Starting phenix.real_space_refine on Sat Mar 7 08:47:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dlp_27509/03_2026/8dlp_27509.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlp_27509/03_2026/8dlp_27509.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dlp_27509/03_2026/8dlp_27509.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlp_27509/03_2026/8dlp_27509.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dlp_27509/03_2026/8dlp_27509.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlp_27509/03_2026/8dlp_27509.map" } resolution = 2.64 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= 0.042 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 198 5.16 5 C 25572 2.51 5 N 6546 2.21 5 O 7779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40095 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8139 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 55, 'TRANS': 984} Chain breaks: 7 Chain: "B" Number of atoms: 8139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8139 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 55, 'TRANS': 984} Chain breaks: 7 Chain: "C" Number of atoms: 8139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8139 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 55, 'TRANS': 984} Chain breaks: 7 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 8.99, per 1000 atoms: 0.22 Number of scatterers: 40095 At special positions: 0 Unit cell: (179, 158, 237, 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 198 16.00 O 7779 8.00 N 6546 7.00 C 25572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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 166 " 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=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " 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=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 90 " " NAG D 703 " - " ASN D 103 " " NAG D 704 " - " ASN D 322 " " NAG D 705 " - " ASN D 432 " " NAG D 706 " - " ASN D 546 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " ASN E 546 " " NAG F 701 " - " ASN F 53 " " NAG F 702 " - " ASN F 90 " " NAG F 703 " - " ASN F 103 " " NAG F 704 " - " ASN F 322 " " NAG F 705 " - " ASN F 432 " " NAG F 706 " - " ASN F 546 " " NAG G 1 " - " ASN A 17 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1074 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN B 17 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1074 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN C 17 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C 801 " " NAG V 1 " - " ASN C1074 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 1.7 seconds 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9228 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 58 sheets defined 41.5% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.500A pdb=" N LYS A 386 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.758A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.099A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.641A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.900A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.082A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.718A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.084A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.621A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.891A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.035A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.512A pdb=" N LYS C 386 " --> pdb=" O SER C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.722A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 4.071A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (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: 3.638A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (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 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.898A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 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 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.013A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.707A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.658A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.812A pdb=" N GLU D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.070A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 Proline residue: D 178 - end of helix removed outlier: 3.722A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 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 218 through 252 removed outlier: 3.738A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (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 275 through 279 removed outlier: 3.814A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 301 Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.572A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.720A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 397 through 413 removed outlier: 4.295A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.622A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.409A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.542A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.805A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.411A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.873A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.714A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.630A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.800A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 4.079A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 145 through 155 removed outlier: 3.775A pdb=" N GLU E 150 " --> pdb=" O PRO E 146 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.714A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 218 through 252 removed outlier: 3.753A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.817A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 301 Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.564A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.680A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 397 through 413 removed outlier: 4.235A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.617A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.431A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 removed outlier: 3.507A pdb=" N GLU E 479 " --> pdb=" O LYS E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.792A pdb=" N SER E 502 " --> pdb=" O ASP E 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.436A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.884A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.713A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 81 removed outlier: 3.631A pdb=" N GLN F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 88 removed outlier: 3.809A pdb=" N GLU F 87 " --> pdb=" O PRO F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 Processing helix chain 'F' and resid 103 through 108 removed outlier: 4.085A pdb=" N VAL F 107 " --> pdb=" O GLY F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 155 Processing helix chain 'F' and resid 157 through 194 Proline residue: F 178 - end of helix removed outlier: 3.705A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 218 through 252 removed outlier: 3.685A pdb=" N LEU F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU F 232 " --> pdb=" O HIS F 228 " (cutoff:3.500A) Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 275 through 279 removed outlier: 3.799A pdb=" N TYR F 279 " --> pdb=" O THR F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 301 Processing helix chain 'F' and resid 303 through 318 Processing helix chain 'F' and resid 324 through 331 removed outlier: 3.567A pdb=" N TRP F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.711A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 388 No H-bonds generated for 'chain 'F' and resid 386 through 388' Processing helix chain 'F' and resid 389 through 393 Processing helix chain 'F' and resid 397 through 413 removed outlier: 4.250A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.601A pdb=" N GLU F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 465 removed outlier: 4.430A pdb=" N PHE F 452 " --> pdb=" O GLY F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 469 through 471 No H-bonds generated for 'chain 'F' and resid 469 through 471' Processing helix chain 'F' and resid 472 through 484 removed outlier: 3.530A pdb=" N GLU F 479 " --> pdb=" O LYS F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 502 removed outlier: 3.789A pdb=" N SER F 502 " --> pdb=" O ASP F 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 499 through 502' Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 512 through 533 removed outlier: 4.430A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.841A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 574 Processing helix chain 'F' and resid 581 through 588 Processing helix chain 'F' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.149A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.012A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.045A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.664A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 11.350A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.909A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.154A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.233A pdb=" N TYR A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.548A pdb=" N PHE A 157 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 11.572A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.664A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.674A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.993A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.420A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.919A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.776A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.524A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.992A 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: 6.669A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.524A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.310A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.652A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.145A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.046A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.669A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 11.377A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.960A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.194A pdb=" N TYR B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N PHE B 157 " --> pdb=" O TYR B 138 " (cutoff:3.500A) removed outlier: 11.587A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.669A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 318 removed outlier: 6.744A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.261A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.069A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.787A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.759A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.507A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.507A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.309A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.065A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.022A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.544A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 11.434A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.016A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.245A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.208A pdb=" N TYR C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.492A pdb=" N PHE C 157 " --> pdb=" O TYR C 138 " (cutoff:3.500A) removed outlier: 11.539A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.544A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.679A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.258A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.871A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.524A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.524A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.315A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF6, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.502A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.058A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.363A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.003A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.350A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 131 through 132 removed outlier: 3.669A pdb=" N VAL F 132 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU F 142 " --> pdb=" O VAL F 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'F' and resid 262 through 263 removed outlier: 6.068A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.369A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) 1959 hydrogen bonds defined for protein. 5532 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: 12.63 Time building geometry restraints manager: 4.47 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: 12627 1.34 - 1.47: 10498 1.47 - 1.59: 17666 1.59 - 1.72: 0 1.72 - 1.84: 288 Bond restraints: 41079 Sorted by residual: bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.59e+00 bond pdb=" C1 NAG F 702 " pdb=" O5 NAG F 702 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.08e+00 bond pdb=" C1 NAG D 702 " pdb=" O5 NAG D 702 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.98e+00 bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.83e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.56e+00 ... (remaining 41074 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 53803 1.92 - 3.83: 1824 3.83 - 5.75: 178 5.75 - 7.67: 49 7.67 - 9.59: 24 Bond angle restraints: 55878 Sorted by residual: angle pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " pdb=" CG TYR B 495 " ideal model delta sigma weight residual 113.90 123.16 -9.26 1.80e+00 3.09e-01 2.65e+01 angle pdb=" CA TYR A 495 " pdb=" CB TYR A 495 " pdb=" CG TYR A 495 " ideal model delta sigma weight residual 113.90 122.79 -8.89 1.80e+00 3.09e-01 2.44e+01 angle pdb=" CA TYR C 495 " pdb=" CB TYR C 495 " pdb=" CG TYR C 495 " ideal model delta sigma weight residual 113.90 122.59 -8.69 1.80e+00 3.09e-01 2.33e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.22 -5.52 1.22e+00 6.72e-01 2.05e+01 angle pdb=" C SER C 359 " pdb=" N ASN C 360 " pdb=" CA ASN C 360 " ideal model delta sigma weight residual 122.82 129.24 -6.42 1.42e+00 4.96e-01 2.04e+01 ... (remaining 55873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 23260 17.72 - 35.44: 1699 35.44 - 53.16: 288 53.16 - 70.88: 93 70.88 - 88.60: 52 Dihedral angle restraints: 25392 sinusoidal: 11052 harmonic: 14340 Sorted by residual: dihedral pdb=" CA GLU E 145 " pdb=" C GLU E 145 " pdb=" N PRO E 146 " pdb=" CA PRO E 146 " ideal model delta harmonic sigma weight residual -180.00 -150.57 -29.43 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CB CYS F 133 " pdb=" SG CYS F 133 " pdb=" SG CYS F 141 " pdb=" CB CYS F 141 " ideal model delta sinusoidal sigma weight residual -86.00 -49.22 -36.78 1 1.00e+01 1.00e-02 1.91e+01 dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual -86.00 -49.70 -36.30 1 1.00e+01 1.00e-02 1.86e+01 ... (remaining 25389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4926 0.060 - 0.120: 1202 0.120 - 0.179: 214 0.179 - 0.239: 26 0.239 - 0.299: 4 Chirality restraints: 6372 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 6369 not shown) Planarity restraints: 7188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 169 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.26e+00 pdb=" C ARG F 169 " 0.047 2.00e-02 2.50e+03 pdb=" O ARG F 169 " -0.017 2.00e-02 2.50e+03 pdb=" N SER F 170 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " -0.030 2.00e-02 2.50e+03 1.90e-02 7.25e+00 pdb=" CG TYR B 495 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 169 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" C ARG D 169 " 0.045 2.00e-02 2.50e+03 pdb=" O ARG D 169 " -0.017 2.00e-02 2.50e+03 pdb=" N SER D 170 " -0.015 2.00e-02 2.50e+03 ... (remaining 7185 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 9955 2.80 - 3.33: 34919 3.33 - 3.85: 68717 3.85 - 4.38: 78818 4.38 - 4.90: 136249 Nonbonded interactions: 328658 Sorted by model distance: nonbonded pdb=" OG1 THR A 430 " pdb=" O PHE A 515 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.294 3.040 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.314 3.040 ... (remaining 328653 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 40.190 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.200 Set refine NCS operators: 0.010 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:10.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 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 : 0.005 0.057 41205 Z= 0.231 Angle : 0.821 16.115 56208 Z= 0.437 Chirality : 0.054 0.299 6372 Planarity : 0.006 0.060 7128 Dihedral : 13.235 88.597 16020 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.16 % Favored : 97.80 % Rotamer: Outliers : 0.12 % Allowed : 2.74 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.11), residues: 4854 helix: 0.49 (0.11), residues: 1751 sheet: 0.83 (0.18), residues: 747 loop : -0.79 (0.11), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 460 TYR 0.043 0.002 TYR B 495 PHE 0.027 0.002 PHE E 369 TRP 0.025 0.002 TRP B 886 HIS 0.006 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00463 (41079) covalent geometry : angle 0.79196 (55878) SS BOND : bond 0.00271 ( 48) SS BOND : angle 1.78713 ( 96) hydrogen bonds : bond 0.12525 ( 1867) hydrogen bonds : angle 6.74677 ( 5532) link_BETA1-4 : bond 0.00560 ( 18) link_BETA1-4 : angle 1.45311 ( 54) link_NAG-ASN : bond 0.00638 ( 60) link_NAG-ASN : angle 3.64927 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 369 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.8098 (m-80) cc_final: 0.7879 (m-80) REVERT: A 144 TYR cc_start: 0.4380 (m-10) cc_final: 0.3847 (m-80) REVERT: A 532 ASN cc_start: 0.8558 (m-40) cc_final: 0.7980 (t0) REVERT: B 200 TYR cc_start: 0.8748 (m-10) cc_final: 0.8522 (t80) REVERT: B 378 LYS cc_start: 0.9219 (tptt) cc_final: 0.8879 (tptp) REVERT: B 387 LEU cc_start: 0.9029 (mt) cc_final: 0.8638 (mt) REVERT: B 517 LEU cc_start: 0.9274 (tt) cc_final: 0.9050 (mm) REVERT: C 1029 MET cc_start: 0.8751 (tpp) cc_final: 0.8402 (tpp) REVERT: D 117 ASN cc_start: 0.6612 (t0) cc_final: 0.6079 (p0) REVERT: D 120 LEU cc_start: 0.1886 (mt) cc_final: 0.1607 (mt) REVERT: D 310 GLU cc_start: 0.4735 (mm-30) cc_final: 0.4104 (tm-30) REVERT: D 323 MET cc_start: 0.5366 (mmp) cc_final: 0.4096 (mmt) REVERT: D 332 MET cc_start: 0.2665 (ttp) cc_final: 0.1492 (ptm) REVERT: D 435 GLU cc_start: 0.1446 (mm-30) cc_final: 0.0600 (pt0) REVERT: D 577 LYS cc_start: 0.3685 (mtpt) cc_final: 0.2839 (pttm) REVERT: E 117 ASN cc_start: 0.7877 (t0) cc_final: 0.7666 (p0) REVERT: E 154 ASN cc_start: 0.6409 (m110) cc_final: 0.5824 (p0) REVERT: E 323 MET cc_start: 0.7588 (mmp) cc_final: 0.7359 (mmm) REVERT: E 332 MET cc_start: 0.5080 (ttp) cc_final: 0.4311 (ppp) REVERT: E 474 MET cc_start: 0.2080 (mmt) cc_final: 0.0519 (mmt) REVERT: F 234 LYS cc_start: 0.5297 (tttt) cc_final: 0.5020 (mttm) REVERT: F 291 ILE cc_start: 0.2581 (pt) cc_final: 0.2233 (mt) REVERT: F 383 MET cc_start: 0.2125 (mtp) cc_final: 0.0021 (tpt) REVERT: F 462 MET cc_start: 0.1806 (mtp) cc_final: 0.1606 (tpp) REVERT: F 480 MET cc_start: 0.3267 (mtp) cc_final: 0.2816 (mtt) REVERT: F 556 ASN cc_start: 0.6355 (m-40) cc_final: 0.6120 (p0) outliers start: 5 outliers final: 1 residues processed: 374 average time/residue: 0.8087 time to fit residues: 361.5710 Evaluate side-chains 184 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 213 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 0.8980 chunk 470 optimal weight: 0.0870 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 245 HIS B 519 HIS ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS E 374 HIS F 374 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.153359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.103992 restraints weight = 146367.143| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 5.22 r_work: 0.3205 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 41205 Z= 0.175 Angle : 0.603 12.126 56208 Z= 0.304 Chirality : 0.044 0.295 6372 Planarity : 0.005 0.072 7128 Dihedral : 6.027 95.077 6911 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.44 % Allowed : 6.56 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.11), residues: 4854 helix: 1.45 (0.12), residues: 1775 sheet: 0.84 (0.18), residues: 736 loop : -0.57 (0.12), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 214 TYR 0.022 0.001 TYR A1067 PHE 0.018 0.001 PHE F 314 TRP 0.019 0.001 TRP F 165 HIS 0.007 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00387 (41079) covalent geometry : angle 0.57958 (55878) SS BOND : bond 0.00216 ( 48) SS BOND : angle 1.25368 ( 96) hydrogen bonds : bond 0.04343 ( 1867) hydrogen bonds : angle 5.35024 ( 5532) link_BETA1-4 : bond 0.00109 ( 18) link_BETA1-4 : angle 1.09528 ( 54) link_NAG-ASN : bond 0.00525 ( 60) link_NAG-ASN : angle 2.84054 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 192 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.8546 (t80) cc_final: 0.8142 (t80) REVERT: A 532 ASN cc_start: 0.8555 (m-40) cc_final: 0.8249 (t0) REVERT: A 740 MET cc_start: 0.9293 (OUTLIER) cc_final: 0.9078 (tpp) REVERT: B 340 GLU cc_start: 0.8832 (mp0) cc_final: 0.8595 (pm20) REVERT: B 378 LYS cc_start: 0.9070 (tptt) cc_final: 0.8810 (tptp) REVERT: B 387 LEU cc_start: 0.8944 (mt) cc_final: 0.8665 (mt) REVERT: C 153 MET cc_start: 0.4976 (pp-130) cc_final: 0.4521 (ttp) REVERT: D 117 ASN cc_start: 0.6717 (t0) cc_final: 0.6488 (p0) REVERT: D 177 ARG cc_start: 0.1867 (tpt-90) cc_final: 0.1180 (ppt170) REVERT: D 310 GLU cc_start: 0.3992 (mm-30) cc_final: 0.3705 (tm-30) REVERT: D 332 MET cc_start: 0.2573 (ttp) cc_final: 0.1912 (ptm) REVERT: D 340 GLN cc_start: 0.3154 (tt0) cc_final: 0.2465 (tm130) REVERT: D 435 GLU cc_start: 0.1669 (mm-30) cc_final: 0.1031 (pt0) REVERT: D 510 TYR cc_start: -0.0210 (OUTLIER) cc_final: -0.0489 (m-80) REVERT: D 577 LYS cc_start: 0.2935 (mtpt) cc_final: 0.2464 (ttpt) REVERT: E 213 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7807 (p0) REVERT: E 332 MET cc_start: 0.5452 (ttp) cc_final: 0.4470 (ppp) REVERT: E 376 MET cc_start: 0.8243 (tpt) cc_final: 0.7260 (tpp) REVERT: E 383 MET cc_start: 0.8684 (tmm) cc_final: 0.7933 (mtm) REVERT: E 474 MET cc_start: 0.2236 (mmt) cc_final: 0.1431 (mmt) REVERT: F 291 ILE cc_start: 0.2486 (pt) cc_final: 0.2181 (mt) REVERT: F 383 MET cc_start: 0.2553 (mtp) cc_final: 0.1428 (tpt) REVERT: F 480 MET cc_start: 0.3430 (mtp) cc_final: 0.3152 (ptp) REVERT: F 557 MET cc_start: 0.3325 (OUTLIER) cc_final: 0.2913 (ptm) outliers start: 62 outliers final: 15 residues processed: 224 average time/residue: 0.7615 time to fit residues: 207.0505 Evaluate side-chains 179 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 557 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 320 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 254 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 265 optimal weight: 2.9990 chunk 445 optimal weight: 20.0000 chunk 434 optimal weight: 40.0000 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN B 907 ASN C 245 HIS C1010 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN F 121 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.153664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.104240 restraints weight = 154397.385| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 5.54 r_work: 0.3168 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 41205 Z= 0.164 Angle : 0.560 11.591 56208 Z= 0.281 Chirality : 0.043 0.274 6372 Planarity : 0.004 0.062 7128 Dihedral : 5.418 62.201 6911 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.21 % Allowed : 7.86 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.12), residues: 4854 helix: 1.80 (0.12), residues: 1787 sheet: 0.75 (0.18), residues: 728 loop : -0.43 (0.12), residues: 2339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 214 TYR 0.023 0.001 TYR A1067 PHE 0.027 0.001 PHE E 327 TRP 0.021 0.001 TRP D 566 HIS 0.009 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00361 (41079) covalent geometry : angle 0.53927 (55878) SS BOND : bond 0.00211 ( 48) SS BOND : angle 1.16627 ( 96) hydrogen bonds : bond 0.03974 ( 1867) hydrogen bonds : angle 5.05938 ( 5532) link_BETA1-4 : bond 0.00207 ( 18) link_BETA1-4 : angle 1.00209 ( 54) link_NAG-ASN : bond 0.00497 ( 60) link_NAG-ASN : angle 2.60535 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 181 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ILE cc_start: 0.9203 (mp) cc_final: 0.8956 (tp) REVERT: A 532 ASN cc_start: 0.8944 (m-40) cc_final: 0.8301 (t0) REVERT: A 565 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.6904 (m-10) REVERT: A 740 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.8470 (tmm) REVERT: B 378 LYS cc_start: 0.9043 (tptt) cc_final: 0.8681 (tptp) REVERT: B 387 LEU cc_start: 0.9022 (mt) cc_final: 0.8731 (mt) REVERT: B 517 LEU cc_start: 0.9163 (mm) cc_final: 0.8887 (tm) REVERT: C 153 MET cc_start: 0.6213 (pp-130) cc_final: 0.5773 (ttp) REVERT: C 762 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8326 (mm-40) REVERT: D 82 MET cc_start: 0.5471 (tpp) cc_final: 0.5235 (tpp) REVERT: D 117 ASN cc_start: 0.6606 (t0) cc_final: 0.6315 (p0) REVERT: D 177 ARG cc_start: 0.1523 (tpt-90) cc_final: 0.0955 (ppt170) REVERT: D 310 GLU cc_start: 0.4180 (mm-30) cc_final: 0.3767 (tm-30) REVERT: D 332 MET cc_start: 0.2615 (ttp) cc_final: 0.1794 (ptm) REVERT: D 340 GLN cc_start: 0.3067 (tt0) cc_final: 0.2379 (tm130) REVERT: D 435 GLU cc_start: 0.1455 (mm-30) cc_final: 0.0696 (pt0) REVERT: D 510 TYR cc_start: 0.0007 (OUTLIER) cc_final: -0.0411 (m-80) REVERT: D 555 PHE cc_start: 0.2908 (t80) cc_final: 0.2507 (t80) REVERT: D 577 LYS cc_start: 0.3145 (mtpt) cc_final: 0.2568 (tttt) REVERT: E 323 MET cc_start: 0.7713 (mmm) cc_final: 0.6375 (tpt) REVERT: E 332 MET cc_start: 0.5539 (ttp) cc_final: 0.4491 (ppp) REVERT: E 383 MET cc_start: 0.8705 (tmm) cc_final: 0.7978 (mtm) REVERT: E 408 MET cc_start: 0.8787 (mmp) cc_final: 0.8576 (mmm) REVERT: E 474 MET cc_start: 0.2445 (mmt) cc_final: 0.1773 (mmp) REVERT: F 249 MET cc_start: 0.5276 (mmt) cc_final: 0.3509 (tmt) REVERT: F 291 ILE cc_start: 0.2420 (pt) cc_final: 0.2085 (mt) REVERT: F 297 MET cc_start: -0.3742 (ptp) cc_final: -0.4418 (mpp) REVERT: F 383 MET cc_start: 0.2425 (mtp) cc_final: 0.1241 (tpt) REVERT: F 480 MET cc_start: 0.3162 (mtp) cc_final: 0.2940 (ptm) outliers start: 52 outliers final: 16 residues processed: 208 average time/residue: 0.7157 time to fit residues: 181.9766 Evaluate side-chains 179 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 574 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 30.0000 chunk 157 optimal weight: 10.0000 chunk 403 optimal weight: 2.9990 chunk 419 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 209 optimal weight: 8.9990 chunk 148 optimal weight: 20.0000 chunk 299 optimal weight: 0.9980 chunk 245 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN C1010 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS D 535 HIS E 524 GLN F 121 ASN F 535 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.151494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.101519 restraints weight = 143238.214| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 5.09 r_work: 0.3160 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 41205 Z= 0.215 Angle : 0.576 11.318 56208 Z= 0.287 Chirality : 0.044 0.274 6372 Planarity : 0.004 0.060 7128 Dihedral : 5.390 89.330 6911 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.60 % Allowed : 8.37 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.12), residues: 4854 helix: 1.88 (0.12), residues: 1810 sheet: 0.62 (0.19), residues: 669 loop : -0.40 (0.12), residues: 2375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 169 TYR 0.022 0.001 TYR A1067 PHE 0.021 0.001 PHE C 823 TRP 0.019 0.001 TRP D 566 HIS 0.020 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00481 (41079) covalent geometry : angle 0.55654 (55878) SS BOND : bond 0.00219 ( 48) SS BOND : angle 1.09608 ( 96) hydrogen bonds : bond 0.03989 ( 1867) hydrogen bonds : angle 5.04541 ( 5532) link_BETA1-4 : bond 0.00173 ( 18) link_BETA1-4 : angle 1.11490 ( 54) link_NAG-ASN : bond 0.00521 ( 60) link_NAG-ASN : angle 2.53721 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 163 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 ASN cc_start: 0.8920 (m-40) cc_final: 0.8389 (t0) REVERT: B 378 LYS cc_start: 0.9108 (tptt) cc_final: 0.8578 (tptp) REVERT: B 387 LEU cc_start: 0.8925 (mt) cc_final: 0.8618 (mt) REVERT: C 153 MET cc_start: 0.4480 (OUTLIER) cc_final: 0.3782 (mtm) REVERT: D 117 ASN cc_start: 0.6677 (t0) cc_final: 0.6448 (p0) REVERT: D 177 ARG cc_start: 0.1887 (tpt-90) cc_final: 0.1164 (ppt170) REVERT: D 309 LYS cc_start: 0.4707 (OUTLIER) cc_final: 0.4384 (pttp) REVERT: D 310 GLU cc_start: 0.4007 (mm-30) cc_final: 0.3652 (tm-30) REVERT: D 332 MET cc_start: 0.2437 (ttp) cc_final: 0.1909 (ptm) REVERT: D 435 GLU cc_start: 0.1492 (mm-30) cc_final: 0.1235 (pp20) REVERT: D 455 MET cc_start: 0.0505 (OUTLIER) cc_final: 0.0264 (tpt) REVERT: D 488 VAL cc_start: 0.3974 (p) cc_final: 0.3666 (m) REVERT: D 510 TYR cc_start: -0.0043 (OUTLIER) cc_final: -0.0381 (m-80) REVERT: D 555 PHE cc_start: 0.2996 (t80) cc_final: 0.2559 (t80) REVERT: D 577 LYS cc_start: 0.3279 (mtpt) cc_final: 0.2769 (ttpt) REVERT: E 267 LEU cc_start: 0.6004 (OUTLIER) cc_final: 0.4518 (tm) REVERT: E 323 MET cc_start: 0.7581 (mmm) cc_final: 0.6601 (tpt) REVERT: E 332 MET cc_start: 0.5364 (ttp) cc_final: 0.4841 (ppp) REVERT: E 474 MET cc_start: 0.2502 (mmt) cc_final: 0.1635 (mmt) REVERT: E 480 MET cc_start: 0.5768 (OUTLIER) cc_final: 0.5472 (mpp) REVERT: E 579 MET cc_start: 0.3640 (OUTLIER) cc_final: 0.1876 (mtp) REVERT: F 208 GLU cc_start: 0.0000 (OUTLIER) cc_final: -0.0294 (tm-30) REVERT: F 249 MET cc_start: 0.5307 (mmt) cc_final: 0.3760 (tmt) REVERT: F 291 ILE cc_start: 0.2990 (pt) cc_final: 0.2643 (mt) REVERT: F 383 MET cc_start: 0.2731 (mtp) cc_final: 0.1677 (tpt) outliers start: 69 outliers final: 24 residues processed: 207 average time/residue: 0.7537 time to fit residues: 195.2713 Evaluate side-chains 179 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 309 LYS Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 497 TYR Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 480 MET Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 208 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 560 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 273 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 482 optimal weight: 7.9990 chunk 116 optimal weight: 30.0000 chunk 123 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 362 optimal weight: 20.0000 chunk 184 optimal weight: 0.7980 chunk 171 optimal weight: 5.9990 chunk 242 optimal weight: 20.0000 chunk 267 optimal weight: 6.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 824 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 493 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN F 121 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.151036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.107992 restraints weight = 152315.161| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 7.54 r_work: 0.3051 rms_B_bonded: 5.70 restraints_weight: 2.0000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 41205 Z= 0.330 Angle : 0.657 11.291 56208 Z= 0.327 Chirality : 0.046 0.286 6372 Planarity : 0.004 0.060 7128 Dihedral : 5.685 85.747 6911 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.53 % Allowed : 9.70 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.12), residues: 4854 helix: 1.69 (0.12), residues: 1820 sheet: 0.35 (0.19), residues: 668 loop : -0.52 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 21 TYR 0.022 0.002 TYR A1067 PHE 0.024 0.002 PHE B 79 TRP 0.019 0.002 TRP D 566 HIS 0.008 0.002 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00742 (41079) covalent geometry : angle 0.63831 (55878) SS BOND : bond 0.00470 ( 48) SS BOND : angle 1.09503 ( 96) hydrogen bonds : bond 0.04327 ( 1867) hydrogen bonds : angle 5.24393 ( 5532) link_BETA1-4 : bond 0.00274 ( 18) link_BETA1-4 : angle 1.27440 ( 54) link_NAG-ASN : bond 0.00675 ( 60) link_NAG-ASN : angle 2.66012 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 161 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 ASN cc_start: 0.9004 (m-40) cc_final: 0.8546 (t0) REVERT: B 200 TYR cc_start: 0.8776 (OUTLIER) cc_final: 0.8495 (t80) REVERT: B 387 LEU cc_start: 0.8987 (mt) cc_final: 0.8634 (mt) REVERT: B 517 LEU cc_start: 0.8999 (mm) cc_final: 0.8638 (tm) REVERT: B 1092 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8702 (pp20) REVERT: C 153 MET cc_start: 0.4901 (OUTLIER) cc_final: 0.4473 (ttm) REVERT: D 278 LEU cc_start: 0.2407 (OUTLIER) cc_final: 0.1539 (tp) REVERT: D 310 GLU cc_start: 0.3745 (mm-30) cc_final: 0.3472 (tm-30) REVERT: D 332 MET cc_start: 0.2081 (ttp) cc_final: 0.1580 (pmm) REVERT: D 435 GLU cc_start: 0.1498 (mm-30) cc_final: 0.1282 (pp20) REVERT: D 488 VAL cc_start: 0.3506 (p) cc_final: 0.3199 (m) REVERT: D 510 TYR cc_start: -0.0232 (OUTLIER) cc_final: -0.0478 (m-80) REVERT: D 555 PHE cc_start: 0.3287 (t80) cc_final: 0.2903 (t80) REVERT: D 577 LYS cc_start: 0.3142 (mtpt) cc_final: 0.2757 (ptmm) REVERT: E 267 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.4571 (tm) REVERT: E 323 MET cc_start: 0.7726 (mmm) cc_final: 0.6582 (tpt) REVERT: E 383 MET cc_start: 0.8791 (tmm) cc_final: 0.7970 (mtm) REVERT: E 408 MET cc_start: 0.8722 (mmp) cc_final: 0.8476 (mmm) REVERT: E 455 MET cc_start: 0.2817 (tmt) cc_final: 0.2173 (pp-130) REVERT: E 474 MET cc_start: 0.2815 (mmt) cc_final: 0.1872 (tpp) REVERT: E 579 MET cc_start: 0.3549 (OUTLIER) cc_final: 0.1614 (mtt) REVERT: F 208 GLU cc_start: -0.0134 (OUTLIER) cc_final: -0.0366 (tm-30) REVERT: F 249 MET cc_start: 0.5586 (mmt) cc_final: 0.4298 (tmt) REVERT: F 291 ILE cc_start: 0.2884 (pt) cc_final: 0.2453 (mt) REVERT: F 383 MET cc_start: 0.2920 (mtp) cc_final: 0.2076 (tpt) REVERT: F 453 THR cc_start: 0.0653 (m) cc_final: 0.0361 (m) REVERT: F 460 ARG cc_start: 0.0984 (mtm180) cc_final: -0.0254 (mmt180) outliers start: 66 outliers final: 22 residues processed: 199 average time/residue: 0.6888 time to fit residues: 168.0603 Evaluate side-chains 174 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain F residue 208 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 560 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 346 optimal weight: 1.9990 chunk 243 optimal weight: 20.0000 chunk 226 optimal weight: 0.0470 chunk 283 optimal weight: 1.9990 chunk 333 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 220 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 175 optimal weight: 1.9990 chunk 271 optimal weight: 0.6980 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 GLN C 115 GLN C 907 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 524 GLN F 121 ASN F 524 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.152769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.110405 restraints weight = 153467.274| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 6.68 r_work: 0.3149 rms_B_bonded: 5.19 restraints_weight: 2.0000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 41205 Z= 0.108 Angle : 0.533 11.217 56208 Z= 0.265 Chirality : 0.042 0.295 6372 Planarity : 0.004 0.060 7128 Dihedral : 5.266 93.512 6911 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.28 % Allowed : 10.28 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.12), residues: 4854 helix: 1.98 (0.12), residues: 1794 sheet: 0.50 (0.19), residues: 665 loop : -0.40 (0.12), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 192 TYR 0.021 0.001 TYR A1067 PHE 0.018 0.001 PHE C 823 TRP 0.024 0.001 TRP D 566 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00231 (41079) covalent geometry : angle 0.51537 (55878) SS BOND : bond 0.00155 ( 48) SS BOND : angle 0.88318 ( 96) hydrogen bonds : bond 0.03609 ( 1867) hydrogen bonds : angle 4.94604 ( 5532) link_BETA1-4 : bond 0.00322 ( 18) link_BETA1-4 : angle 0.87490 ( 54) link_NAG-ASN : bond 0.00405 ( 60) link_NAG-ASN : angle 2.34764 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 159 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 ASN cc_start: 0.8874 (m-40) cc_final: 0.8406 (t0) REVERT: A 565 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.7400 (m-10) REVERT: A 1010 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8466 (pp30) REVERT: B 200 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.8343 (t80) REVERT: B 378 LYS cc_start: 0.9212 (tptt) cc_final: 0.8912 (tptp) REVERT: B 387 LEU cc_start: 0.8995 (mt) cc_final: 0.8607 (mt) REVERT: B 517 LEU cc_start: 0.8957 (mm) cc_final: 0.8554 (tm) REVERT: C 153 MET cc_start: 0.4261 (OUTLIER) cc_final: 0.3469 (mtm) REVERT: D 310 GLU cc_start: 0.3866 (mm-30) cc_final: 0.3527 (tm-30) REVERT: D 332 MET cc_start: 0.2170 (ttp) cc_final: 0.1554 (pmm) REVERT: D 358 ILE cc_start: -0.1548 (OUTLIER) cc_final: -0.2632 (mm) REVERT: D 435 GLU cc_start: 0.1580 (mm-30) cc_final: 0.1286 (pp20) REVERT: D 488 VAL cc_start: 0.3848 (p) cc_final: 0.3504 (m) REVERT: D 510 TYR cc_start: -0.0072 (OUTLIER) cc_final: -0.0363 (m-80) REVERT: D 555 PHE cc_start: 0.3265 (t80) cc_final: 0.2883 (t80) REVERT: E 267 LEU cc_start: 0.5967 (OUTLIER) cc_final: 0.4840 (tt) REVERT: E 323 MET cc_start: 0.7612 (mmm) cc_final: 0.6410 (tpt) REVERT: E 332 MET cc_start: 0.5628 (ttp) cc_final: 0.4764 (ppp) REVERT: E 383 MET cc_start: 0.8798 (tmm) cc_final: 0.8012 (mtm) REVERT: E 474 MET cc_start: 0.2838 (mmt) cc_final: 0.1929 (tpp) REVERT: E 579 MET cc_start: 0.3530 (OUTLIER) cc_final: 0.1731 (mtp) REVERT: F 208 GLU cc_start: 0.0120 (OUTLIER) cc_final: -0.0173 (tm-30) REVERT: F 249 MET cc_start: 0.5560 (mmt) cc_final: 0.4287 (tmt) REVERT: F 291 ILE cc_start: 0.2846 (pt) cc_final: 0.2361 (mt) REVERT: F 383 MET cc_start: 0.2846 (mtp) cc_final: 0.1875 (tpt) REVERT: F 460 ARG cc_start: 0.0880 (mtm180) cc_final: -0.0403 (mmt180) outliers start: 55 outliers final: 12 residues processed: 192 average time/residue: 0.7057 time to fit residues: 166.8779 Evaluate side-chains 170 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain F residue 208 GLU Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 484 ILE Chi-restraints excluded: chain F residue 574 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 222 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 464 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 366 optimal weight: 5.9990 chunk 458 optimal weight: 3.9990 chunk 279 optimal weight: 0.3980 chunk 115 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 250 optimal weight: 20.0000 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1010 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN F 81 GLN F 121 ASN ** F 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 524 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.151426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.107067 restraints weight = 152268.969| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 8.24 r_work: 0.3069 rms_B_bonded: 6.19 restraints_weight: 2.0000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 41205 Z= 0.223 Angle : 0.588 12.117 56208 Z= 0.292 Chirality : 0.044 0.306 6372 Planarity : 0.004 0.066 7128 Dihedral : 5.150 56.415 6909 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.11 % Allowed : 10.90 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.12), residues: 4854 helix: 1.95 (0.12), residues: 1802 sheet: 0.32 (0.19), residues: 664 loop : -0.42 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 177 TYR 0.021 0.001 TYR A1067 PHE 0.036 0.002 PHE A 135 TRP 0.015 0.001 TRP D 566 HIS 0.006 0.001 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00497 (41079) covalent geometry : angle 0.57134 (55878) SS BOND : bond 0.00194 ( 48) SS BOND : angle 0.94402 ( 96) hydrogen bonds : bond 0.03936 ( 1867) hydrogen bonds : angle 5.04170 ( 5532) link_BETA1-4 : bond 0.00166 ( 18) link_BETA1-4 : angle 1.17572 ( 54) link_NAG-ASN : bond 0.00528 ( 60) link_NAG-ASN : angle 2.43078 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 153 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 ASN cc_start: 0.9028 (m-40) cc_final: 0.8532 (t0) REVERT: A 565 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7374 (m-10) REVERT: B 200 TYR cc_start: 0.8852 (OUTLIER) cc_final: 0.8521 (t80) REVERT: B 378 LYS cc_start: 0.9204 (tptt) cc_final: 0.8683 (tptp) REVERT: B 387 LEU cc_start: 0.8990 (mt) cc_final: 0.8553 (mt) REVERT: B 517 LEU cc_start: 0.9194 (mm) cc_final: 0.8833 (tm) REVERT: C 100 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.7068 (mp) REVERT: C 153 MET cc_start: 0.4732 (OUTLIER) cc_final: 0.4148 (ttm) REVERT: D 87 GLU cc_start: 0.2095 (pm20) cc_final: 0.1882 (mm-30) REVERT: D 310 GLU cc_start: 0.3514 (mm-30) cc_final: 0.3253 (tm-30) REVERT: D 332 MET cc_start: 0.2143 (ttp) cc_final: 0.1604 (pmm) REVERT: D 359 LEU cc_start: -0.1641 (OUTLIER) cc_final: -0.1992 (tp) REVERT: D 510 TYR cc_start: -0.0237 (OUTLIER) cc_final: -0.0514 (m-80) REVERT: D 555 PHE cc_start: 0.3268 (t80) cc_final: 0.2898 (t80) REVERT: E 267 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.4463 (tm) REVERT: E 323 MET cc_start: 0.7594 (mmm) cc_final: 0.6482 (tpt) REVERT: E 332 MET cc_start: 0.5665 (ttp) cc_final: 0.4756 (ppp) REVERT: E 376 MET cc_start: 0.7905 (tpt) cc_final: 0.7038 (tpp) REVERT: E 383 MET cc_start: 0.8870 (tmm) cc_final: 0.8637 (ppp) REVERT: E 455 MET cc_start: 0.2957 (tmt) cc_final: 0.2274 (pp-130) REVERT: E 474 MET cc_start: 0.2908 (mmt) cc_final: 0.2062 (tpp) REVERT: E 579 MET cc_start: 0.3878 (OUTLIER) cc_final: 0.2271 (mtp) REVERT: F 208 GLU cc_start: 0.0007 (OUTLIER) cc_final: -0.0252 (tt0) REVERT: F 249 MET cc_start: 0.5660 (mmt) cc_final: 0.4454 (tmt) REVERT: F 291 ILE cc_start: 0.2825 (pt) cc_final: 0.2401 (mt) REVERT: F 332 MET cc_start: 0.2038 (ppp) cc_final: 0.0142 (mpm) REVERT: F 383 MET cc_start: 0.2711 (mtp) cc_final: 0.1844 (tpt) REVERT: F 453 THR cc_start: 0.0656 (m) cc_final: 0.0408 (m) REVERT: F 460 ARG cc_start: 0.1037 (mtm180) cc_final: -0.0313 (mmt180) outliers start: 48 outliers final: 13 residues processed: 185 average time/residue: 0.7149 time to fit residues: 162.8386 Evaluate side-chains 164 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain F residue 208 GLU Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 560 LEU Chi-restraints excluded: chain F residue 574 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 22 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 184 optimal weight: 0.8980 chunk 330 optimal weight: 20.0000 chunk 110 optimal weight: 8.9990 chunk 483 optimal weight: 5.9990 chunk 464 optimal weight: 6.9990 chunk 231 optimal weight: 2.9990 chunk 246 optimal weight: 20.0000 chunk 411 optimal weight: 9.9990 chunk 247 optimal weight: 8.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A 957 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS B 245 HIS C1010 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 HIS E 442 GLN F 81 GLN F 121 ASN F 250 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.149849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.100137 restraints weight = 151928.881| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 4.73 r_work: 0.3081 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 41205 Z= 0.341 Angle : 0.704 13.849 56208 Z= 0.348 Chirality : 0.047 0.454 6372 Planarity : 0.004 0.064 7128 Dihedral : 5.828 58.889 6909 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.07 % Allowed : 11.53 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.12), residues: 4854 helix: 1.73 (0.12), residues: 1791 sheet: 0.06 (0.19), residues: 657 loop : -0.57 (0.12), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 177 TYR 0.022 0.002 TYR C 265 PHE 0.025 0.002 PHE C 823 TRP 0.029 0.002 TRP E 203 HIS 0.007 0.002 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00766 (41079) covalent geometry : angle 0.68036 (55878) SS BOND : bond 0.00307 ( 48) SS BOND : angle 1.12400 ( 96) hydrogen bonds : bond 0.04462 ( 1867) hydrogen bonds : angle 5.34004 ( 5532) link_BETA1-4 : bond 0.00292 ( 18) link_BETA1-4 : angle 1.34995 ( 54) link_NAG-ASN : bond 0.00751 ( 60) link_NAG-ASN : angle 3.10893 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 162 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 ASN cc_start: 0.9037 (m-40) cc_final: 0.8669 (t0) REVERT: B 200 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.8505 (t80) REVERT: B 387 LEU cc_start: 0.9031 (mt) cc_final: 0.8664 (mt) REVERT: B 517 LEU cc_start: 0.9163 (mm) cc_final: 0.8856 (tm) REVERT: C 95 THR cc_start: 0.8059 (p) cc_final: 0.7841 (p) REVERT: C 100 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7369 (mp) REVERT: C 153 MET cc_start: 0.4698 (OUTLIER) cc_final: 0.4126 (ttm) REVERT: C 546 LEU cc_start: 0.8836 (tt) cc_final: 0.8595 (pp) REVERT: D 87 GLU cc_start: 0.1912 (pm20) cc_final: 0.1509 (mm-30) REVERT: D 117 ASN cc_start: 0.6167 (t0) cc_final: 0.5958 (p0) REVERT: D 310 GLU cc_start: 0.3960 (mm-30) cc_final: 0.3571 (tm-30) REVERT: D 332 MET cc_start: 0.1985 (ttp) cc_final: 0.1403 (pmm) REVERT: D 359 LEU cc_start: -0.1212 (OUTLIER) cc_final: -0.1577 (tp) REVERT: D 510 TYR cc_start: -0.0130 (OUTLIER) cc_final: -0.0469 (m-80) REVERT: D 555 PHE cc_start: 0.3207 (t80) cc_final: 0.2820 (t80) REVERT: E 383 MET cc_start: 0.8852 (tmm) cc_final: 0.8584 (ppp) REVERT: E 408 MET cc_start: 0.8473 (mmp) cc_final: 0.8014 (tpp) REVERT: E 455 MET cc_start: 0.3040 (tmt) cc_final: 0.2389 (pp-130) REVERT: E 474 MET cc_start: 0.2788 (mmt) cc_final: 0.2023 (tpp) REVERT: E 510 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.8088 (t80) REVERT: E 579 MET cc_start: 0.4344 (OUTLIER) cc_final: 0.2929 (mtp) REVERT: F 208 GLU cc_start: 0.0157 (OUTLIER) cc_final: -0.0176 (tt0) REVERT: F 249 MET cc_start: 0.5661 (mmt) cc_final: 0.4034 (tmt) REVERT: F 291 ILE cc_start: 0.3231 (pt) cc_final: 0.2832 (mt) REVERT: F 383 MET cc_start: 0.2333 (mtp) cc_final: 0.1234 (tpt) outliers start: 46 outliers final: 17 residues processed: 191 average time/residue: 0.7068 time to fit residues: 165.5566 Evaluate side-chains 165 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 510 TYR Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain F residue 208 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 560 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 310 optimal weight: 0.8980 chunk 362 optimal weight: 30.0000 chunk 318 optimal weight: 40.0000 chunk 277 optimal weight: 0.5980 chunk 333 optimal weight: 20.0000 chunk 304 optimal weight: 0.9980 chunk 265 optimal weight: 0.7980 chunk 287 optimal weight: 0.6980 chunk 270 optimal weight: 0.6980 chunk 257 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS D 265 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 ASN E 417 HIS ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 HIS F 380 GLN ** F 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.151799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.109110 restraints weight = 152967.572| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 8.16 r_work: 0.3109 rms_B_bonded: 5.95 restraints_weight: 2.0000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 41205 Z= 0.117 Angle : 0.573 12.278 56208 Z= 0.283 Chirality : 0.043 0.374 6372 Planarity : 0.004 0.063 7128 Dihedral : 5.287 57.555 6909 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.74 % Allowed : 12.25 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.12), residues: 4854 helix: 1.97 (0.12), residues: 1786 sheet: 0.17 (0.19), residues: 647 loop : -0.41 (0.12), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 34 TYR 0.020 0.001 TYR A1067 PHE 0.024 0.001 PHE A 135 TRP 0.023 0.001 TRP E 203 HIS 0.004 0.001 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00255 (41079) covalent geometry : angle 0.55323 (55878) SS BOND : bond 0.00143 ( 48) SS BOND : angle 0.90400 ( 96) hydrogen bonds : bond 0.03691 ( 1867) hydrogen bonds : angle 5.04781 ( 5532) link_BETA1-4 : bond 0.00255 ( 18) link_BETA1-4 : angle 0.90067 ( 54) link_NAG-ASN : bond 0.00435 ( 60) link_NAG-ASN : angle 2.64196 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 ASN cc_start: 0.9031 (m-40) cc_final: 0.8609 (t0) REVERT: A 565 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.7649 (m-10) REVERT: B 200 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.8432 (t80) REVERT: B 387 LEU cc_start: 0.9026 (mt) cc_final: 0.8712 (mt) REVERT: B 517 LEU cc_start: 0.9128 (mm) cc_final: 0.8787 (tm) REVERT: C 100 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.7246 (mp) REVERT: C 153 MET cc_start: 0.4122 (OUTLIER) cc_final: 0.3697 (ttp) REVERT: D 87 GLU cc_start: 0.2198 (pm20) cc_final: 0.1870 (mm-30) REVERT: D 117 ASN cc_start: 0.6618 (t0) cc_final: 0.6404 (p0) REVERT: D 310 GLU cc_start: 0.3719 (mm-30) cc_final: 0.3400 (tm-30) REVERT: D 332 MET cc_start: 0.1989 (ttp) cc_final: 0.1425 (pmm) REVERT: D 358 ILE cc_start: -0.1572 (OUTLIER) cc_final: -0.2943 (mm) REVERT: D 510 TYR cc_start: -0.0182 (OUTLIER) cc_final: -0.0444 (m-80) REVERT: D 555 PHE cc_start: 0.3320 (t80) cc_final: 0.2970 (t80) REVERT: E 332 MET cc_start: 0.5990 (ttp) cc_final: 0.4560 (tmt) REVERT: E 376 MET cc_start: 0.8035 (tpt) cc_final: 0.7175 (tpp) REVERT: E 383 MET cc_start: 0.8853 (tmm) cc_final: 0.8570 (ppp) REVERT: E 408 MET cc_start: 0.8414 (mmp) cc_final: 0.7976 (mmm) REVERT: E 474 MET cc_start: 0.2799 (mmt) cc_final: 0.2062 (tpp) REVERT: E 510 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7943 (t80) REVERT: E 579 MET cc_start: 0.4045 (OUTLIER) cc_final: 0.2400 (mtp) REVERT: E 600 LYS cc_start: 0.4166 (mmmt) cc_final: 0.2781 (mttt) REVERT: F 249 MET cc_start: 0.5633 (mmt) cc_final: 0.4354 (tmt) REVERT: F 291 ILE cc_start: 0.3133 (pt) cc_final: 0.2641 (mt) REVERT: F 332 MET cc_start: 0.1750 (ppp) cc_final: -0.0427 (mpm) REVERT: F 383 MET cc_start: 0.2570 (mtp) cc_final: 0.1472 (tpt) REVERT: F 460 ARG cc_start: 0.1160 (mtm180) cc_final: -0.0222 (mmt180) outliers start: 32 outliers final: 13 residues processed: 173 average time/residue: 0.6947 time to fit residues: 147.9021 Evaluate side-chains 165 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 510 TYR Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 560 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 212 optimal weight: 1.9990 chunk 463 optimal weight: 40.0000 chunk 452 optimal weight: 50.0000 chunk 368 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 430 optimal weight: 9.9990 chunk 279 optimal weight: 0.3980 chunk 210 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 374 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS D 96 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 ASN ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 HIS F 380 GLN ** F 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.151691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.107752 restraints weight = 151962.064| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 7.62 r_work: 0.3157 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 41205 Z= 0.130 Angle : 0.571 15.708 56208 Z= 0.279 Chirality : 0.043 0.312 6372 Planarity : 0.004 0.062 7128 Dihedral : 5.035 57.408 6909 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.56 % Allowed : 12.71 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.12), residues: 4854 helix: 2.05 (0.12), residues: 1790 sheet: 0.27 (0.19), residues: 619 loop : -0.38 (0.12), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 177 TYR 0.020 0.001 TYR A1067 PHE 0.022 0.001 PHE D 603 TRP 0.023 0.001 TRP E 203 HIS 0.005 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00288 (41079) covalent geometry : angle 0.55157 (55878) SS BOND : bond 0.00136 ( 48) SS BOND : angle 0.85802 ( 96) hydrogen bonds : bond 0.03615 ( 1867) hydrogen bonds : angle 4.96919 ( 5532) link_BETA1-4 : bond 0.00188 ( 18) link_BETA1-4 : angle 0.99323 ( 54) link_NAG-ASN : bond 0.00441 ( 60) link_NAG-ASN : angle 2.58206 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 ASN cc_start: 0.9076 (m-40) cc_final: 0.8624 (t0) REVERT: A 565 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7702 (m-10) REVERT: B 200 TYR cc_start: 0.8877 (OUTLIER) cc_final: 0.8515 (t80) REVERT: B 387 LEU cc_start: 0.9045 (mt) cc_final: 0.8740 (mt) REVERT: B 517 LEU cc_start: 0.9245 (mm) cc_final: 0.9020 (tm) REVERT: C 100 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.7137 (mp) REVERT: C 153 MET cc_start: 0.5464 (OUTLIER) cc_final: 0.4720 (ttp) REVERT: D 87 GLU cc_start: 0.1720 (pm20) cc_final: 0.1130 (mm-30) REVERT: D 117 ASN cc_start: 0.6555 (t0) cc_final: 0.6202 (p0) REVERT: D 310 GLU cc_start: 0.4484 (mm-30) cc_final: 0.3824 (tm-30) REVERT: D 332 MET cc_start: 0.2320 (ttp) cc_final: 0.1381 (pmm) REVERT: D 358 ILE cc_start: -0.1434 (OUTLIER) cc_final: -0.2717 (mm) REVERT: D 510 TYR cc_start: 0.0002 (OUTLIER) cc_final: -0.0744 (m-80) REVERT: D 555 PHE cc_start: 0.2865 (t80) cc_final: 0.2476 (t80) REVERT: E 332 MET cc_start: 0.5991 (ttp) cc_final: 0.4601 (tmt) REVERT: E 376 MET cc_start: 0.8090 (tpt) cc_final: 0.7141 (tpp) REVERT: E 383 MET cc_start: 0.8896 (tmm) cc_final: 0.8597 (ppp) REVERT: E 408 MET cc_start: 0.8425 (mmp) cc_final: 0.8108 (mmm) REVERT: E 474 MET cc_start: 0.2840 (mmt) cc_final: 0.2078 (tpp) REVERT: E 510 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.8029 (t80) REVERT: E 579 MET cc_start: 0.3522 (OUTLIER) cc_final: 0.1798 (mtt) REVERT: E 600 LYS cc_start: 0.4400 (mmmt) cc_final: 0.2930 (mttt) REVERT: F 190 MET cc_start: -0.0553 (ppp) cc_final: -0.1131 (pmm) REVERT: F 249 MET cc_start: 0.5323 (mmt) cc_final: 0.3244 (tmt) REVERT: F 291 ILE cc_start: 0.2865 (pt) cc_final: 0.2582 (mt) REVERT: F 332 MET cc_start: 0.1222 (ppp) cc_final: -0.1353 (mpm) REVERT: F 383 MET cc_start: 0.2048 (mtp) cc_final: 0.0515 (tpt) REVERT: F 455 MET cc_start: 0.2168 (tmm) cc_final: 0.1900 (tmm) REVERT: F 460 ARG cc_start: 0.0683 (mtm180) cc_final: -0.0651 (mmt180) REVERT: F 480 MET cc_start: 0.2518 (tpp) cc_final: 0.2091 (mmm) outliers start: 24 outliers final: 10 residues processed: 161 average time/residue: 0.7108 time to fit residues: 141.0609 Evaluate side-chains 159 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain E residue 510 TYR Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 560 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 145 optimal weight: 4.9990 chunk 427 optimal weight: 7.9990 chunk 470 optimal weight: 0.5980 chunk 430 optimal weight: 30.0000 chunk 60 optimal weight: 2.9990 chunk 158 optimal weight: 0.4980 chunk 37 optimal weight: 30.0000 chunk 313 optimal weight: 30.0000 chunk 431 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 chunk 458 optimal weight: 9.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 HIS ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 HIS ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN F 195 HIS ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.150352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.107474 restraints weight = 152993.196| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 7.09 r_work: 0.3136 rms_B_bonded: 5.42 restraints_weight: 2.0000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 41205 Z= 0.257 Angle : 0.633 12.767 56208 Z= 0.311 Chirality : 0.045 0.327 6372 Planarity : 0.004 0.060 7128 Dihedral : 5.258 57.268 6909 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.67 % Allowed : 12.73 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.12), residues: 4854 helix: 1.94 (0.12), residues: 1790 sheet: 0.12 (0.19), residues: 657 loop : -0.48 (0.12), residues: 2407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 177 TYR 0.022 0.001 TYR A1067 PHE 0.026 0.002 PHE C 823 TRP 0.024 0.002 TRP E 203 HIS 0.005 0.001 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00580 (41079) covalent geometry : angle 0.61350 (55878) SS BOND : bond 0.00218 ( 48) SS BOND : angle 0.96582 ( 96) hydrogen bonds : bond 0.04037 ( 1867) hydrogen bonds : angle 5.15619 ( 5532) link_BETA1-4 : bond 0.00160 ( 18) link_BETA1-4 : angle 1.20739 ( 54) link_NAG-ASN : bond 0.00584 ( 60) link_NAG-ASN : angle 2.71667 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26254.16 seconds wall clock time: 444 minutes 2.57 seconds (26642.57 seconds total)