482.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wgb_32482/07_2026/7wgb_32482.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wgb_32482/07_2026/7wgb_32482.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.074 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 175 5.16 5 C 23421 2.51 5 N 6003 2.21 5 O 7120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36719 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1041} Chain breaks: 4 Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "C" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1041} Chain breaks: 4 Chain: "D" Number of atoms: 4852 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 566} Conformer: "B" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 566} bond proxies already assigned to first conformer: 4972 Chain: "F" Number of atoms: 4852 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 566} Conformer: "B" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 566} bond proxies already assigned to first conformer: 4972 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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 chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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 chiralities: 3 Chain: "R" 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 chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 chiralities: 2 Chain: "Y" 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 chiralities: 3 Chain: "Z" 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 chiralities: 3 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 9.43, per 1000 atoms: 0.26 Number of scatterers: 36719 At special positions: 0 Unit cell: (138.03, 163.71, 263.22, 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 175 16.00 O 7120 8.00 N 6003 7.00 C 23421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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=2.03 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 B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 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 D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.04 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " 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=6, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " NAG-ASN " NAG A1303 " - " ASN A 343 " " NAG A1305 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 145 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 709 " " NAG D 701 " - " ASN D 546 " " NAG D 702 " - " ASN D 90 " " NAG D 703 " - " ASN D 322 " " NAG D 704 " - " ASN D 53 " " NAG F 701 " - " ASN F 546 " " NAG F 702 " - " ASN F 90 " " NAG F 703 " - " ASN F 322 " " NAG F 704 " - " ASN F 53 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN B 331 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C1074 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " NAG-SER " NAG C1302 " - " SER C 254 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.7 seconds 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8450 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 43 sheets defined 36.2% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.681A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.997A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 390' Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.614A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.588A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 634 through 638 removed outlier: 3.704A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 744 removed outlier: 4.352A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.641A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.618A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 854 removed outlier: 4.216A pdb=" N LYS A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 850 through 854' Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 removed outlier: 4.149A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.750A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.775A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.177A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 984 removed outlier: 3.946A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1032 removed outlier: 4.398A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 4.346A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU A1151 " --> pdb=" O SER A1147 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.137A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.574A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 5.342A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 633 through 637 removed outlier: 3.666A pdb=" N TYR B 636 " --> pdb=" O TRP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.587A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 757 through 783 removed outlier: 4.056A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 854 Processing helix chain 'B' and resid 866 through 882 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.522A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 removed outlier: 4.151A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.757A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.029A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 937 " --> pdb=" O LYS B 933 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.764A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 984 removed outlier: 3.945A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.639A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 3.759A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.824A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.337A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.669A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.795A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.599A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.712A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.898A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 4.058A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.847A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.529A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (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 984 removed outlier: 3.566A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.082A pdb=" N GLU C 990 " --> pdb=" O LYS C 986 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1160 removed outlier: 4.231A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU C1151 " --> pdb=" O SER C1147 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 53 Processing helix chain 'D' and resid 55 through 82 removed outlier: 4.592A pdb=" N MET D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.699A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 158 through 169 removed outlier: 4.178A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 176 through 194 Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.720A pdb=" N TYR D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 219 through 252 removed outlier: 4.333A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 277 through 283 removed outlier: 4.024A pdb=" N VAL D 283 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.999A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 324 through 328 Processing helix chain 'D' and resid 365 through 386 Processing helix chain 'D' and resid 387 through 388 No H-bonds generated for 'chain 'D' and resid 387 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 412 removed outlier: 3.534A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 removed outlier: 4.179A pdb=" N LEU D 418 " --> pdb=" O THR D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.718A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 471 through 474 removed outlier: 3.841A pdb=" N MET D 474 " --> pdb=" O ASP D 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 471 through 474' Processing helix chain 'D' and resid 475 through 484 Processing helix chain 'D' and resid 498 through 503 Processing helix chain 'D' and resid 505 through 509 removed outlier: 3.914A pdb=" N ASP D 509 " --> pdb=" O VAL D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 532 Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.687A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 558 Processing helix chain 'D' and resid 565 through 574 removed outlier: 4.130A pdb=" N ALA D 569 " --> pdb=" O PRO D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'F' and resid 20 through 53 removed outlier: 4.605A pdb=" N GLN F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 82 removed outlier: 3.952A pdb=" N MET F 82 " --> pdb=" O THR F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 102 removed outlier: 3.503A pdb=" N LYS F 94 " --> pdb=" O ASN F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 removed outlier: 3.778A pdb=" N SER F 113 " --> pdb=" O SER F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 154 removed outlier: 3.713A pdb=" N ASN F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 173 removed outlier: 4.329A pdb=" N ARG F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER F 170 " --> pdb=" O GLU F 166 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU F 171 " --> pdb=" O SER F 167 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL F 172 " --> pdb=" O TRP F 168 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY F 173 " --> pdb=" O ARG F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 194 Processing helix chain 'F' and resid 198 through 205 Processing helix chain 'F' and resid 218 through 250 Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 263 through 267 removed outlier: 3.592A pdb=" N LEU F 267 " --> pdb=" O ALA F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 299 removed outlier: 3.724A pdb=" N MET F 297 " --> pdb=" O VAL F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 Processing helix chain 'F' and resid 325 through 330 removed outlier: 4.181A pdb=" N GLU F 329 " --> pdb=" O GLN F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.876A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 412 removed outlier: 4.072A pdb=" N GLY F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 removed outlier: 3.623A pdb=" N LEU F 418 " --> pdb=" O THR F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 447 Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 472 through 485 removed outlier: 3.861A pdb=" N LYS F 476 " --> pdb=" O GLN F 472 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU F 479 " --> pdb=" O LYS F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 502 Processing helix chain 'F' and resid 503 through 508 removed outlier: 3.555A pdb=" N SER F 507 " --> pdb=" O LEU F 503 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN F 508 " --> pdb=" O PHE F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 508' Processing helix chain 'F' and resid 513 through 531 Processing helix chain 'F' and resid 532 through 534 No H-bonds generated for 'chain 'F' and resid 532 through 534' Processing helix chain 'F' and resid 547 through 561 removed outlier: 4.001A pdb=" N GLY F 551 " --> pdb=" O SER F 547 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU F 560 " --> pdb=" O ASN F 556 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY F 561 " --> pdb=" O MET F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 574 Processing helix chain 'F' and resid 581 through 586 Processing helix chain 'F' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.984A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 203 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 229 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N SER A 205 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.711A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.762A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 318 removed outlier: 4.622A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.587A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.868A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.392A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB1, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.913A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB3, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.689A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N SER B 202 " --> pdb=" O PRO B 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.787A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.251A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 10.945A pdb=" N VAL B 126 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 9.633A pdb=" N GLU B 166 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N ILE B 128 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N THR B 164 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL B 130 " --> pdb=" O ASN B 162 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ASN B 162 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU B 132 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA B 160 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLN B 134 " --> pdb=" O SER B 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 311 through 318 removed outlier: 4.551A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.581A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.607A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.904A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC2, first strand: chain 'B' and resid 551 through 554 Processing sheet with id=AC3, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.800A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 694 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 656 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AC5, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.536A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 735 through 736 removed outlier: 3.678A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AC8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AC9, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.724A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE C 201 " --> pdb=" O ASP C 230 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP C 230 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE C 203 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU C 226 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.647A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD3, first strand: chain 'C' and resid 116 through 122 Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.883A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AD6, first strand: chain 'C' and resid 453 through 454 removed outlier: 3.509A pdb=" N TYR C 453 " --> pdb=" O ARG C 493 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 537 through 539 removed outlier: 3.741A pdb=" N LYS C 537 " --> pdb=" O LEU C 552 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU C 552 " --> pdb=" O LYS C 537 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.621A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE1, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.899A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.336A 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=AE2, first strand: chain 'C' and resid 735 through 736 removed outlier: 3.585A pdb=" N SER C 735 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE5, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.735A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.320A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 347 through 349 1480 hydrogen bonds defined for protein. 4153 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: 7.48 Time building geometry restraints manager: 4.24 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: 11588 1.34 - 1.46: 9491 1.46 - 1.59: 16284 1.59 - 1.71: 0 1.71 - 1.84: 247 Bond restraints: 37610 Sorted by residual: bond pdb=" N ASN B 145 " pdb=" CA ASN B 145 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.13e+00 bond pdb=" C ASP B 138 " pdb=" N PRO B 139 " ideal model delta sigma weight residual 1.330 1.361 -0.031 1.19e-02 7.06e+03 6.83e+00 bond pdb=" N HIS B 143 " pdb=" CA HIS B 143 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.82e+00 bond pdb=" N PHE B 140 " pdb=" CA PHE B 140 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.24e-02 6.50e+03 6.44e+00 bond pdb=" N SER B 148 " pdb=" CA SER B 148 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.37e+00 ... (remaining 37605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 50335 2.29 - 4.58: 721 4.58 - 6.88: 69 6.88 - 9.17: 12 9.17 - 11.46: 1 Bond angle restraints: 51138 Sorted by residual: angle pdb=" N GLY B 103 " pdb=" CA GLY B 103 " pdb=" C GLY B 103 " ideal model delta sigma weight residual 111.14 117.60 -6.46 1.46e+00 4.69e-01 1.96e+01 angle pdb=" CA LYS B 144 " pdb=" C LYS B 144 " pdb=" O LYS B 144 " ideal model delta sigma weight residual 122.31 116.70 5.61 1.31e+00 5.83e-01 1.84e+01 angle pdb=" N ILE C 468 " pdb=" CA ILE C 468 " pdb=" C ILE C 468 " ideal model delta sigma weight residual 113.53 109.42 4.11 9.80e-01 1.04e+00 1.76e+01 angle pdb=" N HIS B 143 " pdb=" CA HIS B 143 " pdb=" C HIS B 143 " ideal model delta sigma weight residual 108.41 114.80 -6.39 1.61e+00 3.86e-01 1.58e+01 angle pdb=" N LEU B 141 " pdb=" CA LEU B 141 " pdb=" C LEU B 141 " ideal model delta sigma weight residual 113.38 108.61 4.77 1.23e+00 6.61e-01 1.50e+01 ... (remaining 51133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 19401 18.02 - 36.05: 1935 36.05 - 54.07: 327 54.07 - 72.10: 46 72.10 - 90.12: 33 Dihedral angle restraints: 21742 sinusoidal: 8625 harmonic: 13117 Sorted by residual: dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 -177.99 -89.01 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 8.66 84.34 1 1.00e+01 1.00e-02 8.65e+01 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 93.00 165.66 -72.66 1 1.00e+01 1.00e-02 6.74e+01 ... (remaining 21739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 5212 0.075 - 0.149: 631 0.149 - 0.224: 20 0.224 - 0.298: 11 0.298 - 0.373: 3 Chirality restraints: 5877 Sorted by residual: chirality pdb=" CA ASN B 146 " pdb=" N ASN B 146 " pdb=" C ASN B 146 " pdb=" CB ASN B 146 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 5874 not shown) Planarity restraints: 6534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 329 " 0.050 5.00e-02 4.00e+02 7.55e-02 9.12e+00 pdb=" N PRO C 330 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 83 " 0.048 5.00e-02 4.00e+02 7.27e-02 8.47e+00 pdb=" N PRO D 84 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO D 84 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 84 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 214 " -0.046 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO A 215 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " -0.039 5.00e-02 4.00e+02 ... (remaining 6531 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 925 2.68 - 3.24: 37003 3.24 - 3.79: 56762 3.79 - 4.35: 72179 4.35 - 4.90: 117190 Nonbonded interactions: 284059 Sorted by model distance: nonbonded pdb=" OG SER D 109 " pdb=" OD1 ASP D 111 " model vdw 2.126 3.040 nonbonded pdb=" OG1 THR D 55 " pdb=" OD1 ASN D 58 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR B 489 " pdb=" OH TYR F 83 " model vdw 2.157 3.040 nonbonded pdb=" OG1 THR C 581 " pdb=" OE1 GLU C 583 " model vdw 2.166 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.168 3.040 ... (remaining 284054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 14 through 1308) selection = (chain 'C' and resid 14 through 1308) } ncs_group { reference = (chain 'D' and (resid 19 through 227 or resid 229 through 704)) selection = (chain 'F' and (resid 19 through 227 or resid 229 through 704)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Q' selection = chain 'R' selection = chain 'Y' selection = chain 'Z' } 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=0.50 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: 2.930 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: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 33.730 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 0.073 37728 Z= 0.190 Angle : 0.667 11.460 51428 Z= 0.334 Chirality : 0.047 0.373 5877 Planarity : 0.004 0.076 6494 Dihedral : 14.412 90.123 13157 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.86 % Favored : 93.05 % Rotamer: Outliers : 0.05 % Allowed : 0.43 % Favored : 99.52 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.13), residues: 4450 helix: 0.82 (0.14), residues: 1423 sheet: 0.22 (0.21), residues: 606 loop : -1.87 (0.12), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1019 TYR 0.032 0.001 TYR D 199 PHE 0.030 0.001 PHE F 452 TRP 0.024 0.001 TRP F 566 HIS 0.006 0.001 HIS B1159 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (37610) covalent geometry : angle 0.65433 / 0.33 (51138) SS BOND : bond 0.00337 / 0.21 ( 45) SS BOND : angle 1.26895 / 0.79 ( 90) hydrogen bonds : bond 0.12965 / 8.34 ( 1480) hydrogen bonds : angle 6.09980 / 4.19 ( 4153) Misc. bond : bond 0.00081 / 0.04 ( 6) link_BETA1-4 : bond 0.00501 / 0.33 ( 26) link_BETA1-4 : angle 1.72439 / 1.04 ( 78) link_NAG-ASN : bond 0.00388 / 0.24 ( 40) link_NAG-ASN : angle 2.30707 / 1.86 ( 120) link_NAG-SER : bond 0.00009 / 0.00 ( 1) link_NAG-SER : angle 1.19007 / 0.64 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1017 GLU cc_start: 0.8233 (tm-30) cc_final: 0.8032 (tm-30) REVERT: C 759 PHE cc_start: 0.7236 (t80) cc_final: 0.6891 (t80) REVERT: D 69 TRP cc_start: 0.2001 (t-100) cc_final: 0.0958 (t60) REVERT: D 249 MET cc_start: 0.3632 (mtt) cc_final: 0.3430 (mmt) REVERT: F 498 CYS cc_start: 0.6572 (t) cc_final: 0.6250 (t) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.2026 time to fit residues: 58.3951 Evaluate side-chains 126 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 30.0000 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1159 HIS B 134 GLN C 220 GLN C 370 ASN C 955 ASN C1119 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.119156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.085211 restraints weight = 169921.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.086314 restraints weight = 83719.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.085966 restraints weight = 55706.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.086228 restraints weight = 56074.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.086439 restraints weight = 46553.616| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 37728 Z= 0.196 Angle : 0.642 10.153 51428 Z= 0.326 Chirality : 0.045 0.389 5877 Planarity : 0.005 0.075 6494 Dihedral : 4.889 30.632 4817 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.99 % Favored : 92.92 % Rotamer: Outliers : 0.38 % Allowed : 7.58 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.12), residues: 4450 helix: 0.81 (0.14), residues: 1424 sheet: 0.25 (0.21), residues: 611 loop : -1.87 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 169 TYR 0.022 0.001 TYR A 453 PHE 0.030 0.002 PHE D 369 TRP 0.045 0.002 TRP D 203 HIS 0.006 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (37610) covalent geometry : angle 0.62915 / 0.32 (51138) SS BOND : bond 0.00379 / 0.24 ( 45) SS BOND : angle 1.20490 / 0.78 ( 90) hydrogen bonds : bond 0.04985 / 3.28 ( 1480) hydrogen bonds : angle 5.32888 / 3.65 ( 4153) Misc. bond : bond 0.00041 / 0.02 ( 6) link_BETA1-4 : bond 0.00414 / 0.31 ( 26) link_BETA1-4 : angle 1.55278 / 1.01 ( 78) link_NAG-ASN : bond 0.00485 / 0.34 ( 40) link_NAG-ASN : angle 2.25708 / 1.75 ( 120) link_NAG-SER : bond 0.00098 / 0.05 ( 1) link_NAG-SER : angle 0.99007 / 0.53 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 697 MET cc_start: 0.7254 (mpp) cc_final: 0.7006 (mpp) REVERT: D 249 MET cc_start: 0.2899 (mtt) cc_final: 0.2489 (mtt) REVERT: F 270 MET cc_start: 0.5000 (mpp) cc_final: 0.4748 (mpp) REVERT: F 498 CYS cc_start: 0.6350 (t) cc_final: 0.6091 (t) outliers start: 14 outliers final: 8 residues processed: 145 average time/residue: 0.1821 time to fit residues: 46.7792 Evaluate side-chains 131 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 144 optimal weight: 7.9990 chunk 129 optimal weight: 30.0000 chunk 150 optimal weight: 10.0000 chunk 176 optimal weight: 0.9980 chunk 437 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 413 optimal weight: 9.9990 chunk 363 optimal weight: 8.9990 chunk 212 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 345 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.118137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.083654 restraints weight = 187346.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.084815 restraints weight = 88500.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.084718 restraints weight = 54868.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.084976 restraints weight = 52009.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.085053 restraints weight = 45380.149| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 37728 Z= 0.235 Angle : 0.665 10.220 51428 Z= 0.337 Chirality : 0.045 0.402 5877 Planarity : 0.005 0.075 6494 Dihedral : 5.033 24.231 4817 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.64 % Favored : 92.27 % Rotamer: Outliers : 0.91 % Allowed : 11.44 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.12), residues: 4450 helix: 0.67 (0.14), residues: 1423 sheet: 0.12 (0.21), residues: 609 loop : -1.92 (0.12), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 815 TYR 0.020 0.002 TYR A1067 PHE 0.034 0.002 PHE D 369 TRP 0.060 0.002 TRP D 203 HIS 0.007 0.001 HIS A1159 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.24 (37610) covalent geometry : angle 0.65192 / 0.33 (51138) SS BOND : bond 0.00343 / 0.21 ( 45) SS BOND : angle 1.24148 / 0.81 ( 90) hydrogen bonds : bond 0.05129 / 3.37 ( 1480) hydrogen bonds : angle 5.37845 / 3.68 ( 4153) Misc. bond : bond 0.00040 / 0.02 ( 6) link_BETA1-4 : bond 0.00432 / 0.31 ( 26) link_BETA1-4 : angle 1.52216 / 0.98 ( 78) link_NAG-ASN : bond 0.00571 / 0.40 ( 40) link_NAG-ASN : angle 2.33065 / 1.80 ( 120) link_NAG-SER : bond 0.00140 / 0.07 ( 1) link_NAG-SER : angle 1.74854 / 0.93 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.5427 (m-10) cc_final: 0.5124 (m-80) REVERT: D 249 MET cc_start: 0.2819 (mtt) cc_final: 0.2418 (mtt) REVERT: F 270 MET cc_start: 0.5086 (mpp) cc_final: 0.4685 (mpp) REVERT: F 498 CYS cc_start: 0.6432 (t) cc_final: 0.6112 (t) outliers start: 35 outliers final: 20 residues processed: 163 average time/residue: 0.1932 time to fit residues: 56.7924 Evaluate side-chains 148 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 378 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 222 optimal weight: 2.9990 chunk 405 optimal weight: 6.9990 chunk 63 optimal weight: 0.0470 chunk 86 optimal weight: 5.9990 chunk 231 optimal weight: 0.0170 chunk 136 optimal weight: 4.9990 chunk 272 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 overall best weight: 2.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 GLN A 762 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.118421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.083655 restraints weight = 224581.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.084782 restraints weight = 103734.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.085303 restraints weight = 58480.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.085387 restraints weight = 48778.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.085436 restraints weight = 45864.587| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.3570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 37728 Z= 0.170 Angle : 0.612 10.296 51428 Z= 0.309 Chirality : 0.044 0.389 5877 Planarity : 0.004 0.074 6494 Dihedral : 4.880 23.129 4817 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.72 % Favored : 93.19 % Rotamer: Outliers : 1.27 % Allowed : 13.51 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.12), residues: 4450 helix: 0.81 (0.14), residues: 1421 sheet: 0.05 (0.21), residues: 622 loop : -1.90 (0.12), residues: 2407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 634 TYR 0.020 0.001 TYR D 385 PHE 0.031 0.001 PHE D 369 TRP 0.054 0.002 TRP F 477 HIS 0.007 0.001 HIS A1159 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (37610) covalent geometry : angle 0.59907 / 0.31 (51138) SS BOND : bond 0.00315 / 0.20 ( 45) SS BOND : angle 1.43039 / 0.83 ( 90) hydrogen bonds : bond 0.04652 / 3.05 ( 1480) hydrogen bonds : angle 5.19035 / 3.55 ( 4153) Misc. bond : bond 0.00033 / 0.02 ( 6) link_BETA1-4 : bond 0.00394 / 0.28 ( 26) link_BETA1-4 : angle 1.48325 / 0.94 ( 78) link_NAG-ASN : bond 0.00438 / 0.30 ( 40) link_NAG-ASN : angle 2.18190 / 1.70 ( 120) link_NAG-SER : bond 0.00066 / 0.03 ( 1) link_NAG-SER : angle 1.18021 / 0.63 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 139 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.5425 (m-10) cc_final: 0.5121 (m-80) REVERT: A 271 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7937 (pm20) REVERT: A 1010 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8439 (mp10) REVERT: B 740 MET cc_start: 0.8688 (mtp) cc_final: 0.8469 (mtp) REVERT: C 303 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8268 (tt) REVERT: D 249 MET cc_start: 0.2645 (mtt) cc_final: 0.2159 (mtt) REVERT: D 579 MET cc_start: 0.0288 (mpp) cc_final: -0.1037 (mtm) REVERT: F 217 TYR cc_start: -0.0192 (OUTLIER) cc_final: -0.0781 (m-80) REVERT: F 270 MET cc_start: 0.5155 (mpp) cc_final: 0.4654 (mpp) REVERT: F 376 MET cc_start: 0.3311 (ptp) cc_final: 0.3087 (ptp) REVERT: F 473 TRP cc_start: 0.3051 (m-90) cc_final: 0.2538 (m-90) REVERT: F 498 CYS cc_start: 0.6560 (t) cc_final: 0.6353 (t) outliers start: 49 outliers final: 24 residues processed: 183 average time/residue: 0.2062 time to fit residues: 66.5532 Evaluate side-chains 156 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 61 optimal weight: 0.7980 chunk 363 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 chunk 368 optimal weight: 0.8980 chunk 150 optimal weight: 0.0070 chunk 258 optimal weight: 1.9990 chunk 340 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.119542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.085741 restraints weight = 172549.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.086376 restraints weight = 86565.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.086497 restraints weight = 55437.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.086696 restraints weight = 55627.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.087060 restraints weight = 46732.554| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 37728 Z= 0.120 Angle : 0.585 13.556 51428 Z= 0.293 Chirality : 0.043 0.380 5877 Planarity : 0.004 0.073 6494 Dihedral : 4.678 25.052 4817 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.21 % Favored : 93.71 % Rotamer: Outliers : 1.09 % Allowed : 14.78 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.13), residues: 4450 helix: 0.98 (0.14), residues: 1428 sheet: 0.22 (0.21), residues: 610 loop : -1.79 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 634 TYR 0.021 0.001 TYR D 385 PHE 0.027 0.001 PHE D 369 TRP 0.070 0.001 TRP F 477 HIS 0.018 0.001 HIS F 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (37610) covalent geometry : angle 0.57279 / 0.29 (51138) SS BOND : bond 0.00399 / 0.32 ( 45) SS BOND : angle 1.14448 / 0.70 ( 90) hydrogen bonds : bond 0.04244 / 2.78 ( 1480) hydrogen bonds : angle 4.99944 / 3.42 ( 4153) Misc. bond : bond 0.00037 / 0.02 ( 6) link_BETA1-4 : bond 0.00435 / 0.32 ( 26) link_BETA1-4 : angle 1.46919 / 0.91 ( 78) link_NAG-ASN : bond 0.00376 / 0.24 ( 40) link_NAG-ASN : angle 2.06154 / 1.63 ( 120) link_NAG-SER : bond 0.00008 / 0.00 ( 1) link_NAG-SER : angle 0.58461 / 0.31 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.5406 (m-10) cc_final: 0.5105 (m-80) REVERT: A 1010 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8409 (mp10) REVERT: B 633 TRP cc_start: 0.7277 (p90) cc_final: 0.6971 (p90) REVERT: B 740 MET cc_start: 0.8725 (mtp) cc_final: 0.8464 (mtp) REVERT: C 773 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8248 (mt-10) REVERT: D 69 TRP cc_start: 0.1483 (t-100) cc_final: -0.0096 (t60) REVERT: D 249 MET cc_start: 0.2665 (mtt) cc_final: 0.2284 (mmt) REVERT: F 217 TYR cc_start: -0.0387 (OUTLIER) cc_final: -0.1039 (m-80) REVERT: F 473 TRP cc_start: 0.3286 (m-90) cc_final: 0.2781 (m-90) REVERT: F 498 CYS cc_start: 0.6502 (t) cc_final: 0.6253 (t) outliers start: 42 outliers final: 24 residues processed: 181 average time/residue: 0.2078 time to fit residues: 66.7531 Evaluate side-chains 157 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 275 optimal weight: 0.6980 chunk 286 optimal weight: 0.8980 chunk 245 optimal weight: 0.8980 chunk 255 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 427 optimal weight: 5.9990 chunk 383 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 140 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.118260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.084192 restraints weight = 165268.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.085618 restraints weight = 75940.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.084988 restraints weight = 51468.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.085351 restraints weight = 52413.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.085687 restraints weight = 43058.185| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 37728 Z= 0.175 Angle : 0.615 13.005 51428 Z= 0.308 Chirality : 0.044 0.388 5877 Planarity : 0.004 0.074 6494 Dihedral : 4.743 25.700 4817 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.08 % Favored : 92.81 % Rotamer: Outliers : 1.72 % Allowed : 15.39 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.13), residues: 4450 helix: 0.93 (0.14), residues: 1429 sheet: 0.27 (0.22), residues: 598 loop : -1.85 (0.12), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 44 TYR 0.019 0.001 TYR D 385 PHE 0.032 0.001 PHE A 133 TRP 0.051 0.001 TRP D 203 HIS 0.017 0.001 HIS F 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (37610) covalent geometry : angle 0.60324 / 0.30 (51138) SS BOND : bond 0.00340 / 0.24 ( 45) SS BOND : angle 1.20171 / 0.76 ( 90) hydrogen bonds : bond 0.04464 / 2.93 ( 1480) hydrogen bonds : angle 5.07930 / 3.47 ( 4153) Misc. bond : bond 0.00037 / 0.02 ( 6) link_BETA1-4 : bond 0.00421 / 0.31 ( 26) link_BETA1-4 : angle 1.46320 / 0.92 ( 78) link_NAG-ASN : bond 0.00453 / 0.31 ( 40) link_NAG-ASN : angle 2.14414 / 1.68 ( 120) link_NAG-SER : bond 0.00099 / 0.05 ( 1) link_NAG-SER : angle 1.19655 / 0.63 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 133 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: A 186 PHE cc_start: 0.5473 (m-10) cc_final: 0.5150 (m-80) REVERT: A 455 LEU cc_start: 0.6698 (mm) cc_final: 0.6478 (mp) REVERT: A 1010 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8442 (mp10) REVERT: B 633 TRP cc_start: 0.7253 (p90) cc_final: 0.6913 (p90) REVERT: B 740 MET cc_start: 0.8667 (mtp) cc_final: 0.8390 (mtp) REVERT: C 303 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8231 (tt) REVERT: D 249 MET cc_start: 0.2691 (mtt) cc_final: 0.2311 (mmt) REVERT: F 217 TYR cc_start: -0.0407 (OUTLIER) cc_final: -0.1059 (m-80) REVERT: F 270 MET cc_start: 0.5076 (mpp) cc_final: 0.4600 (mpp) REVERT: F 473 TRP cc_start: 0.3265 (m-90) cc_final: 0.2756 (m-90) REVERT: F 474 MET cc_start: -0.1494 (mmp) cc_final: -0.2470 (mmp) REVERT: F 477 TRP cc_start: -0.2105 (t60) cc_final: -0.2671 (t-100) outliers start: 67 outliers final: 45 residues processed: 194 average time/residue: 0.2070 time to fit residues: 71.2881 Evaluate side-chains 178 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 129 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 80 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 278 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 351 optimal weight: 2.9990 chunk 245 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 256 optimal weight: 8.9990 chunk 140 optimal weight: 20.0000 chunk 361 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.116884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.082058 restraints weight = 194909.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.083603 restraints weight = 87499.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.083577 restraints weight = 52010.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.083778 restraints weight = 49174.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.083955 restraints weight = 42960.204| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 37728 Z= 0.325 Angle : 0.778 13.468 51428 Z= 0.391 Chirality : 0.048 0.426 5877 Planarity : 0.005 0.073 6494 Dihedral : 5.397 25.614 4817 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.31 % Favored : 90.58 % Rotamer: Outliers : 2.00 % Allowed : 16.38 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.12), residues: 4450 helix: 0.47 (0.14), residues: 1430 sheet: -0.07 (0.21), residues: 606 loop : -2.09 (0.12), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 815 TYR 0.022 0.002 TYR A1067 PHE 0.041 0.002 PHE D 369 TRP 0.060 0.002 TRP D 203 HIS 0.029 0.002 HIS F 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00752 / 0.33 (37610) covalent geometry : angle 0.76395 / 0.39 (51138) SS BOND : bond 0.00560 / 0.31 ( 45) SS BOND : angle 1.60466 / 1.01 ( 90) hydrogen bonds : bond 0.05617 / 3.69 ( 1480) hydrogen bonds : angle 5.60231 / 3.83 ( 4153) Misc. bond : bond 0.00058 / 0.03 ( 6) link_BETA1-4 : bond 0.00524 / 0.34 ( 26) link_BETA1-4 : angle 1.62289 / 1.08 ( 78) link_NAG-ASN : bond 0.00831 / 0.59 ( 40) link_NAG-ASN : angle 2.60096 / 1.96 ( 120) link_NAG-SER : bond 0.00351 / 0.18 ( 1) link_NAG-SER : angle 2.62071 / 1.39 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 130 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.5672 (m-10) cc_final: 0.5304 (m-80) REVERT: A 1010 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8512 (mp10) REVERT: B 740 MET cc_start: 0.8660 (mtp) cc_final: 0.8399 (mtp) REVERT: C 190 ARG cc_start: 0.7700 (mtp180) cc_final: 0.6569 (mmm160) REVERT: C 303 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8329 (tt) REVERT: D 249 MET cc_start: 0.2794 (mtt) cc_final: 0.2299 (mtt) REVERT: F 217 TYR cc_start: 0.0095 (OUTLIER) cc_final: -0.0880 (m-80) REVERT: F 270 MET cc_start: 0.5111 (mpp) cc_final: 0.4584 (mpp) outliers start: 78 outliers final: 51 residues processed: 204 average time/residue: 0.2062 time to fit residues: 75.0198 Evaluate side-chains 179 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 125 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 326 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 217 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 417 optimal weight: 4.9990 chunk 273 optimal weight: 0.8980 chunk 295 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN A 762 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN A1119 ASN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 HIS B 487 ASN C 115 GLN ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 HIS ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.118993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.084186 restraints weight = 224222.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.085447 restraints weight = 109978.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.085800 restraints weight = 57106.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.086034 restraints weight = 55136.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.086449 restraints weight = 44404.302| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 37728 Z= 0.129 Angle : 0.624 12.694 51428 Z= 0.310 Chirality : 0.044 0.377 5877 Planarity : 0.004 0.071 6494 Dihedral : 4.920 32.609 4817 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.73 % Favored : 94.18 % Rotamer: Outliers : 1.22 % Allowed : 17.57 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.12), residues: 4450 helix: 0.84 (0.14), residues: 1435 sheet: -0.01 (0.21), residues: 628 loop : -1.90 (0.12), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 357 TYR 0.036 0.001 TYR F 158 PHE 0.028 0.001 PHE D 369 TRP 0.051 0.001 TRP D 203 HIS 0.006 0.001 HIS A1159 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (37610) covalent geometry : angle 0.61085 / 0.31 (51138) SS BOND : bond 0.00334 / 0.22 ( 45) SS BOND : angle 1.26701 / 0.78 ( 90) hydrogen bonds : bond 0.04449 / 2.93 ( 1480) hydrogen bonds : angle 5.11230 / 3.49 ( 4153) Misc. bond : bond 0.00043 / 0.03 ( 6) link_BETA1-4 : bond 0.00460 / 0.33 ( 26) link_BETA1-4 : angle 1.51913 / 0.95 ( 78) link_NAG-ASN : bond 0.00448 / 0.27 ( 40) link_NAG-ASN : angle 2.21676 / 1.70 ( 120) link_NAG-SER : bond 0.00007 / 0.00 ( 1) link_NAG-SER : angle 0.83347 / 0.44 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 140 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.5439 (m-10) cc_final: 0.5128 (m-80) REVERT: A 455 LEU cc_start: 0.7035 (mm) cc_final: 0.6821 (mm) REVERT: A 1010 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8455 (mp10) REVERT: B 740 MET cc_start: 0.8605 (mtp) cc_final: 0.8247 (mtp) REVERT: C 190 ARG cc_start: 0.7526 (mtp180) cc_final: 0.6285 (mmm160) REVERT: C 303 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8233 (tp) REVERT: C 370 ASN cc_start: 0.7167 (t0) cc_final: 0.6396 (p0) REVERT: D 249 MET cc_start: 0.3059 (mtt) cc_final: 0.2642 (mmt) REVERT: F 217 TYR cc_start: -0.0207 (OUTLIER) cc_final: -0.0954 (m-80) REVERT: F 270 MET cc_start: 0.5122 (mpp) cc_final: 0.4599 (mpp) outliers start: 47 outliers final: 34 residues processed: 181 average time/residue: 0.2085 time to fit residues: 66.5908 Evaluate side-chains 166 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 70 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 chunk 274 optimal weight: 8.9990 chunk 151 optimal weight: 20.0000 chunk 365 optimal weight: 6.9990 chunk 321 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 chunk 272 optimal weight: 8.9990 chunk 383 optimal weight: 0.7980 chunk 173 optimal weight: 0.3980 chunk 91 optimal weight: 0.9980 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.118400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.083649 restraints weight = 201122.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.084696 restraints weight = 95307.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.085096 restraints weight = 58797.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.085372 restraints weight = 47444.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.085610 restraints weight = 42756.388| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 37728 Z= 0.151 Angle : 0.630 11.612 51428 Z= 0.313 Chirality : 0.044 0.383 5877 Planarity : 0.004 0.071 6494 Dihedral : 4.871 33.523 4817 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.68 % Favored : 93.21 % Rotamer: Outliers : 1.47 % Allowed : 17.75 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.12), residues: 4450 helix: 0.89 (0.14), residues: 1426 sheet: 0.05 (0.21), residues: 624 loop : -1.89 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 357 TYR 0.032 0.001 TYR F 158 PHE 0.030 0.001 PHE D 369 TRP 0.050 0.001 TRP D 203 HIS 0.011 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (37610) covalent geometry : angle 0.61494 / 0.31 (51138) SS BOND : bond 0.00328 / 0.21 ( 45) SS BOND : angle 1.54289 / 0.88 ( 90) hydrogen bonds : bond 0.04433 / 2.91 ( 1480) hydrogen bonds : angle 5.10224 / 3.48 ( 4153) Misc. bond : bond 0.00031 / 0.02 ( 6) link_BETA1-4 : bond 0.00457 / 0.32 ( 26) link_BETA1-4 : angle 1.52143 / 0.94 ( 78) link_NAG-ASN : bond 0.00446 / 0.29 ( 40) link_NAG-ASN : angle 2.37761 / 1.78 ( 120) link_NAG-SER : bond 0.00132 / 0.07 ( 1) link_NAG-SER : angle 0.94629 / 0.50 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 133 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.5534 (m-10) cc_final: 0.5211 (m-80) REVERT: A 455 LEU cc_start: 0.6948 (mm) cc_final: 0.6684 (mm) REVERT: A 1010 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8447 (mp10) REVERT: B 740 MET cc_start: 0.8624 (mtp) cc_final: 0.8278 (mtp) REVERT: B 1017 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8272 (tm-30) REVERT: C 190 ARG cc_start: 0.7517 (mtp180) cc_final: 0.6268 (mmm160) REVERT: C 303 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8271 (tp) REVERT: C 773 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8125 (mt-10) REVERT: D 249 MET cc_start: 0.3045 (mtt) cc_final: 0.2638 (mmt) REVERT: D 557 MET cc_start: 0.4706 (mmm) cc_final: 0.4357 (tmm) REVERT: F 217 TYR cc_start: -0.0168 (OUTLIER) cc_final: -0.0892 (m-80) REVERT: F 270 MET cc_start: 0.5118 (mpp) cc_final: 0.4605 (mpp) outliers start: 57 outliers final: 44 residues processed: 185 average time/residue: 0.2070 time to fit residues: 67.8987 Evaluate side-chains 177 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 130 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 179 optimal weight: 10.0000 chunk 244 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 442 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 367 optimal weight: 20.0000 chunk 269 optimal weight: 9.9990 chunk 278 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.117629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.083435 restraints weight = 200099.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.084379 restraints weight = 90587.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.084902 restraints weight = 57386.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.084876 restraints weight = 47188.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.085093 restraints weight = 44061.721| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 37728 Z= 0.204 Angle : 0.663 12.740 51428 Z= 0.330 Chirality : 0.045 0.390 5877 Planarity : 0.004 0.071 6494 Dihedral : 4.992 34.657 4817 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.40 % Favored : 92.49 % Rotamer: Outliers : 1.39 % Allowed : 17.93 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.12), residues: 4450 helix: 0.80 (0.14), residues: 1436 sheet: 0.05 (0.21), residues: 612 loop : -1.96 (0.12), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.030 0.001 TYR F 158 PHE 0.033 0.001 PHE D 369 TRP 0.051 0.002 TRP D 203 HIS 0.008 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (37610) covalent geometry : angle 0.64912 / 0.33 (51138) SS BOND : bond 0.00342 / 0.22 ( 45) SS BOND : angle 1.55989 / 0.92 ( 90) hydrogen bonds : bond 0.04655 / 3.06 ( 1480) hydrogen bonds : angle 5.20005 / 3.55 ( 4153) Misc. bond : bond 0.00030 / 0.02 ( 6) link_BETA1-4 : bond 0.00434 / 0.31 ( 26) link_BETA1-4 : angle 1.51627 / 0.95 ( 78) link_NAG-ASN : bond 0.00527 / 0.36 ( 40) link_NAG-ASN : angle 2.39360 / 1.80 ( 120) link_NAG-SER : bond 0.00224 / 0.12 ( 1) link_NAG-SER : angle 1.85301 / 0.98 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 131 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.5445 (m-10) cc_final: 0.5219 (m-80) REVERT: A 455 LEU cc_start: 0.7081 (mm) cc_final: 0.6791 (mm) REVERT: A 1010 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8448 (mp10) REVERT: B 740 MET cc_start: 0.8619 (mtp) cc_final: 0.8294 (mtp) REVERT: B 1017 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8266 (tm-30) REVERT: C 190 ARG cc_start: 0.7623 (mtp180) cc_final: 0.6402 (mmm160) REVERT: C 303 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8315 (tt) REVERT: C 370 ASN cc_start: 0.7135 (t0) cc_final: 0.6405 (p0) REVERT: D 249 MET cc_start: 0.2965 (mtt) cc_final: 0.2481 (mmt) REVERT: D 557 MET cc_start: 0.4642 (mmm) cc_final: 0.4355 (tmm) REVERT: F 217 TYR cc_start: 0.0119 (OUTLIER) cc_final: -0.0823 (m-80) REVERT: F 270 MET cc_start: 0.5107 (mpp) cc_final: 0.4562 (mpp) REVERT: F 464 PHE cc_start: 0.3055 (OUTLIER) cc_final: 0.2675 (t80) outliers start: 54 outliers final: 48 residues processed: 180 average time/residue: 0.2064 time to fit residues: 65.8138 Evaluate side-chains 179 residues out of total 3940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 127 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 464 PHE Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 42 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 431 optimal weight: 10.0000 chunk 287 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 279 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 442 optimal weight: 1.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.119058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.084381 restraints weight = 170810.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.085481 restraints weight = 81319.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.086322 restraints weight = 52112.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.086240 restraints weight = 48424.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.086232 restraints weight = 41603.482| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 37728 Z= 0.155 Angle : 0.631 12.537 51428 Z= 0.313 Chirality : 0.044 0.379 5877 Planarity : 0.004 0.070 6494 Dihedral : 4.897 32.381 4817 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.68 % Favored : 93.21 % Rotamer: Outliers : 1.45 % Allowed : 18.10 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.12), residues: 4450 helix: 0.85 (0.14), residues: 1443 sheet: 0.08 (0.22), residues: 608 loop : -1.91 (0.12), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 357 TYR 0.030 0.001 TYR F 158 PHE 0.031 0.001 PHE D 369 TRP 0.049 0.001 TRP D 203 HIS 0.010 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (37610) covalent geometry : angle 0.61770 / 0.31 (51138) SS BOND : bond 0.00313 / 0.20 ( 45) SS BOND : angle 1.39471 / 0.82 ( 90) hydrogen bonds : bond 0.04449 / 2.93 ( 1480) hydrogen bonds : angle 5.09787 / 3.48 ( 4153) Misc. bond : bond 0.00031 / 0.02 ( 6) link_BETA1-4 : bond 0.00433 / 0.31 ( 26) link_BETA1-4 : angle 1.50922 / 0.93 ( 78) link_NAG-ASN : bond 0.00430 / 0.28 ( 40) link_NAG-ASN : angle 2.27149 / 1.73 ( 120) link_NAG-SER : bond 0.00110 / 0.06 ( 1) link_NAG-SER : angle 1.31531 / 0.69 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8467.20 seconds wall clock time: 146 minutes 59.42 seconds (8819.42 seconds total)