Starting phenix.real_space_refine on Sun Feb 8 03:54:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sy5_25517/02_2026/7sy5_25517.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sy5_25517/02_2026/7sy5_25517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sy5_25517/02_2026/7sy5_25517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sy5_25517/02_2026/7sy5_25517.map" model { file = "/net/cci-nas-00/data/ceres_data/7sy5_25517/02_2026/7sy5_25517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sy5_25517/02_2026/7sy5_25517.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.041 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 25548 2.51 5 N 6561 2.21 5 O 7776 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40083 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} 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: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, '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: 9.77, per 1000 atoms: 0.24 Number of scatterers: 40083 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 7776 8.00 N 6561 7.00 C 25548 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=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 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=2.02 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=2.04 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=2.04 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: 3.49 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 60 sheets defined 41.6% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 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 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.738A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.105A 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: 3.634A 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: 3.917A 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: 4.054A 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 removed outlier: 3.501A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.708A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.087A 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: 3.628A 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: 3.915A 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: 4.082A 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: 3.508A 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: 3.721A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 4.079A 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: 3.635A 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: 3.927A 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: 4.054A 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: 3.720A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.656A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.793A 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: 4.085A 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 146 through 155 removed outlier: 3.934A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 194 Proline residue: D 178 - end of helix removed outlier: 3.702A 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: 3.739A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.803A 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: 3.841A 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: 3.569A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.729A 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: 4.257A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.937A 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: 3.570A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.371A 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: 3.504A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.802A 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: 4.427A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.605A 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: 3.902A 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: 3.740A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.652A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.785A 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: 4.070A 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 146 through 155 removed outlier: 3.961A 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: 3.716A 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: 3.735A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.799A 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: 3.816A 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: 3.552A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.692A 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: 4.259A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.938A 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: 3.553A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.411A 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 Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.805A 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: 4.446A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.596A 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: 3.903A 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: 3.727A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 81 removed outlier: 3.646A pdb=" N GLN F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 88 removed outlier: 3.797A 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: 4.069A 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 146 through 155 removed outlier: 3.935A pdb=" N ILE F 151 " --> pdb=" O GLY F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 194 Proline residue: F 178 - end of helix removed outlier: 3.706A 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: 3.728A pdb=" N LEU F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 3.840A 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: 3.819A 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: 3.564A pdb=" N TRP F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.732A 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: 4.280A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA F 413 " --> pdb=" O SER F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.594A pdb=" N GLU F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 465 removed outlier: 4.396A 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: 3.502A pdb=" N GLU F 479 " --> pdb=" O LYS F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 502 removed outlier: 3.811A 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: 4.406A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.594A 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: 3.907A 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: 8.180A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.873A 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: 5.115A 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: 4.026A 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: 3.541A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 11.261A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.809A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.082A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.668A 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: 4.640A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.509A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.538A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.549A 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: 3.541A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.646A 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: 6.662A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.543A 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: 5.055A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.425A 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: 4.572A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.074A 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: 6.160A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.366A 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: 6.827A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.736A 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: 6.514A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.957A 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: 6.514A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.572A 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: 3.611A 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 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.231A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.040A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.570A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.242A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.570A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 318 removed outlier: 6.713A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.247A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.146A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.205A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.797A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.533A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.533A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.273A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.133A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE3, 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=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.507A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.180A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.298A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.271A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.507A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.685A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.223A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.197A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.510A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.510A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.304A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.522A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.031A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, 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=AG1, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.801A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.977A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.355A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 131 through 132 removed outlier: 3.547A pdb=" N VAL F 132 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU F 142 " --> pdb=" O VAL F 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'F' and resid 262 through 263 removed outlier: 6.053A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.363A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) 1984 hydrogen bonds defined for protein. 5586 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: 12.20 Time building geometry restraints manager: 4.54 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: 12547 1.34 - 1.47: 10450 1.47 - 1.59: 17779 1.59 - 1.71: 0 1.71 - 1.84: 288 Bond restraints: 41064 Sorted by residual: bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.34e+00 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.16e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.12e+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 7.11e+00 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.07e+00 ... (remaining 41059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 53760 1.95 - 3.90: 1844 3.90 - 5.84: 186 5.84 - 7.79: 43 7.79 - 9.74: 27 Bond angle restraints: 55860 Sorted by residual: angle pdb=" CA TYR A 495 " pdb=" CB TYR A 495 " pdb=" CG TYR A 495 " ideal model delta sigma weight residual 113.90 123.36 -9.46 1.80e+00 3.09e-01 2.76e+01 angle pdb=" CA TYR C 495 " pdb=" CB TYR C 495 " pdb=" CG TYR C 495 " ideal model delta sigma weight residual 113.90 123.31 -9.41 1.80e+00 3.09e-01 2.73e+01 angle pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " pdb=" CG TYR B 495 " ideal model delta sigma weight residual 113.90 123.18 -9.28 1.80e+00 3.09e-01 2.66e+01 angle pdb=" C SER C 359 " pdb=" N ASN C 360 " pdb=" CA ASN C 360 " ideal model delta sigma weight residual 122.82 129.28 -6.46 1.42e+00 4.96e-01 2.07e+01 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.82 129.19 -6.37 1.42e+00 4.96e-01 2.01e+01 ... (remaining 55855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 23287 17.74 - 35.48: 1690 35.48 - 53.22: 287 53.22 - 70.95: 86 70.95 - 88.69: 51 Dihedral angle restraints: 25401 sinusoidal: 11067 harmonic: 14334 Sorted by residual: 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 -47.40 -38.60 1 1.00e+01 1.00e-02 2.10e+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 -48.16 -37.84 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual -86.00 -48.34 -37.66 1 1.00e+01 1.00e-02 2.00e+01 ... (remaining 25398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4670 0.055 - 0.109: 1292 0.109 - 0.164: 359 0.164 - 0.218: 41 0.218 - 0.273: 13 Chirality restraints: 6375 Sorted by residual: 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 -2.13 -0.27 2.00e-01 2.50e+01 1.86e+00 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 -2.13 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CB VAL A 576 " pdb=" CA VAL A 576 " pdb=" CG1 VAL A 576 " pdb=" CG2 VAL A 576 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 6372 not shown) Planarity restraints: 7191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 169 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.11e+00 pdb=" C ARG F 169 " 0.049 2.00e-02 2.50e+03 pdb=" O ARG F 169 " -0.018 2.00e-02 2.50e+03 pdb=" N SER F 170 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 169 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" C ARG E 169 " -0.049 2.00e-02 2.50e+03 pdb=" O ARG E 169 " 0.018 2.00e-02 2.50e+03 pdb=" N SER E 170 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 169 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.70e+00 pdb=" C ARG D 169 " 0.048 2.00e-02 2.50e+03 pdb=" O ARG D 169 " -0.018 2.00e-02 2.50e+03 pdb=" N SER D 170 " -0.016 2.00e-02 2.50e+03 ... (remaining 7188 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 10411 2.80 - 3.33: 34881 3.33 - 3.85: 69032 3.85 - 4.38: 79045 4.38 - 4.90: 136628 Nonbonded interactions: 329997 Sorted by model distance: nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.281 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.288 3.040 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.290 3.040 nonbonded pdb=" O ASP A 80 " pdb=" OH TYR A 265 " model vdw 2.294 3.040 ... (remaining 329992 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: 0.03 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: 6.140 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: 0.040 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 42.100 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 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 0.059 41190 Z= 0.238 Angle : 0.850 15.581 56190 Z= 0.456 Chirality : 0.055 0.273 6375 Planarity : 0.006 0.061 7131 Dihedral : 13.112 88.692 16029 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: 0.50 (0.11), residues: 1757 sheet: 0.84 (0.18), residues: 732 loop : -0.80 (0.11), residues: 2365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 460 TYR 0.045 0.002 TYR A 495 PHE 0.028 0.002 PHE D 369 TRP 0.025 0.002 TRP C 886 HIS 0.006 0.001 HIS F 378 Details of bonding type rmsd covalent geometry : bond 0.00477 (41064) covalent geometry : angle 0.81791 (55860) SS BOND : bond 0.00340 ( 48) SS BOND : angle 1.87072 ( 96) hydrogen bonds : bond 0.12765 ( 1888) hydrogen bonds : angle 6.83038 ( 5586) link_BETA1-4 : bond 0.00472 ( 18) link_BETA1-4 : angle 1.70648 ( 54) link_NAG-ASN : bond 0.00704 ( 60) link_NAG-ASN : angle 3.89599 ( 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 456 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.540 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 79 PHE cc_start: 0.5820 (t80) cc_final: 0.4270 (t80) REVERT: A 141 LEU cc_start: 0.8686 (mm) cc_final: 0.8412 (tp) REVERT: B 79 PHE cc_start: 0.6787 (t80) cc_final: 0.5457 (t80) REVERT: B 134 GLN cc_start: 0.8928 (tp40) cc_final: 0.8370 (tm-30) REVERT: B 141 LEU cc_start: 0.8854 (mm) cc_final: 0.8617 (tp) REVERT: B 175 PHE cc_start: 0.6762 (m-10) cc_final: 0.6310 (m-10) REVERT: B 380 TYR cc_start: 0.8682 (m-80) cc_final: 0.8265 (m-80) REVERT: B 440 ASN cc_start: 0.9179 (m-40) cc_final: 0.8611 (t0) REVERT: B 455 LEU cc_start: 0.8893 (tp) cc_final: 0.8580 (tp) REVERT: B 464 PHE cc_start: 0.8100 (m-80) cc_final: 0.7803 (m-80) REVERT: B 983 ARG cc_start: 0.7724 (mtp180) cc_final: 0.7395 (ttm110) REVERT: B 1005 GLN cc_start: 0.7548 (mt0) cc_final: 0.7175 (mt0) REVERT: C 66 HIS cc_start: 0.6499 (m90) cc_final: 0.6237 (m90) REVERT: C 129 LYS cc_start: 0.8401 (mtmt) cc_final: 0.8151 (tttp) REVERT: D 23 GLU cc_start: 0.6141 (tp30) cc_final: 0.4858 (pt0) REVERT: D 82 MET cc_start: 0.6103 (mtp) cc_final: 0.5374 (tmt) REVERT: D 83 TYR cc_start: 0.2189 (m-80) cc_final: 0.0953 (m-80) REVERT: D 150 GLU cc_start: 0.3958 (tm-30) cc_final: 0.3518 (tt0) REVERT: D 168 TRP cc_start: 0.0700 (t-100) cc_final: 0.0306 (m100) REVERT: D 323 MET cc_start: 0.2442 (mmp) cc_final: 0.0905 (mmp) REVERT: D 515 TYR cc_start: 0.3523 (m-80) cc_final: 0.3287 (m-10) REVERT: E 332 MET cc_start: 0.2063 (ttp) cc_final: 0.1650 (ptm) REVERT: E 474 MET cc_start: 0.3312 (mmt) cc_final: 0.2914 (mmp) REVERT: F 266 LEU cc_start: 0.3719 (mt) cc_final: 0.3296 (mt) REVERT: F 579 MET cc_start: -0.0216 (ptm) cc_final: -0.0758 (ptp) outliers start: 0 outliers final: 1 residues processed: 456 average time/residue: 0.7376 time to fit residues: 407.9816 Evaluate side-chains 213 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 432 optimal weight: 40.0000 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 0.9990 chunk 470 optimal weight: 40.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN B 188 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN D 374 HIS E 250 ASN E 374 HIS E 442 GLN E 552 GLN F 374 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.163908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.100152 restraints weight = 118545.741| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 6.94 r_work: 0.3124 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 41190 Z= 0.241 Angle : 0.672 13.035 56190 Z= 0.335 Chirality : 0.045 0.253 6375 Planarity : 0.005 0.062 7131 Dihedral : 5.700 58.292 6908 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.58 % Allowed : 7.65 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.11), residues: 4854 helix: 1.33 (0.12), residues: 1782 sheet: 0.66 (0.18), residues: 739 loop : -0.58 (0.12), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 161 TYR 0.023 0.002 TYR A1067 PHE 0.023 0.002 PHE D 504 TRP 0.018 0.002 TRP B 886 HIS 0.009 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00538 (41064) covalent geometry : angle 0.64453 (55860) SS BOND : bond 0.00280 ( 48) SS BOND : angle 1.44853 ( 96) hydrogen bonds : bond 0.04701 ( 1888) hydrogen bonds : angle 5.47885 ( 5586) link_BETA1-4 : bond 0.00314 ( 18) link_BETA1-4 : angle 1.07564 ( 54) link_NAG-ASN : bond 0.00686 ( 60) link_NAG-ASN : angle 3.27108 ( 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 294 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 226 time to evaluate : 1.525 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: A 141 LEU cc_start: 0.8560 (mm) cc_final: 0.8273 (tp) REVERT: A 565 PHE cc_start: 0.8190 (m-80) cc_final: 0.7968 (m-80) REVERT: B 134 GLN cc_start: 0.8969 (tp40) cc_final: 0.8430 (tm-30) REVERT: B 141 LEU cc_start: 0.8940 (mm) cc_final: 0.8706 (tt) REVERT: B 440 ASN cc_start: 0.9337 (m-40) cc_final: 0.8802 (t0) REVERT: B 517 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8000 (mm) REVERT: B 1010 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8545 (mp10) REVERT: C 129 LYS cc_start: 0.8581 (mtmt) cc_final: 0.8218 (tttp) REVERT: C 740 MET cc_start: 0.9317 (ttp) cc_final: 0.9068 (ttt) REVERT: C 950 ASP cc_start: 0.9006 (m-30) cc_final: 0.8794 (m-30) REVERT: D 23 GLU cc_start: 0.5686 (tp30) cc_final: 0.5092 (pt0) REVERT: D 82 MET cc_start: 0.6004 (mtp) cc_final: 0.5711 (tmt) REVERT: D 83 TYR cc_start: 0.2805 (m-80) cc_final: 0.2352 (m-80) REVERT: D 150 GLU cc_start: 0.3844 (tm-30) cc_final: 0.3550 (tt0) REVERT: D 270 MET cc_start: -0.0667 (OUTLIER) cc_final: -0.2534 (ttp) REVERT: D 332 MET cc_start: 0.2001 (ppp) cc_final: 0.1744 (pmt) REVERT: E 255 TYR cc_start: 0.4088 (m-80) cc_final: 0.3851 (m-10) REVERT: E 475 LYS cc_start: 0.8222 (mmpt) cc_final: 0.7486 (tttt) REVERT: E 579 MET cc_start: 0.1809 (OUTLIER) cc_final: -0.0395 (ttp) REVERT: E 609 ASP cc_start: 0.4788 (p0) cc_final: 0.4576 (p0) REVERT: F 383 MET cc_start: 0.3021 (mtt) cc_final: 0.2457 (mtt) REVERT: F 455 MET cc_start: -0.0196 (ppp) cc_final: -0.0721 (ppp) REVERT: F 480 MET cc_start: 0.2262 (mtp) cc_final: 0.1679 (tpt) REVERT: F 579 MET cc_start: 0.4751 (ptm) cc_final: 0.4346 (ptp) outliers start: 68 outliers final: 15 residues processed: 272 average time/residue: 0.6763 time to fit residues: 227.0001 Evaluate side-chains 203 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 563 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 378 optimal weight: 1.9990 chunk 469 optimal weight: 30.0000 chunk 184 optimal weight: 0.5980 chunk 374 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 384 optimal weight: 20.0000 chunk 363 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 182 optimal weight: 0.7980 chunk 436 optimal weight: 20.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN F 154 ASN F 388 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.163909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.106010 restraints weight = 119989.171| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 7.06 r_work: 0.3141 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 41190 Z= 0.157 Angle : 0.587 13.393 56190 Z= 0.291 Chirality : 0.043 0.263 6375 Planarity : 0.004 0.059 7131 Dihedral : 5.264 52.639 6906 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.44 % Allowed : 8.77 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: 0.77 (0.12), residues: 4854 helix: 1.71 (0.12), residues: 1773 sheet: 0.55 (0.18), residues: 710 loop : -0.39 (0.12), residues: 2371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 482 TYR 0.022 0.001 TYR A1067 PHE 0.020 0.001 PHE E 327 TRP 0.022 0.001 TRP D 168 HIS 0.011 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00343 (41064) covalent geometry : angle 0.56086 (55860) SS BOND : bond 0.00238 ( 48) SS BOND : angle 1.26512 ( 96) hydrogen bonds : bond 0.04128 ( 1888) hydrogen bonds : angle 5.17846 ( 5586) link_BETA1-4 : bond 0.00263 ( 18) link_BETA1-4 : angle 0.94657 ( 54) link_NAG-ASN : bond 0.00606 ( 60) link_NAG-ASN : angle 2.97769 ( 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 263 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 201 time to evaluate : 1.556 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 141 LEU cc_start: 0.8588 (mm) cc_final: 0.8289 (tp) REVERT: B 134 GLN cc_start: 0.9062 (tp40) cc_final: 0.8633 (tm-30) REVERT: B 141 LEU cc_start: 0.8885 (mm) cc_final: 0.8662 (tt) REVERT: B 200 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.8643 (t80) REVERT: B 517 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8504 (mm) REVERT: B 979 ASP cc_start: 0.8586 (t0) cc_final: 0.8379 (t0) REVERT: B 1010 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8565 (mp10) REVERT: B 1017 GLU cc_start: 0.9223 (tt0) cc_final: 0.8905 (tp30) REVERT: C 79 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.7318 (m-10) REVERT: C 129 LYS cc_start: 0.8354 (mtmt) cc_final: 0.7836 (tttp) REVERT: C 153 MET cc_start: 0.5747 (tmt) cc_final: 0.5499 (tmt) REVERT: C 565 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.6956 (m-80) REVERT: C 740 MET cc_start: 0.9345 (ttp) cc_final: 0.9042 (ttt) REVERT: C 950 ASP cc_start: 0.9068 (m-30) cc_final: 0.8804 (m-30) REVERT: D 23 GLU cc_start: 0.5607 (tp30) cc_final: 0.4674 (pt0) REVERT: D 82 MET cc_start: 0.6127 (mtp) cc_final: 0.5604 (tmt) REVERT: D 83 TYR cc_start: 0.3113 (m-80) cc_final: 0.2039 (m-80) REVERT: D 150 GLU cc_start: 0.3883 (tm-30) cc_final: 0.3492 (tt0) REVERT: D 323 MET cc_start: 0.1655 (mtt) cc_final: 0.0369 (mtt) REVERT: D 328 TRP cc_start: 0.0953 (m100) cc_final: 0.0680 (t60) REVERT: E 228 HIS cc_start: 0.5233 (OUTLIER) cc_final: 0.5017 (p90) REVERT: E 255 TYR cc_start: 0.3958 (m-80) cc_final: 0.3692 (m-10) REVERT: E 455 MET cc_start: 0.5903 (ppp) cc_final: 0.5279 (ppp) REVERT: E 480 MET cc_start: 0.4181 (mtt) cc_final: 0.2632 (pp-130) REVERT: E 557 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7645 (tpt) REVERT: E 613 TYR cc_start: 0.4264 (t80) cc_final: 0.3961 (t80) REVERT: F 144 LEU cc_start: 0.2540 (tp) cc_final: 0.1558 (pt) REVERT: F 323 MET cc_start: 0.3983 (mtt) cc_final: 0.3444 (ptp) REVERT: F 392 LEU cc_start: 0.4900 (mt) cc_final: 0.4546 (tp) REVERT: F 480 MET cc_start: 0.1599 (mtp) cc_final: 0.0780 (tpt) outliers start: 62 outliers final: 15 residues processed: 245 average time/residue: 0.6705 time to fit residues: 202.9949 Evaluate side-chains 199 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 367 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 155 optimal weight: 4.9990 chunk 347 optimal weight: 5.9990 chunk 406 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 200 optimal weight: 2.9990 chunk 354 optimal weight: 20.0000 chunk 392 optimal weight: 20.0000 chunk 351 optimal weight: 40.0000 chunk 289 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN C 81 ASN C 137 ASN D 540 HIS E 239 HIS ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 508 ASN F 33 ASN F 388 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.161203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.099778 restraints weight = 116794.864| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 9.09 r_work: 0.3025 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 41190 Z= 0.300 Angle : 0.679 11.335 56190 Z= 0.336 Chirality : 0.046 0.276 6375 Planarity : 0.004 0.059 7131 Dihedral : 5.556 54.762 6906 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.97 % Allowed : 9.05 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: 0.67 (0.12), residues: 4854 helix: 1.63 (0.12), residues: 1782 sheet: 0.28 (0.18), residues: 726 loop : -0.39 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 482 TYR 0.029 0.002 TYR F 521 PHE 0.021 0.002 PHE B 175 TRP 0.027 0.002 TRP D 459 HIS 0.013 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00670 (41064) covalent geometry : angle 0.65655 (55860) SS BOND : bond 0.00314 ( 48) SS BOND : angle 1.24370 ( 96) hydrogen bonds : bond 0.04594 ( 1888) hydrogen bonds : angle 5.30143 ( 5586) link_BETA1-4 : bond 0.00347 ( 18) link_BETA1-4 : angle 1.34736 ( 54) link_NAG-ASN : bond 0.00719 ( 60) link_NAG-ASN : angle 2.92753 ( 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 276 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 191 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.8385 (mm) cc_final: 0.7936 (tp) REVERT: B 134 GLN cc_start: 0.9011 (tp40) cc_final: 0.8456 (tm-30) REVERT: B 141 LEU cc_start: 0.8889 (mm) cc_final: 0.8603 (tt) REVERT: B 200 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.8311 (t80) REVERT: B 517 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8089 (mm) REVERT: B 1010 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8643 (mp10) REVERT: B 1017 GLU cc_start: 0.9316 (tt0) cc_final: 0.8960 (tm-30) REVERT: C 153 MET cc_start: 0.5858 (tmt) cc_final: 0.5574 (tmt) REVERT: C 565 PHE cc_start: 0.7759 (m-80) cc_final: 0.7486 (m-80) REVERT: C 740 MET cc_start: 0.9390 (ttp) cc_final: 0.9165 (ttt) REVERT: D 23 GLU cc_start: 0.5616 (tp30) cc_final: 0.5122 (pp20) REVERT: D 83 TYR cc_start: 0.3254 (m-80) cc_final: 0.2956 (m-10) REVERT: D 150 GLU cc_start: 0.3982 (tm-30) cc_final: 0.3610 (tt0) REVERT: D 323 MET cc_start: 0.2196 (mtt) cc_final: 0.0760 (mtm) REVERT: D 328 TRP cc_start: 0.1226 (m100) cc_final: 0.0763 (t60) REVERT: D 366 MET cc_start: 0.3866 (tmm) cc_final: 0.3312 (tpp) REVERT: D 479 GLU cc_start: 0.4235 (tt0) cc_final: 0.4031 (tm-30) REVERT: D 480 MET cc_start: 0.0667 (OUTLIER) cc_final: 0.0289 (mtt) REVERT: D 543 ASP cc_start: 0.1563 (t0) cc_final: 0.0805 (p0) REVERT: E 236 LEU cc_start: 0.2360 (OUTLIER) cc_final: 0.1666 (pt) REVERT: E 255 TYR cc_start: 0.4266 (m-80) cc_final: 0.3997 (m-10) REVERT: E 557 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7756 (tpt) REVERT: E 579 MET cc_start: 0.0790 (ttp) cc_final: 0.0275 (ttp) REVERT: E 613 TYR cc_start: 0.4543 (t80) cc_final: 0.4326 (t80) REVERT: F 144 LEU cc_start: 0.2542 (tp) cc_final: 0.1682 (pt) REVERT: F 270 MET cc_start: 0.2272 (tpp) cc_final: 0.1929 (tpp) REVERT: F 365 THR cc_start: 0.2019 (OUTLIER) cc_final: 0.1806 (m) REVERT: F 392 LEU cc_start: 0.4358 (mt) cc_final: 0.4000 (mt) REVERT: F 455 MET cc_start: 0.0365 (ppp) cc_final: -0.0227 (ppp) REVERT: F 480 MET cc_start: 0.1932 (mtp) cc_final: 0.1332 (tpt) REVERT: F 516 TYR cc_start: 0.1768 (t80) cc_final: 0.1483 (t80) outliers start: 85 outliers final: 28 residues processed: 258 average time/residue: 0.6258 time to fit residues: 201.1312 Evaluate side-chains 197 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 196 TYR Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 609 ASP Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 570 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 270 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 177 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 276 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 228 optimal weight: 0.9990 chunk 429 optimal weight: 0.0020 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN E 63 ASN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.163109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.103648 restraints weight = 119275.234| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 5.52 r_work: 0.3143 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 41190 Z= 0.116 Angle : 0.568 11.183 56190 Z= 0.281 Chirality : 0.043 0.293 6375 Planarity : 0.004 0.058 7131 Dihedral : 5.168 53.344 6906 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.35 % Allowed : 10.37 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: 1.85 (0.12), residues: 1766 sheet: 0.22 (0.18), residues: 703 loop : -0.26 (0.12), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 214 TYR 0.020 0.001 TYR C1067 PHE 0.015 0.001 PHE B 201 TRP 0.013 0.001 TRP D 459 HIS 0.007 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00247 (41064) covalent geometry : angle 0.54511 (55860) SS BOND : bond 0.00231 ( 48) SS BOND : angle 0.99615 ( 96) hydrogen bonds : bond 0.03885 ( 1888) hydrogen bonds : angle 5.08929 ( 5586) link_BETA1-4 : bond 0.00259 ( 18) link_BETA1-4 : angle 0.99436 ( 54) link_NAG-ASN : bond 0.00492 ( 60) link_NAG-ASN : angle 2.75000 ( 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 238 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 180 time to evaluate : 1.512 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 141 LEU cc_start: 0.8320 (mm) cc_final: 0.7843 (tp) REVERT: B 134 GLN cc_start: 0.8928 (tp40) cc_final: 0.8383 (tm-30) REVERT: B 141 LEU cc_start: 0.8875 (mm) cc_final: 0.8581 (tt) REVERT: B 153 MET cc_start: 0.4320 (OUTLIER) cc_final: 0.4058 (ptt) REVERT: B 200 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.8325 (t80) REVERT: B 773 GLU cc_start: 0.8943 (tt0) cc_final: 0.8694 (tt0) REVERT: C 153 MET cc_start: 0.5737 (tmt) cc_final: 0.5495 (tmt) REVERT: C 565 PHE cc_start: 0.7461 (OUTLIER) cc_final: 0.7158 (m-80) REVERT: C 740 MET cc_start: 0.9311 (ttp) cc_final: 0.9029 (ttt) REVERT: C 754 LEU cc_start: 0.9651 (mt) cc_final: 0.9425 (mt) REVERT: C 950 ASP cc_start: 0.8989 (m-30) cc_final: 0.8690 (m-30) REVERT: D 23 GLU cc_start: 0.5671 (tp30) cc_final: 0.4846 (pt0) REVERT: D 83 TYR cc_start: 0.3345 (m-80) cc_final: 0.2932 (m-10) REVERT: D 150 GLU cc_start: 0.3925 (tm-30) cc_final: 0.3561 (tt0) REVERT: D 323 MET cc_start: 0.1846 (mtm) cc_final: -0.0249 (mtt) REVERT: D 328 TRP cc_start: 0.1036 (m100) cc_final: 0.0653 (t60) REVERT: D 366 MET cc_start: 0.3805 (tmm) cc_final: 0.3225 (tpp) REVERT: D 479 GLU cc_start: 0.4132 (tt0) cc_final: 0.3924 (tm-30) REVERT: D 480 MET cc_start: 0.0643 (OUTLIER) cc_final: 0.0232 (mtt) REVERT: D 543 ASP cc_start: 0.1479 (t0) cc_final: 0.0451 (p0) REVERT: E 228 HIS cc_start: 0.5221 (OUTLIER) cc_final: 0.4939 (p90) REVERT: E 236 LEU cc_start: 0.2419 (OUTLIER) cc_final: 0.1681 (pt) REVERT: E 255 TYR cc_start: 0.4000 (m-80) cc_final: 0.3723 (m-10) REVERT: E 557 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7523 (tpt) REVERT: E 579 MET cc_start: 0.0184 (ttp) cc_final: -0.0022 (ttp) REVERT: E 613 TYR cc_start: 0.4464 (t80) cc_final: 0.4213 (t80) REVERT: F 144 LEU cc_start: 0.2596 (tp) cc_final: 0.1674 (pt) REVERT: F 270 MET cc_start: 0.2331 (tpp) cc_final: 0.2097 (tpp) REVERT: F 323 MET cc_start: 0.2160 (OUTLIER) cc_final: 0.1915 (OUTLIER) REVERT: F 455 MET cc_start: 0.0696 (ppp) cc_final: 0.0274 (ppp) REVERT: F 474 MET cc_start: 0.1733 (mmp) cc_final: 0.1517 (mmt) REVERT: F 480 MET cc_start: 0.1773 (mtp) cc_final: 0.1136 (tpt) REVERT: F 566 TRP cc_start: 0.0691 (p-90) cc_final: 0.0425 (p-90) outliers start: 58 outliers final: 22 residues processed: 222 average time/residue: 0.6784 time to fit residues: 184.2912 Evaluate side-chains 193 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 367 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 184 optimal weight: 0.9980 chunk 203 optimal weight: 0.7980 chunk 37 optimal weight: 30.0000 chunk 23 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 267 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 471 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.161926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.102620 restraints weight = 119906.566| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 6.75 r_work: 0.3102 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 41190 Z= 0.178 Angle : 0.581 13.318 56190 Z= 0.288 Chirality : 0.043 0.272 6375 Planarity : 0.004 0.064 7131 Dihedral : 5.067 54.679 6906 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.35 % Allowed : 10.97 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: 1.89 (0.12), residues: 1763 sheet: 0.21 (0.18), residues: 712 loop : -0.23 (0.12), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 204 TYR 0.023 0.001 TYR B 365 PHE 0.020 0.001 PHE C 79 TRP 0.013 0.001 TRP D 165 HIS 0.006 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00397 (41064) covalent geometry : angle 0.56057 (55860) SS BOND : bond 0.00218 ( 48) SS BOND : angle 0.93619 ( 96) hydrogen bonds : bond 0.03916 ( 1888) hydrogen bonds : angle 5.03711 ( 5586) link_BETA1-4 : bond 0.00274 ( 18) link_BETA1-4 : angle 1.08716 ( 54) link_NAG-ASN : bond 0.00537 ( 60) link_NAG-ASN : angle 2.61839 ( 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 230 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 172 time to evaluate : 1.800 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 141 LEU cc_start: 0.8214 (mm) cc_final: 0.7750 (tp) REVERT: B 134 GLN cc_start: 0.9126 (tp40) cc_final: 0.8697 (tm-30) REVERT: B 141 LEU cc_start: 0.8837 (mm) cc_final: 0.8546 (tt) REVERT: B 200 TYR cc_start: 0.9029 (OUTLIER) cc_final: 0.8661 (t80) REVERT: B 309 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8753 (mp0) REVERT: C 129 LYS cc_start: 0.8621 (mtmt) cc_final: 0.8033 (tttp) REVERT: C 565 PHE cc_start: 0.7486 (OUTLIER) cc_final: 0.7231 (m-80) REVERT: C 740 MET cc_start: 0.9363 (ttp) cc_final: 0.9093 (ttt) REVERT: C 754 LEU cc_start: 0.9659 (mt) cc_final: 0.9428 (mt) REVERT: C 950 ASP cc_start: 0.9039 (m-30) cc_final: 0.8783 (m-30) REVERT: D 23 GLU cc_start: 0.5686 (tp30) cc_final: 0.5134 (pp20) REVERT: D 83 TYR cc_start: 0.3289 (m-80) cc_final: 0.2651 (m-10) REVERT: D 150 GLU cc_start: 0.3941 (tm-30) cc_final: 0.3523 (tt0) REVERT: D 323 MET cc_start: 0.2218 (mtm) cc_final: 0.0912 (mtm) REVERT: D 328 TRP cc_start: 0.0777 (m100) cc_final: 0.0528 (t60) REVERT: D 332 MET cc_start: 0.0607 (pmt) cc_final: -0.2747 (mpt) REVERT: D 366 MET cc_start: 0.4023 (tmm) cc_final: 0.3452 (tpp) REVERT: D 479 GLU cc_start: 0.4167 (tt0) cc_final: 0.3935 (tm-30) REVERT: D 480 MET cc_start: 0.0515 (mpp) cc_final: 0.0092 (mtt) REVERT: E 228 HIS cc_start: 0.5402 (OUTLIER) cc_final: 0.5143 (p90) REVERT: E 236 LEU cc_start: 0.2524 (OUTLIER) cc_final: 0.1774 (pt) REVERT: E 255 TYR cc_start: 0.4102 (m-80) cc_final: 0.3841 (m-10) REVERT: E 366 MET cc_start: 0.3109 (tpt) cc_final: 0.2853 (tpp) REVERT: E 557 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7469 (tpt) REVERT: E 579 MET cc_start: -0.0171 (ttp) cc_final: -0.0446 (ttp) REVERT: E 613 TYR cc_start: 0.4732 (t80) cc_final: 0.4477 (t80) REVERT: F 106 SER cc_start: 0.3498 (p) cc_final: 0.3053 (m) REVERT: F 144 LEU cc_start: 0.2453 (tp) cc_final: 0.1480 (pt) REVERT: F 207 TYR cc_start: 0.0532 (m-80) cc_final: 0.0162 (m-10) REVERT: F 365 THR cc_start: 0.1629 (OUTLIER) cc_final: 0.1349 (m) REVERT: F 474 MET cc_start: 0.1606 (mmp) cc_final: 0.1335 (mmt) REVERT: F 566 TRP cc_start: 0.0629 (p-90) cc_final: 0.0421 (p-90) outliers start: 58 outliers final: 25 residues processed: 214 average time/residue: 0.6963 time to fit residues: 184.6329 Evaluate side-chains 198 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 367 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 111 optimal weight: 8.9990 chunk 477 optimal weight: 0.6980 chunk 318 optimal weight: 40.0000 chunk 8 optimal weight: 6.9990 chunk 220 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 429 optimal weight: 9.9990 chunk 78 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 755 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN D 535 HIS D 586 ASN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.161734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.101529 restraints weight = 119589.329| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 5.85 r_work: 0.3124 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 41190 Z= 0.181 Angle : 0.578 13.652 56190 Z= 0.286 Chirality : 0.043 0.283 6375 Planarity : 0.004 0.062 7131 Dihedral : 5.035 54.948 6906 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.28 % Allowed : 11.32 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: 1.88 (0.12), residues: 1776 sheet: 0.20 (0.18), residues: 713 loop : -0.19 (0.13), residues: 2365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 204 TYR 0.020 0.001 TYR C1067 PHE 0.018 0.001 PHE E 308 TRP 0.014 0.001 TRP F 163 HIS 0.007 0.001 HIS E 493 Details of bonding type rmsd covalent geometry : bond 0.00406 (41064) covalent geometry : angle 0.55936 (55860) SS BOND : bond 0.00196 ( 48) SS BOND : angle 0.84326 ( 96) hydrogen bonds : bond 0.03861 ( 1888) hydrogen bonds : angle 5.02629 ( 5586) link_BETA1-4 : bond 0.00152 ( 18) link_BETA1-4 : angle 1.03348 ( 54) link_NAG-ASN : bond 0.00509 ( 60) link_NAG-ASN : angle 2.54715 ( 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 228 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 173 time to evaluate : 1.561 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 141 LEU cc_start: 0.7974 (mm) cc_final: 0.7361 (tp) REVERT: B 134 GLN cc_start: 0.8628 (tp40) cc_final: 0.8127 (tm-30) REVERT: B 141 LEU cc_start: 0.8845 (mm) cc_final: 0.8548 (tt) REVERT: B 200 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.8411 (t80) REVERT: B 309 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8769 (mp0) REVERT: B 571 ASP cc_start: 0.9100 (OUTLIER) cc_final: 0.8885 (t0) REVERT: C 565 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.7265 (m-80) REVERT: C 740 MET cc_start: 0.9339 (ttp) cc_final: 0.9081 (ttt) REVERT: C 754 LEU cc_start: 0.9658 (mt) cc_final: 0.9425 (mt) REVERT: C 950 ASP cc_start: 0.8999 (m-30) cc_final: 0.8730 (m-30) REVERT: D 23 GLU cc_start: 0.5584 (tp30) cc_final: 0.5109 (pp20) REVERT: D 83 TYR cc_start: 0.3437 (m-80) cc_final: 0.3101 (m-10) REVERT: D 150 GLU cc_start: 0.3933 (tm-30) cc_final: 0.3583 (tt0) REVERT: D 323 MET cc_start: 0.2205 (mtm) cc_final: 0.0625 (mtm) REVERT: D 328 TRP cc_start: 0.1005 (m100) cc_final: 0.0657 (t60) REVERT: D 332 MET cc_start: 0.1016 (pmt) cc_final: -0.2147 (mpt) REVERT: D 366 MET cc_start: 0.4339 (tmm) cc_final: 0.3843 (tpp) REVERT: D 480 MET cc_start: 0.0856 (OUTLIER) cc_final: 0.0491 (mtt) REVERT: E 228 HIS cc_start: 0.5453 (OUTLIER) cc_final: 0.5213 (p90) REVERT: E 236 LEU cc_start: 0.2610 (OUTLIER) cc_final: 0.1875 (pt) REVERT: E 255 TYR cc_start: 0.4397 (m-80) cc_final: 0.4170 (m-10) REVERT: E 366 MET cc_start: 0.3198 (tpt) cc_final: 0.2971 (tpp) REVERT: E 557 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7608 (tpt) REVERT: E 579 MET cc_start: 0.0023 (ttp) cc_final: -0.0185 (ttp) REVERT: E 613 TYR cc_start: 0.4893 (t80) cc_final: 0.4690 (t80) REVERT: F 106 SER cc_start: 0.3472 (p) cc_final: 0.3121 (m) REVERT: F 207 TYR cc_start: 0.0041 (m-80) cc_final: -0.0544 (m-10) REVERT: F 365 THR cc_start: 0.1888 (OUTLIER) cc_final: 0.1664 (m) REVERT: F 474 MET cc_start: 0.2232 (mmp) cc_final: 0.2007 (mmt) REVERT: F 557 MET cc_start: 0.1315 (OUTLIER) cc_final: 0.0914 (tmt) outliers start: 55 outliers final: 23 residues processed: 213 average time/residue: 0.6763 time to fit residues: 178.4013 Evaluate side-chains 197 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 557 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 384 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 310 optimal weight: 0.3980 chunk 380 optimal weight: 9.9990 chunk 480 optimal weight: 30.0000 chunk 79 optimal weight: 0.5980 chunk 367 optimal weight: 0.0000 chunk 132 optimal weight: 6.9990 chunk 226 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 535 HIS ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.162765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.103745 restraints weight = 122103.196| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 5.61 r_work: 0.3135 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 41190 Z= 0.105 Angle : 0.552 15.637 56190 Z= 0.273 Chirality : 0.042 0.279 6375 Planarity : 0.004 0.063 7131 Dihedral : 4.801 54.870 6906 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.21 % Allowed : 11.60 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.12), residues: 4854 helix: 2.02 (0.12), residues: 1749 sheet: 0.34 (0.19), residues: 676 loop : -0.10 (0.13), residues: 2429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 214 TYR 0.019 0.001 TYR A1067 PHE 0.014 0.001 PHE C 79 TRP 0.050 0.001 TRP F 566 HIS 0.006 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00226 (41064) covalent geometry : angle 0.53457 (55860) SS BOND : bond 0.00414 ( 48) SS BOND : angle 0.79844 ( 96) hydrogen bonds : bond 0.03556 ( 1888) hydrogen bonds : angle 4.89296 ( 5586) link_BETA1-4 : bond 0.00294 ( 18) link_BETA1-4 : angle 0.93172 ( 54) link_NAG-ASN : bond 0.00456 ( 60) link_NAG-ASN : angle 2.44028 ( 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 240 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 188 time to evaluate : 1.504 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 141 LEU cc_start: 0.8093 (mm) cc_final: 0.7582 (tp) REVERT: B 134 GLN cc_start: 0.9130 (tp40) cc_final: 0.8763 (tm-30) REVERT: B 141 LEU cc_start: 0.8804 (mm) cc_final: 0.8509 (tt) REVERT: B 200 TYR cc_start: 0.9122 (OUTLIER) cc_final: 0.8755 (t80) REVERT: B 309 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8653 (mp0) REVERT: B 571 ASP cc_start: 0.9097 (OUTLIER) cc_final: 0.8877 (t0) REVERT: C 565 PHE cc_start: 0.7350 (OUTLIER) cc_final: 0.7105 (m-80) REVERT: C 740 MET cc_start: 0.9258 (ttp) cc_final: 0.9033 (ttt) REVERT: C 754 LEU cc_start: 0.9618 (mt) cc_final: 0.9371 (mt) REVERT: C 776 LYS cc_start: 0.9377 (ttmt) cc_final: 0.9151 (tttm) REVERT: C 950 ASP cc_start: 0.8965 (m-30) cc_final: 0.8643 (m-30) REVERT: D 23 GLU cc_start: 0.5685 (tp30) cc_final: 0.5219 (pp20) REVERT: D 83 TYR cc_start: 0.3358 (m-80) cc_final: 0.3052 (m-10) REVERT: D 150 GLU cc_start: 0.4007 (tm-30) cc_final: 0.3634 (tt0) REVERT: D 323 MET cc_start: 0.2656 (mtm) cc_final: 0.0943 (mtm) REVERT: D 328 TRP cc_start: 0.1002 (m100) cc_final: 0.0632 (t60) REVERT: D 332 MET cc_start: 0.0840 (pmt) cc_final: -0.2244 (mpt) REVERT: D 366 MET cc_start: 0.4307 (tmm) cc_final: 0.3849 (tpp) REVERT: E 228 HIS cc_start: 0.5450 (OUTLIER) cc_final: 0.5235 (p90) REVERT: E 236 LEU cc_start: 0.2968 (OUTLIER) cc_final: 0.2221 (pt) REVERT: E 455 MET cc_start: 0.5668 (ppp) cc_final: 0.5047 (ppp) REVERT: E 480 MET cc_start: 0.4792 (mpt) cc_final: 0.3414 (pp-130) REVERT: E 557 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7609 (tpt) REVERT: F 106 SER cc_start: 0.3842 (p) cc_final: 0.3500 (m) REVERT: F 144 LEU cc_start: 0.1875 (OUTLIER) cc_final: 0.0830 (pt) REVERT: F 275 TRP cc_start: 0.2194 (m-10) cc_final: 0.1925 (m-10) REVERT: F 365 THR cc_start: 0.1837 (OUTLIER) cc_final: 0.1548 (m) REVERT: F 392 LEU cc_start: 0.4145 (OUTLIER) cc_final: 0.3413 (tp) REVERT: F 474 MET cc_start: 0.2147 (mmp) cc_final: 0.1917 (mmt) outliers start: 52 outliers final: 24 residues processed: 224 average time/residue: 0.6480 time to fit residues: 181.0452 Evaluate side-chains 201 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 485 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 232 optimal weight: 7.9990 chunk 392 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 193 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 344 optimal weight: 20.0000 chunk 398 optimal weight: 8.9990 chunk 208 optimal weight: 20.0000 chunk 305 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN D 373 HIS ** E 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.160535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.104816 restraints weight = 119587.519| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 6.63 r_work: 0.3066 rms_B_bonded: 5.32 restraints_weight: 2.0000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 41190 Z= 0.308 Angle : 0.664 16.906 56190 Z= 0.329 Chirality : 0.046 0.286 6375 Planarity : 0.004 0.062 7131 Dihedral : 5.245 56.451 6906 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.32 % Allowed : 12.06 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: 1.79 (0.12), residues: 1777 sheet: 0.09 (0.18), residues: 723 loop : -0.23 (0.13), residues: 2354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 214 TYR 0.022 0.002 TYR A1067 PHE 0.019 0.002 PHE D 369 TRP 0.028 0.002 TRP F 163 HIS 0.007 0.001 HIS E 493 Details of bonding type rmsd covalent geometry : bond 0.00697 (41064) covalent geometry : angle 0.64694 (55860) SS BOND : bond 0.00295 ( 48) SS BOND : angle 0.95952 ( 96) hydrogen bonds : bond 0.04288 ( 1888) hydrogen bonds : angle 5.17256 ( 5586) link_BETA1-4 : bond 0.00272 ( 18) link_BETA1-4 : angle 1.30614 ( 54) link_NAG-ASN : bond 0.00643 ( 60) link_NAG-ASN : angle 2.58702 ( 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 226 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 169 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.7819 (mm) cc_final: 0.7189 (tp) REVERT: A 1010 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8871 (mp10) REVERT: B 134 GLN cc_start: 0.8508 (tp40) cc_final: 0.8070 (tm-30) REVERT: B 200 TYR cc_start: 0.9011 (OUTLIER) cc_final: 0.8584 (t80) REVERT: B 571 ASP cc_start: 0.9225 (OUTLIER) cc_final: 0.9001 (t70) REVERT: C 129 LYS cc_start: 0.8720 (mtmt) cc_final: 0.8116 (tttp) REVERT: C 153 MET cc_start: 0.4552 (tpt) cc_final: 0.3671 (tpp) REVERT: C 565 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.7391 (m-80) REVERT: C 740 MET cc_start: 0.9409 (ttp) cc_final: 0.9189 (ttt) REVERT: D 82 MET cc_start: 0.3230 (mtt) cc_final: 0.1993 (tmt) REVERT: D 83 TYR cc_start: 0.3241 (m-80) cc_final: 0.1475 (m-10) REVERT: D 150 GLU cc_start: 0.4128 (tm-30) cc_final: 0.3776 (tt0) REVERT: D 323 MET cc_start: 0.2517 (mtm) cc_final: 0.0262 (mtt) REVERT: D 328 TRP cc_start: 0.1076 (m100) cc_final: 0.0706 (t60) REVERT: D 332 MET cc_start: 0.1318 (pmt) cc_final: -0.1729 (mpt) REVERT: D 366 MET cc_start: 0.4308 (tmm) cc_final: 0.3913 (tpp) REVERT: E 228 HIS cc_start: 0.5486 (OUTLIER) cc_final: 0.5196 (p90) REVERT: E 236 LEU cc_start: 0.2506 (OUTLIER) cc_final: 0.1779 (pt) REVERT: E 557 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7708 (tpt) REVERT: E 580 ASN cc_start: 0.7666 (m-40) cc_final: 0.6652 (p0) REVERT: F 106 SER cc_start: 0.3298 (p) cc_final: 0.2996 (m) REVERT: F 144 LEU cc_start: 0.1785 (OUTLIER) cc_final: 0.0900 (pt) REVERT: F 249 MET cc_start: 0.0298 (pmm) cc_final: 0.0073 (pp-130) REVERT: F 275 TRP cc_start: 0.2209 (m-10) cc_final: 0.1969 (m-10) REVERT: F 365 THR cc_start: 0.1900 (OUTLIER) cc_final: 0.1633 (m) REVERT: F 392 LEU cc_start: 0.3628 (OUTLIER) cc_final: 0.3001 (tp) outliers start: 57 outliers final: 23 residues processed: 208 average time/residue: 0.6555 time to fit residues: 168.4564 Evaluate side-chains 196 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 375 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 263 optimal weight: 0.9980 chunk 356 optimal weight: 9.9990 chunk 332 optimal weight: 6.9990 chunk 161 optimal weight: 0.0670 chunk 255 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 427 optimal weight: 2.9990 chunk 229 optimal weight: 8.9990 chunk 234 optimal weight: 0.7980 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS ** E 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.162007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.103500 restraints weight = 119827.642| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 7.01 r_work: 0.3117 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 41190 Z= 0.124 Angle : 0.579 14.486 56190 Z= 0.287 Chirality : 0.043 0.294 6375 Planarity : 0.004 0.062 7131 Dihedral : 4.987 55.528 6906 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.81 % Allowed : 12.71 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: 0.94 (0.12), residues: 4854 helix: 1.88 (0.12), residues: 1770 sheet: 0.12 (0.19), residues: 680 loop : -0.12 (0.13), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 214 TYR 0.020 0.001 TYR C1067 PHE 0.014 0.001 PHE E 369 TRP 0.036 0.001 TRP F 163 HIS 0.004 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00270 (41064) covalent geometry : angle 0.55990 (55860) SS BOND : bond 0.00173 ( 48) SS BOND : angle 0.83495 ( 96) hydrogen bonds : bond 0.03716 ( 1888) hydrogen bonds : angle 4.99871 ( 5586) link_BETA1-4 : bond 0.00280 ( 18) link_BETA1-4 : angle 0.93632 ( 54) link_NAG-ASN : bond 0.00433 ( 60) link_NAG-ASN : angle 2.57551 ( 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 204 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 1.520 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: A 141 LEU cc_start: 0.8055 (mm) cc_final: 0.7444 (tp) REVERT: A 1010 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8699 (mp10) REVERT: B 134 GLN cc_start: 0.8814 (tp40) cc_final: 0.8349 (tm-30) REVERT: B 200 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.8509 (t80) REVERT: B 571 ASP cc_start: 0.9075 (OUTLIER) cc_final: 0.8847 (t0) REVERT: B 773 GLU cc_start: 0.8938 (tt0) cc_final: 0.8692 (tt0) REVERT: B 1092 GLU cc_start: 0.9032 (pt0) cc_final: 0.8815 (pm20) REVERT: C 153 MET cc_start: 0.4431 (tpt) cc_final: 0.3493 (tpp) REVERT: C 565 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.7263 (m-80) REVERT: C 740 MET cc_start: 0.9310 (ttp) cc_final: 0.9047 (ttt) REVERT: C 754 LEU cc_start: 0.9668 (mt) cc_final: 0.9436 (mt) REVERT: C 934 ILE cc_start: 0.8915 (mm) cc_final: 0.8702 (mp) REVERT: C 950 ASP cc_start: 0.8998 (m-30) cc_final: 0.8744 (m-30) REVERT: D 83 TYR cc_start: 0.3170 (m-80) cc_final: 0.2939 (m-10) REVERT: D 150 GLU cc_start: 0.4024 (tm-30) cc_final: 0.3655 (tt0) REVERT: D 209 VAL cc_start: 0.1383 (t) cc_final: 0.1154 (p) REVERT: D 323 MET cc_start: 0.2420 (mtm) cc_final: 0.0378 (mtm) REVERT: D 328 TRP cc_start: 0.0890 (m100) cc_final: 0.0590 (t60) REVERT: D 332 MET cc_start: 0.1226 (pmt) cc_final: -0.1771 (mpt) REVERT: D 366 MET cc_start: 0.4431 (tmm) cc_final: 0.3952 (tpp) REVERT: E 228 HIS cc_start: 0.5455 (OUTLIER) cc_final: 0.5184 (p90) REVERT: E 236 LEU cc_start: 0.3048 (OUTLIER) cc_final: 0.2307 (pt) REVERT: E 366 MET cc_start: 0.2754 (tpp) cc_final: 0.2517 (mtp) REVERT: E 557 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7809 (tpt) REVERT: E 580 ASN cc_start: 0.7660 (m-40) cc_final: 0.6623 (p0) REVERT: F 123 MET cc_start: 0.0443 (ttt) cc_final: 0.0020 (ptp) REVERT: F 144 LEU cc_start: 0.1984 (OUTLIER) cc_final: 0.1098 (pt) REVERT: F 392 LEU cc_start: 0.3866 (OUTLIER) cc_final: 0.3197 (tp) REVERT: F 455 MET cc_start: -0.0670 (ppp) cc_final: -0.2413 (mmt) REVERT: F 480 MET cc_start: 0.2556 (ptm) cc_final: 0.2287 (mtm) REVERT: F 557 MET cc_start: 0.1214 (OUTLIER) cc_final: 0.0861 (tmt) REVERT: F 579 MET cc_start: 0.3073 (ptp) cc_final: 0.2872 (ptt) outliers start: 35 outliers final: 19 residues processed: 193 average time/residue: 0.7123 time to fit residues: 168.9194 Evaluate side-chains 196 residues out of total 4311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 557 MET Chi-restraints excluded: chain F residue 563 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 471 optimal weight: 30.0000 chunk 142 optimal weight: 6.9990 chunk 283 optimal weight: 0.9980 chunk 446 optimal weight: 6.9990 chunk 147 optimal weight: 30.0000 chunk 207 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 463 optimal weight: 40.0000 chunk 191 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 289 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.162012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.099499 restraints weight = 119375.351| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 6.88 r_work: 0.3080 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 41190 Z= 0.157 Angle : 0.590 18.251 56190 Z= 0.291 Chirality : 0.043 0.288 6375 Planarity : 0.004 0.063 7131 Dihedral : 4.937 56.325 6906 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.81 % Allowed : 12.92 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: 0.93 (0.12), residues: 4854 helix: 1.88 (0.12), residues: 1770 sheet: 0.08 (0.19), residues: 689 loop : -0.12 (0.13), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 214 TYR 0.019 0.001 TYR A1067 PHE 0.016 0.001 PHE C 898 TRP 0.059 0.002 TRP D 566 HIS 0.004 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00350 (41064) covalent geometry : angle 0.57154 (55860) SS BOND : bond 0.00180 ( 48) SS BOND : angle 0.82452 ( 96) hydrogen bonds : bond 0.03769 ( 1888) hydrogen bonds : angle 4.98179 ( 5586) link_BETA1-4 : bond 0.00162 ( 18) link_BETA1-4 : angle 1.06283 ( 54) link_NAG-ASN : bond 0.00469 ( 60) link_NAG-ASN : angle 2.53892 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30678.69 seconds wall clock time: 518 minutes 47.58 seconds (31127.58 seconds total)