Starting phenix.real_space_refine on Wed Jun 25 11:11:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wwl_32869/06_2025/7wwl_32869.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wwl_32869/06_2025/7wwl_32869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wwl_32869/06_2025/7wwl_32869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wwl_32869/06_2025/7wwl_32869.map" model { file = "/net/cci-nas-00/data/ceres_data/7wwl_32869/06_2025/7wwl_32869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wwl_32869/06_2025/7wwl_32869.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 18859 2.51 5 N 4890 2.21 5 O 5829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.63s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29704 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 7765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7765 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 53, 'TRANS': 940} Chain breaks: 8 Chain: "B" Number of atoms: 7759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7759 Classifications: {'peptide': 993} Link IDs: {'PTRANS': 53, 'TRANS': 939} Chain breaks: 8 Chain: "C" Number of atoms: 7759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7759 Classifications: {'peptide': 993} Link IDs: {'PTRANS': 53, 'TRANS': 939} Chain breaks: 8 Chain: "H" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 967 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "L" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 842 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "I" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 967 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "M" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 842 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "J" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 967 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "N" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 842 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: "F" 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: "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: "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: "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: "Y" 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: "Z" 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: 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: "b" 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: "c" 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 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: "f" 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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 Time building chain proxies: 18.24, per 1000 atoms: 0.61 Number of scatterers: 29704 At special positions: 0 Unit cell: (134.788, 153.267, 200.008, 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 126 16.00 O 5829 8.00 N 4890 7.00 C 18859 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 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=2.31 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 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=2.17 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=2.63 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=1.75 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 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=2.17 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=2.53 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.12 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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=2.10 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 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=2.17 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=2.52 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 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 Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 331 " " NAG R 1 " - " ASN B 343 " " NAG S 1 " - " ASN B 709 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 331 " " NAG Y 1 " - " ASN C 343 " " NAG Z 1 " - " ASN C 709 " " NAG a 1 " - " ASN C 717 " " NAG b 1 " - " ASN C 801 " " NAG c 1 " - " ASN C1074 " " NAG d 1 " - " ASN C1098 " " NAG e 1 " - " ASN C1134 " " NAG f 1 " - " ASN B1074 " Time building additional restraints: 7.82 Conformation dependent library (CDL) restraints added in 3.6 seconds 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6836 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 60 sheets defined 19.1% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.578A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.630A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) 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: 3.773A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.634A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.774A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.573A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.993A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.626A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.879A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.632A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.578A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.694A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) 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: 3.964A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.545A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.009A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.245A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.578A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 572 removed outlier: 3.849A pdb=" N THR C 572 " --> pdb=" O ILE C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.717A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) 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: 3.560A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.698A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.590A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.355A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.221A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'H' and resid 103 through 107 removed outlier: 3.563A pdb=" N ILE H 106 " --> pdb=" O TRP H 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 107 removed outlier: 3.563A pdb=" N ILE I 106 " --> pdb=" O TRP I 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 107 removed outlier: 3.563A pdb=" N ILE J 106 " --> pdb=" O TRP J 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.858A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.012A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.524A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 653 through 655 Processing sheet with id=AB2, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.417A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.857A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.732A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.037A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.554A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR B 573 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP B 568 " --> pdb=" O THR B 573 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.526A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.264A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.579A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.858A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.908A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.525A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.851A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.569A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.606A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.632A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.574A pdb=" N LEU L 11 " --> pdb=" O LYS L 104 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 46 through 48 removed outlier: 6.666A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.606A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 5 through 6 Processing sheet with id=AF9, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.574A pdb=" N LEU M 11 " --> pdb=" O LYS M 104 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 46 through 48 removed outlier: 6.666A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AG3, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.606A pdb=" N ALA J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 5 through 6 removed outlier: 3.632A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.574A pdb=" N LEU N 11 " --> pdb=" O LYS N 104 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 46 through 48 removed outlier: 6.665A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 1038 hydrogen bonds defined for protein. 2805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.11 Time building geometry restraints manager: 9.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6613 1.33 - 1.45: 7696 1.45 - 1.58: 15896 1.58 - 1.70: 0 1.70 - 1.83: 159 Bond restraints: 30364 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.444 0.078 1.20e-02 6.94e+03 4.26e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.264 0.068 1.59e-02 3.96e+03 1.80e+01 bond pdb=" N PRO A 589 " pdb=" CD PRO A 589 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.80e+01 bond pdb=" N PRO B 589 " pdb=" CD PRO B 589 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.77e+01 bond pdb=" N PRO C 589 " pdb=" CD PRO C 589 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.77e+01 ... (remaining 30359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 40308 2.74 - 5.48: 875 5.48 - 8.22: 100 8.22 - 10.96: 2 10.96 - 13.70: 11 Bond angle restraints: 41296 Sorted by residual: angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.73 -11.19 1.91e+00 2.74e-01 3.43e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.73 -11.19 1.91e+00 2.74e-01 3.43e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.72 -11.18 1.91e+00 2.74e-01 3.43e+01 angle pdb=" N PHE B 565 " pdb=" CA PHE B 565 " pdb=" C PHE B 565 " ideal model delta sigma weight residual 108.86 116.78 -7.92 1.41e+00 5.03e-01 3.15e+01 angle pdb=" C SER C 31 " pdb=" N PHE C 32 " pdb=" CA PHE C 32 " ideal model delta sigma weight residual 122.56 115.23 7.33 1.50e+00 4.44e-01 2.39e+01 ... (remaining 41291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 16409 17.93 - 35.87: 1795 35.87 - 53.80: 581 53.80 - 71.74: 154 71.74 - 89.67: 52 Dihedral angle restraints: 18991 sinusoidal: 8350 harmonic: 10641 Sorted by residual: dihedral pdb=" CB CYS I 22 " pdb=" SG CYS I 22 " pdb=" SG CYS I 96 " pdb=" CB CYS I 96 " ideal model delta sinusoidal sigma weight residual -86.00 -171.51 85.51 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS J 22 " pdb=" SG CYS J 22 " pdb=" SG CYS J 96 " pdb=" CB CYS J 96 " ideal model delta sinusoidal sigma weight residual -86.00 -171.50 85.50 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual -86.00 -171.50 85.50 1 1.00e+01 1.00e-02 8.85e+01 ... (remaining 18988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 4835 0.329 - 0.659: 3 0.659 - 0.988: 5 0.988 - 1.318: 0 1.318 - 1.647: 1 Chirality restraints: 4844 Sorted by residual: chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.17e+03 chirality pdb=" C1 NAG e 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG e 1 " pdb=" O5 NAG e 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.78e+01 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.44e+01 ... (remaining 4841 not shown) Planarity restraints: 5304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.077 2.00e-02 2.50e+03 1.03e-01 1.33e+02 pdb=" CG ASN B 331 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.180 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " 0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " -0.047 2.00e-02 2.50e+03 5.80e-02 4.20e+01 pdb=" CG ASN A 709 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " 0.099 2.00e-02 2.50e+03 pdb=" C1 NAG A1409 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.053 2.00e-02 2.50e+03 5.69e-02 4.05e+01 pdb=" CG ASN C 331 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.091 2.00e-02 2.50e+03 pdb=" C1 NAG X 1 " -0.068 2.00e-02 2.50e+03 ... (remaining 5301 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 228 2.51 - 3.11: 20919 3.11 - 3.70: 42180 3.70 - 4.30: 63969 4.30 - 4.90: 107487 Nonbonded interactions: 234783 Sorted by model distance: nonbonded pdb=" O VAL A 227 " pdb=" OD1 ASP A 228 " model vdw 1.911 3.040 nonbonded pdb=" OD1 ASN A 532 " pdb=" N LEU A 533 " model vdw 2.043 3.120 nonbonded pdb=" O GLY M 64 " pdb=" OG SER M 65 " model vdw 2.067 3.040 nonbonded pdb=" O ILE B 332 " pdb=" OG1 THR B 333 " model vdw 2.080 3.040 nonbonded pdb=" O THR B 523 " pdb=" O VAL B 524 " model vdw 2.090 3.040 ... (remaining 234778 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 939 or resid 944 through 1146 or resid 1401 thr \ ough 1408)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'K' 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' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 1.330 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: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 70.230 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.230 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:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 : 0.012 0.598 30480 Z= 0.532 Angle : 1.212 50.389 41599 Z= 0.638 Chirality : 0.072 1.647 4844 Planarity : 0.007 0.096 5256 Dihedral : 17.166 89.673 12020 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 2.30 % Allowed : 9.48 % Favored : 88.22 % Rotamer: Outliers : 9.75 % Allowed : 15.91 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.11), residues: 3607 helix: -2.34 (0.16), residues: 677 sheet: -1.76 (0.15), residues: 1015 loop : -3.32 (0.11), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP H 103 HIS 0.009 0.002 HIS A1048 PHE 0.025 0.003 PHE A 898 TYR 0.027 0.002 TYR B1067 ARG 0.008 0.001 ARG M 45 Details of bonding type rmsd link_NAG-ASN : bond 0.02572 ( 48) link_NAG-ASN : angle 8.47801 ( 144) link_BETA1-4 : bond 0.04096 ( 23) link_BETA1-4 : angle 4.12244 ( 69) hydrogen bonds : bond 0.18155 ( 1002) hydrogen bonds : angle 7.62733 ( 2805) SS BOND : bond 0.15435 ( 45) SS BOND : angle 8.65718 ( 90) covalent geometry : bond 0.00978 (30364) covalent geometry : angle 1.01844 (41296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 312 poor density : 472 time to evaluate : 3.223 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 SER cc_start: 0.6367 (OUTLIER) cc_final: 0.6043 (m) REVERT: A 164 ASN cc_start: 0.5162 (OUTLIER) cc_final: 0.4704 (OUTLIER) REVERT: A 389 ASP cc_start: 0.5828 (OUTLIER) cc_final: 0.5053 (m-30) REVERT: A 444 LYS cc_start: 0.6508 (pttt) cc_final: 0.5627 (tttp) REVERT: A 529 LYS cc_start: 0.6692 (OUTLIER) cc_final: 0.5697 (mtpt) REVERT: A 530 SER cc_start: 0.5179 (OUTLIER) cc_final: 0.4565 (t) REVERT: A 531 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8315 (p) REVERT: A 1039 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8792 (mtp180) REVERT: B 403 ARG cc_start: 0.7271 (ttp-170) cc_final: 0.6961 (ttp80) REVERT: B 523 THR cc_start: 0.3941 (OUTLIER) cc_final: 0.3730 (p) REVERT: B 554 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: B 599 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8678 (t) REVERT: B 811 LYS cc_start: 0.6393 (OUTLIER) cc_final: 0.5701 (mtpp) REVERT: C 195 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8830 (ptmt) REVERT: C 324 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6974 (pm20) REVERT: C 354 ASN cc_start: 0.7076 (t0) cc_final: 0.6828 (t0) REVERT: J 51 ILE cc_start: 0.1272 (OUTLIER) cc_final: 0.0601 (tp) outliers start: 312 outliers final: 82 residues processed: 729 average time/residue: 1.2964 time to fit residues: 1157.0130 Evaluate side-chains 340 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 245 time to evaluate : 4.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain I residue 27 PHE Chi-restraints excluded: chain J residue 31 ASN Chi-restraints excluded: chain J residue 51 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 306 optimal weight: 4.9990 chunk 275 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 284 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 329 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 137 ASN A 188 ASN A 317 ASN A 422 ASN A 498 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A 540 ASN A 644 GLN A 703 ASN A 762 GLN A 804 GLN A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 969 ASN A 992 GLN A1010 GLN A1058 HIS B 134 GLN B 137 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 450 ASN B 498 GLN B 540 ASN B 644 GLN B 703 ASN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 954 GLN B 992 GLN B1054 GLN C 137 ASN C 422 ASN C 440 ASN C 542 ASN C 644 GLN C 703 ASN C 751 ASN C 784 GLN C 901 GLN C 914 ASN C 926 GLN C 992 GLN C1010 GLN C1071 GLN C1101 HIS ** H 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN L 37 GLN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.173738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.118423 restraints weight = 45880.563| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.60 r_work: 0.3231 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30480 Z= 0.147 Angle : 0.763 15.083 41599 Z= 0.375 Chirality : 0.050 0.746 4844 Planarity : 0.006 0.066 5256 Dihedral : 9.683 59.966 5591 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.99 % Favored : 92.82 % Rotamer: Outliers : 6.22 % Allowed : 20.35 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.13), residues: 3607 helix: -0.15 (0.20), residues: 656 sheet: -1.24 (0.15), residues: 1018 loop : -2.67 (0.12), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 103 HIS 0.005 0.001 HIS H 112 PHE 0.026 0.002 PHE A 559 TYR 0.028 0.001 TYR B 200 ARG 0.008 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00507 ( 48) link_NAG-ASN : angle 3.27501 ( 144) link_BETA1-4 : bond 0.00724 ( 23) link_BETA1-4 : angle 2.40355 ( 69) hydrogen bonds : bond 0.04543 ( 1002) hydrogen bonds : angle 5.63364 ( 2805) SS BOND : bond 0.00368 ( 45) SS BOND : angle 1.80907 ( 90) covalent geometry : bond 0.00327 (30364) covalent geometry : angle 0.72968 (41296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 270 time to evaluate : 3.101 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: symmetry clash REVERT: A 63 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.8094 (m) REVERT: A 117 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6859 (tt) REVERT: A 444 LYS cc_start: 0.3794 (pttt) cc_final: 0.2945 (tttp) REVERT: A 449 TYR cc_start: 0.5894 (OUTLIER) cc_final: 0.5164 (t80) REVERT: A 452 ARG cc_start: 0.5895 (OUTLIER) cc_final: 0.4285 (mtp85) REVERT: A 529 LYS cc_start: 0.6586 (OUTLIER) cc_final: 0.5781 (mtpt) REVERT: A 531 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7522 (p) REVERT: A 544 ASN cc_start: 0.6762 (p0) cc_final: 0.5980 (p0) REVERT: A 878 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8924 (mt) REVERT: A 995 ARG cc_start: 0.8087 (mtt-85) cc_final: 0.7856 (mtt180) REVERT: A 1038 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8353 (mptt) REVERT: B 396 TYR cc_start: 0.8506 (m-80) cc_final: 0.8299 (m-80) REVERT: B 403 ARG cc_start: 0.8020 (ttp-170) cc_final: 0.7704 (ttp80) REVERT: B 544 ASN cc_start: 0.7633 (p0) cc_final: 0.6989 (p0) REVERT: B 554 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: B 787 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.7897 (mm-40) REVERT: B 867 ASP cc_start: 0.8573 (p0) cc_final: 0.8132 (m-30) REVERT: B 990 GLU cc_start: 0.7369 (tt0) cc_final: 0.6900 (tm-30) REVERT: C 41 LYS cc_start: 0.7258 (OUTLIER) cc_final: 0.7040 (mmtp) REVERT: C 135 PHE cc_start: 0.6860 (m-80) cc_final: 0.6161 (m-80) REVERT: C 323 THR cc_start: 0.7459 (p) cc_final: 0.7132 (t) REVERT: C 324 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7121 (pm20) REVERT: C 354 ASN cc_start: 0.7254 (t0) cc_final: 0.6823 (t0) REVERT: C 368 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8568 (mp) REVERT: C 449 TYR cc_start: 0.7709 (m-80) cc_final: 0.7503 (m-80) REVERT: C 988 GLU cc_start: 0.7908 (tp30) cc_final: 0.7634 (tp30) REVERT: H 3 GLN cc_start: 0.7658 (tp-100) cc_final: 0.7414 (tp-100) REVERT: H 19 ARG cc_start: 0.6249 (ttt180) cc_final: 0.6027 (ttt-90) REVERT: H 54 ASP cc_start: 0.6311 (OUTLIER) cc_final: 0.6073 (m-30) REVERT: H 77 ASN cc_start: 0.6729 (m110) cc_final: 0.6413 (m-40) REVERT: H 99 ASP cc_start: 0.7966 (t70) cc_final: 0.7700 (t70) REVERT: L 101 GLN cc_start: 0.6939 (OUTLIER) cc_final: 0.5843 (mp10) REVERT: I 39 GLN cc_start: 0.3319 (tt0) cc_final: 0.2917 (mp-120) REVERT: J 71 SER cc_start: 0.5521 (p) cc_final: 0.5287 (m) outliers start: 199 outliers final: 79 residues processed: 434 average time/residue: 1.2684 time to fit residues: 675.7297 Evaluate side-chains 309 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 215 time to evaluate : 3.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain M residue 10 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 267 optimal weight: 0.0000 chunk 151 optimal weight: 0.9990 chunk 15 optimal weight: 0.0470 chunk 139 optimal weight: 4.9990 chunk 205 optimal weight: 7.9990 chunk 303 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 276 optimal weight: 0.6980 chunk 200 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 340 optimal weight: 9.9990 overall best weight: 0.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A1010 GLN B 207 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 121 ASN C 134 GLN C 498 GLN C 519 HIS H 59 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.174013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.119991 restraints weight = 45935.600| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.62 r_work: 0.3228 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 30480 Z= 0.118 Angle : 0.679 13.816 41599 Z= 0.330 Chirality : 0.048 0.646 4844 Planarity : 0.004 0.047 5256 Dihedral : 8.374 59.698 5500 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.88 % Favored : 92.96 % Rotamer: Outliers : 5.00 % Allowed : 21.79 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.13), residues: 3607 helix: 0.67 (0.21), residues: 658 sheet: -1.06 (0.16), residues: 1055 loop : -2.27 (0.12), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 33 HIS 0.004 0.001 HIS B 207 PHE 0.022 0.001 PHE A 92 TYR 0.018 0.001 TYR A1067 ARG 0.005 0.000 ARG H 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00659 ( 48) link_NAG-ASN : angle 2.76043 ( 144) link_BETA1-4 : bond 0.00658 ( 23) link_BETA1-4 : angle 2.16350 ( 69) hydrogen bonds : bond 0.03756 ( 1002) hydrogen bonds : angle 5.19048 ( 2805) SS BOND : bond 0.00381 ( 45) SS BOND : angle 1.98257 ( 90) covalent geometry : bond 0.00254 (30364) covalent geometry : angle 0.64932 (41296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 252 time to evaluate : 3.395 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 63 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.8043 (m) REVERT: A 117 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6957 (tt) REVERT: A 444 LYS cc_start: 0.3901 (pttt) cc_final: 0.2998 (tttp) REVERT: A 449 TYR cc_start: 0.5765 (OUTLIER) cc_final: 0.4866 (t80) REVERT: A 529 LYS cc_start: 0.6541 (OUTLIER) cc_final: 0.5821 (mtpt) REVERT: A 531 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7616 (p) REVERT: A 878 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8902 (mt) REVERT: A 1038 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8388 (mptt) REVERT: B 324 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6970 (pm20) REVERT: B 331 ASN cc_start: 0.6651 (OUTLIER) cc_final: 0.5883 (m-40) REVERT: B 335 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8032 (tm) REVERT: B 403 ARG cc_start: 0.8138 (ttp-170) cc_final: 0.7786 (ttp80) REVERT: B 406 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7419 (pt0) REVERT: B 417 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7455 (tptm) REVERT: B 544 ASN cc_start: 0.7626 (p0) cc_final: 0.6869 (p0) REVERT: B 554 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: B 787 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8002 (mt0) REVERT: B 867 ASP cc_start: 0.8350 (p0) cc_final: 0.8108 (m-30) REVERT: B 990 GLU cc_start: 0.7254 (tt0) cc_final: 0.6885 (tm-30) REVERT: C 41 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6958 (mmtp) REVERT: C 200 TYR cc_start: 0.6804 (OUTLIER) cc_final: 0.5860 (t80) REVERT: C 354 ASN cc_start: 0.7262 (t0) cc_final: 0.6832 (t0) REVERT: C 368 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8595 (mp) REVERT: C 534 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8300 (m) REVERT: C 988 GLU cc_start: 0.7933 (tp30) cc_final: 0.7519 (tp30) REVERT: H 19 ARG cc_start: 0.6512 (ttt180) cc_final: 0.6193 (ttt90) REVERT: H 77 ASN cc_start: 0.6789 (m110) cc_final: 0.6495 (m-40) REVERT: H 86 LEU cc_start: 0.5454 (mt) cc_final: 0.5136 (mp) REVERT: L 98 THR cc_start: 0.8959 (m) cc_final: 0.8585 (p) REVERT: L 101 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.6091 (mp10) REVERT: I 39 GLN cc_start: 0.3131 (tt0) cc_final: 0.2808 (mp-120) REVERT: J 51 ILE cc_start: -0.1937 (OUTLIER) cc_final: -0.2323 (tp) outliers start: 160 outliers final: 66 residues processed: 382 average time/residue: 1.1357 time to fit residues: 542.3407 Evaluate side-chains 289 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 204 time to evaluate : 3.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain J residue 51 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 353 optimal weight: 6.9990 chunk 305 optimal weight: 20.0000 chunk 79 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 319 optimal weight: 9.9990 chunk 291 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 336 optimal weight: 0.0870 chunk 17 optimal weight: 8.9990 chunk 269 optimal weight: 0.6980 overall best weight: 2.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 506 GLN B1005 GLN B1106 GLN C 81 ASN C 196 ASN C 317 ASN C 501 ASN H 82 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 GLN J 74 ASN N 28 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.168031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.112288 restraints weight = 45708.090| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.65 r_work: 0.3123 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 30480 Z= 0.182 Angle : 0.725 14.734 41599 Z= 0.353 Chirality : 0.050 0.610 4844 Planarity : 0.005 0.059 5256 Dihedral : 7.822 59.952 5480 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.88 % Favored : 92.99 % Rotamer: Outliers : 5.35 % Allowed : 21.48 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.13), residues: 3607 helix: 1.01 (0.21), residues: 638 sheet: -0.67 (0.16), residues: 1008 loop : -2.13 (0.12), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 103 HIS 0.039 0.002 HIS B 207 PHE 0.021 0.002 PHE C 86 TYR 0.020 0.001 TYR A1067 ARG 0.013 0.001 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 48) link_NAG-ASN : angle 2.84946 ( 144) link_BETA1-4 : bond 0.00411 ( 23) link_BETA1-4 : angle 2.26572 ( 69) hydrogen bonds : bond 0.04573 ( 1002) hydrogen bonds : angle 5.21829 ( 2805) SS BOND : bond 0.00464 ( 45) SS BOND : angle 2.16263 ( 90) covalent geometry : bond 0.00438 (30364) covalent geometry : angle 0.69449 (41296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 235 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7881 (m) REVERT: A 237 ARG cc_start: 0.7798 (mtp85) cc_final: 0.7304 (mtm-85) REVERT: A 269 TYR cc_start: 0.8082 (m-80) cc_final: 0.7789 (m-10) REVERT: A 324 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6981 (pm20) REVERT: A 480 CYS cc_start: 0.1564 (OUTLIER) cc_final: 0.0920 (t) REVERT: A 529 LYS cc_start: 0.6669 (OUTLIER) cc_final: 0.5888 (mtpt) REVERT: A 531 THR cc_start: 0.7883 (OUTLIER) cc_final: 0.7522 (p) REVERT: A 563 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6994 (mp10) REVERT: A 787 GLN cc_start: 0.9371 (OUTLIER) cc_final: 0.9022 (mt0) REVERT: A 878 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.9013 (mt) REVERT: A 985 ASP cc_start: 0.6028 (p0) cc_final: 0.5407 (p0) REVERT: A 988 GLU cc_start: 0.7985 (mp0) cc_final: 0.7473 (mp0) REVERT: A 1038 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8449 (mppt) REVERT: B 324 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7198 (pm20) REVERT: B 403 ARG cc_start: 0.8116 (ttp-170) cc_final: 0.7728 (ttp80) REVERT: B 417 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7127 (tptp) REVERT: B 452 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8255 (mtt180) REVERT: B 544 ASN cc_start: 0.7947 (p0) cc_final: 0.7205 (p0) REVERT: B 554 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: B 571 ASP cc_start: 0.8010 (m-30) cc_final: 0.7628 (t0) REVERT: B 811 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6365 (mtpp) REVERT: B 867 ASP cc_start: 0.8439 (p0) cc_final: 0.8172 (m-30) REVERT: C 41 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7374 (mmtp) REVERT: C 81 ASN cc_start: 0.5818 (OUTLIER) cc_final: 0.5595 (m-40) REVERT: C 135 PHE cc_start: 0.6198 (m-80) cc_final: 0.5907 (m-80) REVERT: C 200 TYR cc_start: 0.6967 (OUTLIER) cc_final: 0.6044 (t80) REVERT: C 355 ARG cc_start: 0.8232 (ttt90) cc_final: 0.7963 (ttm170) REVERT: C 368 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8554 (mp) REVERT: C 493 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.7008 (tt0) REVERT: C 529 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8063 (ttpt) REVERT: C 697 MET cc_start: 0.9289 (ptm) cc_final: 0.8996 (ptm) REVERT: C 756 TYR cc_start: 0.9289 (m-80) cc_final: 0.8936 (m-80) REVERT: C 988 GLU cc_start: 0.7921 (tp30) cc_final: 0.7601 (tp30) REVERT: H 19 ARG cc_start: 0.6946 (ttt180) cc_final: 0.5711 (ttt-90) REVERT: H 82 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6883 (tp40) REVERT: H 106 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.7823 (tt) REVERT: L 1 ASP cc_start: 0.5428 (OUTLIER) cc_final: 0.5147 (t0) REVERT: L 18 ARG cc_start: 0.7808 (mmm160) cc_final: 0.7519 (mtp-110) REVERT: L 98 THR cc_start: 0.9044 (m) cc_final: 0.8702 (p) REVERT: L 101 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.6674 (mp10) REVERT: I 39 GLN cc_start: 0.2651 (tt0) cc_final: 0.2422 (mp-120) REVERT: M 1 ASP cc_start: 0.1164 (OUTLIER) cc_final: 0.0896 (p0) REVERT: J 51 ILE cc_start: -0.1653 (OUTLIER) cc_final: -0.2738 (mt) REVERT: J 67 ARG cc_start: 0.5296 (OUTLIER) cc_final: 0.4701 (ttt180) REVERT: J 106 ILE cc_start: 0.4655 (OUTLIER) cc_final: 0.4439 (mm) outliers start: 171 outliers final: 74 residues processed: 372 average time/residue: 1.0747 time to fit residues: 495.1280 Evaluate side-chains 312 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 210 time to evaluate : 3.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain M residue 1 ASP Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 105 optimal weight: 7.9990 chunk 361 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 174 optimal weight: 0.7980 chunk 343 optimal weight: 0.0970 chunk 72 optimal weight: 0.8980 chunk 305 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 42 optimal weight: 20.0000 chunk 295 optimal weight: 0.5980 chunk 329 optimal weight: 7.9990 overall best weight: 1.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A1010 GLN B 81 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN B1005 GLN C 115 GLN C 239 GLN C 450 ASN C 804 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.167173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.111961 restraints weight = 45190.317| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.55 r_work: 0.3144 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30480 Z= 0.134 Angle : 0.679 13.511 41599 Z= 0.330 Chirality : 0.048 0.564 4844 Planarity : 0.004 0.050 5256 Dihedral : 7.395 59.774 5475 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.24 % Favored : 93.62 % Rotamer: Outliers : 4.97 % Allowed : 22.66 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 3607 helix: 1.32 (0.22), residues: 636 sheet: -0.50 (0.16), residues: 1001 loop : -1.99 (0.12), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 103 HIS 0.003 0.001 HIS B 207 PHE 0.015 0.001 PHE M 99 TYR 0.017 0.001 TYR C1067 ARG 0.004 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 48) link_NAG-ASN : angle 2.55883 ( 144) link_BETA1-4 : bond 0.00484 ( 23) link_BETA1-4 : angle 2.10157 ( 69) hydrogen bonds : bond 0.03982 ( 1002) hydrogen bonds : angle 5.10608 ( 2805) SS BOND : bond 0.00483 ( 45) SS BOND : angle 2.56237 ( 90) covalent geometry : bond 0.00314 (30364) covalent geometry : angle 0.64848 (41296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 233 time to evaluate : 2.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.7901 (m-30) cc_final: 0.7140 (p0) REVERT: A 237 ARG cc_start: 0.7740 (mtp85) cc_final: 0.7198 (mtm-85) REVERT: A 269 TYR cc_start: 0.8096 (m-80) cc_final: 0.7814 (m-10) REVERT: A 324 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7044 (pm20) REVERT: A 444 LYS cc_start: 0.4223 (pttt) cc_final: 0.3238 (tttp) REVERT: A 449 TYR cc_start: 0.6128 (p90) cc_final: 0.4895 (t80) REVERT: A 480 CYS cc_start: 0.1131 (OUTLIER) cc_final: 0.0604 (t) REVERT: A 529 LYS cc_start: 0.6679 (OUTLIER) cc_final: 0.5912 (mtpt) REVERT: A 531 THR cc_start: 0.7830 (OUTLIER) cc_final: 0.7516 (p) REVERT: A 563 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7158 (mp10) REVERT: A 869 MET cc_start: 0.9078 (mtt) cc_final: 0.8877 (mtt) REVERT: A 878 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8955 (mt) REVERT: A 1038 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8450 (mppt) REVERT: B 231 ILE cc_start: 0.6903 (mp) cc_final: 0.6662 (mp) REVERT: B 331 ASN cc_start: 0.6725 (OUTLIER) cc_final: 0.6003 (m-40) REVERT: B 403 ARG cc_start: 0.8126 (ttp-170) cc_final: 0.7744 (ttp80) REVERT: B 417 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7473 (tptm) REVERT: B 544 ASN cc_start: 0.7968 (p0) cc_final: 0.7238 (p0) REVERT: B 554 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: B 571 ASP cc_start: 0.7936 (m-30) cc_final: 0.7713 (t0) REVERT: B 787 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8164 (mt0) REVERT: C 135 PHE cc_start: 0.6437 (m-80) cc_final: 0.6156 (m-80) REVERT: C 200 TYR cc_start: 0.6992 (OUTLIER) cc_final: 0.6281 (t80) REVERT: C 228 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8074 (t0) REVERT: C 368 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8552 (mp) REVERT: C 493 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7105 (tt0) REVERT: C 529 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8137 (ttpt) REVERT: C 534 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8357 (m) REVERT: C 988 GLU cc_start: 0.7924 (tp30) cc_final: 0.7516 (tp30) REVERT: H 19 ARG cc_start: 0.7202 (ttt180) cc_final: 0.6271 (ttt-90) REVERT: H 82 GLN cc_start: 0.7764 (tm-30) cc_final: 0.7491 (tp-100) REVERT: L 1 ASP cc_start: 0.5432 (OUTLIER) cc_final: 0.5154 (t70) REVERT: L 18 ARG cc_start: 0.7819 (mmm160) cc_final: 0.7598 (mtp-110) REVERT: L 98 THR cc_start: 0.9069 (m) cc_final: 0.8742 (p) REVERT: L 101 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.6743 (mp10) REVERT: J 51 ILE cc_start: -0.1665 (OUTLIER) cc_final: -0.2736 (mt) REVERT: J 71 SER cc_start: 0.5908 (p) cc_final: 0.5689 (m) outliers start: 159 outliers final: 76 residues processed: 365 average time/residue: 1.1094 time to fit residues: 503.3070 Evaluate side-chains 303 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 207 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 64 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 251 optimal weight: 7.9990 chunk 215 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 353 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 256 optimal weight: 1.9990 chunk 294 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 234 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A1010 GLN B 81 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 394 ASN ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B1005 GLN C 81 ASN C 99 ASN C 751 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN J 74 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.162967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.110209 restraints weight = 45578.132| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.56 r_work: 0.3090 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 30480 Z= 0.203 Angle : 0.740 15.119 41599 Z= 0.360 Chirality : 0.051 0.572 4844 Planarity : 0.005 0.055 5256 Dihedral : 7.406 59.441 5470 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.04 % Favored : 92.79 % Rotamer: Outliers : 5.56 % Allowed : 22.38 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 3607 helix: 1.13 (0.21), residues: 656 sheet: -0.49 (0.16), residues: 1018 loop : -1.96 (0.12), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 113 HIS 0.006 0.001 HIS B1064 PHE 0.020 0.002 PHE B 86 TYR 0.021 0.001 TYR C1067 ARG 0.010 0.001 ARG J 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 48) link_NAG-ASN : angle 2.81921 ( 144) link_BETA1-4 : bond 0.00397 ( 23) link_BETA1-4 : angle 2.23483 ( 69) hydrogen bonds : bond 0.04830 ( 1002) hydrogen bonds : angle 5.31546 ( 2805) SS BOND : bond 0.00526 ( 45) SS BOND : angle 2.45311 ( 90) covalent geometry : bond 0.00494 (30364) covalent geometry : angle 0.70898 (41296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 235 time to evaluate : 3.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7109 (ttmt) cc_final: 0.6525 (tttt) REVERT: A 161 SER cc_start: 0.7404 (OUTLIER) cc_final: 0.6862 (t) REVERT: A 198 ASP cc_start: 0.8159 (m-30) cc_final: 0.7388 (p0) REVERT: A 202 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8457 (mtpp) REVERT: A 237 ARG cc_start: 0.7722 (mtp85) cc_final: 0.7075 (ttp-110) REVERT: A 269 TYR cc_start: 0.8093 (m-80) cc_final: 0.7805 (m-10) REVERT: A 324 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: A 439 ASN cc_start: 0.7422 (t0) cc_final: 0.7100 (t0) REVERT: A 444 LYS cc_start: 0.4628 (pttt) cc_final: 0.3560 (tttp) REVERT: A 452 ARG cc_start: 0.5952 (OUTLIER) cc_final: 0.4643 (mtp85) REVERT: A 480 CYS cc_start: 0.1534 (OUTLIER) cc_final: 0.0863 (t) REVERT: A 529 LYS cc_start: 0.6821 (OUTLIER) cc_final: 0.6050 (mtpt) REVERT: A 531 THR cc_start: 0.7789 (OUTLIER) cc_final: 0.7499 (p) REVERT: A 869 MET cc_start: 0.9133 (mtt) cc_final: 0.8884 (mtt) REVERT: A 916 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8999 (tp) REVERT: B 280 ASN cc_start: 0.8164 (t0) cc_final: 0.7508 (t0) REVERT: B 331 ASN cc_start: 0.6731 (OUTLIER) cc_final: 0.5941 (m-40) REVERT: B 403 ARG cc_start: 0.8083 (ttp-170) cc_final: 0.7554 (ttp80) REVERT: B 417 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7458 (tppt) REVERT: B 452 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8243 (mtt180) REVERT: B 787 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8250 (mt0) REVERT: B 811 LYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6226 (mtpp) REVERT: C 122 ASN cc_start: 0.4275 (OUTLIER) cc_final: 0.3420 (m-40) REVERT: C 135 PHE cc_start: 0.6604 (m-80) cc_final: 0.6341 (m-80) REVERT: C 200 TYR cc_start: 0.7012 (OUTLIER) cc_final: 0.6192 (t80) REVERT: C 228 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.7974 (t0) REVERT: C 340 GLU cc_start: 0.8619 (mp0) cc_final: 0.8328 (pm20) REVERT: C 368 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8510 (mp) REVERT: C 487 ASN cc_start: 0.6454 (m-40) cc_final: 0.5461 (p0) REVERT: C 493 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.6995 (tt0) REVERT: C 529 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8109 (ttpt) REVERT: C 756 TYR cc_start: 0.9283 (m-80) cc_final: 0.8914 (m-80) REVERT: C 995 ARG cc_start: 0.8548 (mtp180) cc_final: 0.8294 (mtt-85) REVERT: H 19 ARG cc_start: 0.7628 (ttt180) cc_final: 0.7136 (ttt-90) REVERT: H 77 ASN cc_start: 0.6628 (m-40) cc_final: 0.6337 (m-40) REVERT: L 18 ARG cc_start: 0.8004 (mmm160) cc_final: 0.7793 (mtp-110) REVERT: L 74 THR cc_start: 0.7844 (m) cc_final: 0.7552 (t) REVERT: L 98 THR cc_start: 0.9079 (m) cc_final: 0.8767 (p) REVERT: I 34 MET cc_start: 0.1865 (pmm) cc_final: 0.1616 (pmm) REVERT: J 51 ILE cc_start: -0.1197 (OUTLIER) cc_final: -0.2166 (mt) REVERT: J 106 ILE cc_start: 0.5252 (OUTLIER) cc_final: 0.5000 (mm) outliers start: 178 outliers final: 87 residues processed: 382 average time/residue: 1.1589 time to fit residues: 543.7847 Evaluate side-chains 321 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 213 time to evaluate : 3.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 208 optimal weight: 3.9990 chunk 258 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 286 optimal weight: 0.6980 chunk 4 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 251 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 81 ASN B 218 GLN B 394 ASN B 440 ASN B1005 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.162809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.107807 restraints weight = 45531.832| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.64 r_work: 0.3100 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30480 Z= 0.170 Angle : 0.699 13.250 41599 Z= 0.339 Chirality : 0.049 0.522 4844 Planarity : 0.004 0.053 5256 Dihedral : 7.107 59.428 5461 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.10 % Favored : 93.73 % Rotamer: Outliers : 4.69 % Allowed : 23.66 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.14), residues: 3607 helix: 1.34 (0.21), residues: 655 sheet: -0.38 (0.16), residues: 1045 loop : -1.89 (0.13), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 94 HIS 0.016 0.001 HIS I 59 PHE 0.015 0.002 PHE B 86 TYR 0.018 0.001 TYR C1067 ARG 0.005 0.001 ARG M 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 48) link_NAG-ASN : angle 2.51858 ( 144) link_BETA1-4 : bond 0.00431 ( 23) link_BETA1-4 : angle 2.08331 ( 69) hydrogen bonds : bond 0.04294 ( 1002) hydrogen bonds : angle 5.20344 ( 2805) SS BOND : bond 0.00475 ( 45) SS BOND : angle 2.15238 ( 90) covalent geometry : bond 0.00410 (30364) covalent geometry : angle 0.67265 (41296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 225 time to evaluate : 3.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7107 (ttmt) cc_final: 0.6500 (tttt) REVERT: A 161 SER cc_start: 0.7480 (OUTLIER) cc_final: 0.6971 (t) REVERT: A 198 ASP cc_start: 0.8219 (m-30) cc_final: 0.7374 (p0) REVERT: A 202 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8520 (mtpp) REVERT: A 237 ARG cc_start: 0.7679 (mtp85) cc_final: 0.6958 (ttp-110) REVERT: A 269 TYR cc_start: 0.8103 (m-80) cc_final: 0.7863 (m-10) REVERT: A 304 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8439 (ttpt) REVERT: A 324 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7339 (pm20) REVERT: A 439 ASN cc_start: 0.7604 (t0) cc_final: 0.7079 (t0) REVERT: A 452 ARG cc_start: 0.5994 (OUTLIER) cc_final: 0.4652 (mtp85) REVERT: A 480 CYS cc_start: 0.1480 (OUTLIER) cc_final: 0.0912 (t) REVERT: A 529 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6085 (mtpt) REVERT: A 869 MET cc_start: 0.9103 (mtt) cc_final: 0.8870 (mtt) REVERT: B 280 ASN cc_start: 0.8213 (t0) cc_final: 0.7555 (t0) REVERT: B 331 ASN cc_start: 0.6747 (OUTLIER) cc_final: 0.5981 (m-40) REVERT: B 403 ARG cc_start: 0.8167 (ttp-170) cc_final: 0.7702 (ttp80) REVERT: B 787 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8269 (mt0) REVERT: B 811 LYS cc_start: 0.6984 (OUTLIER) cc_final: 0.6596 (mttt) REVERT: B 1113 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8524 (mt0) REVERT: C 122 ASN cc_start: 0.4732 (OUTLIER) cc_final: 0.4035 (m-40) REVERT: C 135 PHE cc_start: 0.6427 (m-80) cc_final: 0.6098 (m-80) REVERT: C 200 TYR cc_start: 0.7037 (OUTLIER) cc_final: 0.6258 (t80) REVERT: C 228 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8160 (t0) REVERT: C 340 GLU cc_start: 0.8691 (mp0) cc_final: 0.8261 (pm20) REVERT: C 402 ILE cc_start: 0.8732 (pt) cc_final: 0.8486 (pp) REVERT: C 487 ASN cc_start: 0.6698 (m-40) cc_final: 0.5748 (p0) REVERT: C 529 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8142 (ttpt) REVERT: C 534 VAL cc_start: 0.8688 (OUTLIER) cc_final: 0.8412 (m) REVERT: C 995 ARG cc_start: 0.8465 (mtp180) cc_final: 0.8204 (mtt-85) REVERT: H 19 ARG cc_start: 0.7763 (ttt180) cc_final: 0.7443 (ttt90) REVERT: L 18 ARG cc_start: 0.8064 (mmm160) cc_final: 0.7835 (mtp-110) REVERT: L 74 THR cc_start: 0.7802 (m) cc_final: 0.7477 (t) REVERT: L 98 THR cc_start: 0.9095 (m) cc_final: 0.8876 (p) REVERT: I 64 VAL cc_start: 0.4408 (t) cc_final: 0.4190 (p) REVERT: M 12 SER cc_start: 0.3454 (OUTLIER) cc_final: 0.3249 (t) REVERT: J 51 ILE cc_start: -0.0591 (OUTLIER) cc_final: -0.1586 (mt) REVERT: J 106 ILE cc_start: 0.5374 (OUTLIER) cc_final: 0.5139 (mm) outliers start: 150 outliers final: 82 residues processed: 348 average time/residue: 1.1023 time to fit residues: 476.7099 Evaluate side-chains 307 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 206 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 331 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 338 optimal weight: 9.9990 chunk 228 optimal weight: 10.0000 chunk 315 optimal weight: 0.6980 chunk 43 optimal weight: 9.9990 chunk 245 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 285 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 81 ASN B 121 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 188 ASN H 82 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN ** I 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.163087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.108439 restraints weight = 45321.571| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.57 r_work: 0.3122 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30480 Z= 0.135 Angle : 0.677 12.737 41599 Z= 0.327 Chirality : 0.048 0.497 4844 Planarity : 0.004 0.058 5256 Dihedral : 6.846 59.839 5457 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.35 % Favored : 93.48 % Rotamer: Outliers : 4.13 % Allowed : 24.38 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3607 helix: 1.56 (0.21), residues: 654 sheet: -0.40 (0.16), residues: 1052 loop : -1.77 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 33 HIS 0.005 0.001 HIS I 59 PHE 0.019 0.001 PHE C 133 TYR 0.018 0.001 TYR C1067 ARG 0.006 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 48) link_NAG-ASN : angle 2.39303 ( 144) link_BETA1-4 : bond 0.00440 ( 23) link_BETA1-4 : angle 2.02514 ( 69) hydrogen bonds : bond 0.03962 ( 1002) hydrogen bonds : angle 5.07902 ( 2805) SS BOND : bond 0.00444 ( 45) SS BOND : angle 1.90863 ( 90) covalent geometry : bond 0.00316 (30364) covalent geometry : angle 0.65353 (41296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 215 time to evaluate : 5.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7091 (ttmt) cc_final: 0.6273 (ttmm) REVERT: A 161 SER cc_start: 0.7372 (OUTLIER) cc_final: 0.6873 (t) REVERT: A 198 ASP cc_start: 0.8122 (m-30) cc_final: 0.7339 (p0) REVERT: A 202 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8518 (mttm) REVERT: A 237 ARG cc_start: 0.7614 (mtp85) cc_final: 0.6893 (ttp-110) REVERT: A 269 TYR cc_start: 0.8076 (m-80) cc_final: 0.7710 (m-10) REVERT: A 304 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8408 (ttpt) REVERT: A 324 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7276 (pm20) REVERT: A 439 ASN cc_start: 0.7545 (t0) cc_final: 0.7288 (t0) REVERT: A 452 ARG cc_start: 0.5915 (OUTLIER) cc_final: 0.4601 (mtp85) REVERT: A 480 CYS cc_start: 0.1477 (OUTLIER) cc_final: 0.0951 (t) REVERT: A 529 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6178 (mtpt) REVERT: A 869 MET cc_start: 0.9091 (mtt) cc_final: 0.8821 (mtt) REVERT: B 331 ASN cc_start: 0.6772 (OUTLIER) cc_final: 0.5978 (m-40) REVERT: B 452 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8240 (mtt180) REVERT: B 787 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8227 (mt0) REVERT: B 811 LYS cc_start: 0.6974 (OUTLIER) cc_final: 0.6579 (mttt) REVERT: C 95 THR cc_start: 0.8627 (p) cc_final: 0.8351 (p) REVERT: C 135 PHE cc_start: 0.6565 (m-80) cc_final: 0.6241 (m-80) REVERT: C 200 TYR cc_start: 0.6977 (OUTLIER) cc_final: 0.6188 (t80) REVERT: C 228 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8161 (t0) REVERT: C 340 GLU cc_start: 0.8655 (mp0) cc_final: 0.8099 (pm20) REVERT: C 402 ILE cc_start: 0.8684 (pt) cc_final: 0.8435 (pp) REVERT: C 487 ASN cc_start: 0.6611 (m-40) cc_final: 0.5679 (p0) REVERT: C 529 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8145 (ttpt) REVERT: H 11 LEU cc_start: 0.5968 (tm) cc_final: 0.5567 (mm) REVERT: H 19 ARG cc_start: 0.7756 (ttt180) cc_final: 0.7420 (ttt90) REVERT: L 18 ARG cc_start: 0.8084 (mmm160) cc_final: 0.7851 (mtp-110) REVERT: L 82 ASP cc_start: 0.8614 (m-30) cc_final: 0.8346 (m-30) REVERT: L 98 THR cc_start: 0.9121 (m) cc_final: 0.8900 (p) REVERT: I 64 VAL cc_start: 0.4320 (t) cc_final: 0.4103 (p) REVERT: I 106 ILE cc_start: 0.5444 (OUTLIER) cc_final: 0.5101 (tp) REVERT: J 51 ILE cc_start: -0.0501 (OUTLIER) cc_final: -0.1479 (mt) REVERT: J 90 ASP cc_start: 0.4494 (p0) cc_final: 0.4091 (OUTLIER) REVERT: J 106 ILE cc_start: 0.5374 (OUTLIER) cc_final: 0.5161 (mm) outliers start: 132 outliers final: 86 residues processed: 328 average time/residue: 1.6426 time to fit residues: 678.8970 Evaluate side-chains 300 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 198 time to evaluate : 4.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 159 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 273 optimal weight: 0.9990 chunk 69 optimal weight: 0.0030 chunk 116 optimal weight: 10.0000 chunk 358 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 221 optimal weight: 0.0970 chunk 236 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 804 GLN A1010 GLN A1142 GLN B 81 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.165216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113271 restraints weight = 45017.194| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.44 r_work: 0.3166 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 30480 Z= 0.108 Angle : 0.648 12.237 41599 Z= 0.314 Chirality : 0.046 0.465 4844 Planarity : 0.004 0.050 5256 Dihedral : 6.468 57.112 5455 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.68 % Favored : 94.18 % Rotamer: Outliers : 2.66 % Allowed : 25.91 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3607 helix: 1.82 (0.21), residues: 650 sheet: -0.32 (0.16), residues: 1054 loop : -1.60 (0.13), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 33 HIS 0.004 0.000 HIS I 59 PHE 0.022 0.001 PHE A 855 TYR 0.017 0.001 TYR B1067 ARG 0.007 0.000 ARG B 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 48) link_NAG-ASN : angle 2.18562 ( 144) link_BETA1-4 : bond 0.00518 ( 23) link_BETA1-4 : angle 1.88060 ( 69) hydrogen bonds : bond 0.03350 ( 1002) hydrogen bonds : angle 4.89867 ( 2805) SS BOND : bond 0.00405 ( 45) SS BOND : angle 1.81700 ( 90) covalent geometry : bond 0.00235 (30364) covalent geometry : angle 0.62687 (41296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 209 time to evaluate : 3.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7147 (ttmt) cc_final: 0.6488 (tttt) REVERT: A 198 ASP cc_start: 0.7898 (m-30) cc_final: 0.7229 (p0) REVERT: A 202 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8540 (mttm) REVERT: A 269 TYR cc_start: 0.8019 (m-80) cc_final: 0.7697 (m-10) REVERT: A 324 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7237 (pm20) REVERT: A 439 ASN cc_start: 0.7613 (t0) cc_final: 0.7337 (t0) REVERT: A 449 TYR cc_start: 0.5959 (OUTLIER) cc_final: 0.4317 (p90) REVERT: A 452 ARG cc_start: 0.6043 (OUTLIER) cc_final: 0.4711 (mtp85) REVERT: A 480 CYS cc_start: 0.1406 (OUTLIER) cc_final: 0.0928 (t) REVERT: A 529 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6180 (mtpt) REVERT: A 869 MET cc_start: 0.9016 (mtt) cc_final: 0.8766 (mtt) REVERT: B 52 GLN cc_start: 0.8148 (tp40) cc_final: 0.7797 (tp-100) REVERT: B 280 ASN cc_start: 0.8178 (t0) cc_final: 0.7556 (t0) REVERT: B 331 ASN cc_start: 0.6770 (OUTLIER) cc_final: 0.6058 (m-40) REVERT: B 787 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8203 (mt0) REVERT: B 811 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6752 (mttt) REVERT: B 1113 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8506 (mt0) REVERT: C 95 THR cc_start: 0.8649 (p) cc_final: 0.8370 (p) REVERT: C 135 PHE cc_start: 0.6576 (m-80) cc_final: 0.6336 (m-80) REVERT: C 200 TYR cc_start: 0.6985 (OUTLIER) cc_final: 0.6320 (t80) REVERT: C 228 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8215 (t0) REVERT: C 340 GLU cc_start: 0.8633 (mp0) cc_final: 0.8113 (pm20) REVERT: C 487 ASN cc_start: 0.6606 (m-40) cc_final: 0.5658 (p0) REVERT: C 523 THR cc_start: 0.5239 (OUTLIER) cc_final: 0.4852 (p) REVERT: C 534 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8432 (m) REVERT: C 776 LYS cc_start: 0.9127 (ttmm) cc_final: 0.8885 (tttm) REVERT: H 11 LEU cc_start: 0.6136 (tm) cc_final: 0.5699 (mm) REVERT: H 19 ARG cc_start: 0.7822 (ttt180) cc_final: 0.7513 (ttt90) REVERT: L 18 ARG cc_start: 0.8102 (mmm160) cc_final: 0.7869 (mtp-110) REVERT: L 48 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8293 (mt) REVERT: L 82 ASP cc_start: 0.8695 (m-30) cc_final: 0.8395 (m-30) REVERT: I 39 GLN cc_start: 0.2251 (tt0) cc_final: 0.2008 (mp-120) REVERT: J 51 ILE cc_start: -0.0534 (OUTLIER) cc_final: -0.1528 (mt) REVERT: J 67 ARG cc_start: 0.6871 (ttp-170) cc_final: 0.6596 (ttt-90) REVERT: J 83 MET cc_start: 0.6036 (pmm) cc_final: 0.5332 (mpp) REVERT: J 84 ASN cc_start: 0.5855 (m-40) cc_final: 0.4877 (p0) REVERT: J 106 ILE cc_start: 0.5390 (OUTLIER) cc_final: 0.5176 (mm) outliers start: 85 outliers final: 52 residues processed: 285 average time/residue: 1.1234 time to fit residues: 398.9432 Evaluate side-chains 265 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 196 time to evaluate : 3.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 15 optimal weight: 6.9990 chunk 219 optimal weight: 0.7980 chunk 157 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 341 optimal weight: 7.9990 chunk 241 optimal weight: 0.0980 chunk 134 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 955 ASN A1010 GLN B 81 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B1005 GLN H 82 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.160106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.106521 restraints weight = 45201.807| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.61 r_work: 0.3072 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 30480 Z= 0.235 Angle : 0.757 14.532 41599 Z= 0.369 Chirality : 0.052 0.526 4844 Planarity : 0.005 0.055 5256 Dihedral : 7.008 59.034 5455 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.18 % Favored : 92.68 % Rotamer: Outliers : 2.91 % Allowed : 25.95 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.14), residues: 3607 helix: 1.39 (0.21), residues: 649 sheet: -0.41 (0.16), residues: 1045 loop : -1.74 (0.13), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 33 HIS 0.005 0.001 HIS I 59 PHE 0.023 0.002 PHE B 43 TYR 0.023 0.002 TYR C1067 ARG 0.009 0.001 ARG B 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00431 ( 48) link_NAG-ASN : angle 2.70453 ( 144) link_BETA1-4 : bond 0.00454 ( 23) link_BETA1-4 : angle 2.22601 ( 69) hydrogen bonds : bond 0.05179 ( 1002) hydrogen bonds : angle 5.33602 ( 2805) SS BOND : bond 0.00556 ( 45) SS BOND : angle 2.30146 ( 90) covalent geometry : bond 0.00577 (30364) covalent geometry : angle 0.72977 (41296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 216 time to evaluate : 3.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7134 (ttmt) cc_final: 0.6521 (tttt) REVERT: A 198 ASP cc_start: 0.8219 (m-30) cc_final: 0.7412 (p0) REVERT: A 202 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8528 (mttm) REVERT: A 237 ARG cc_start: 0.7727 (mtp85) cc_final: 0.7033 (ttp-110) REVERT: A 269 TYR cc_start: 0.8077 (m-80) cc_final: 0.7810 (m-10) REVERT: A 324 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7247 (pm20) REVERT: A 439 ASN cc_start: 0.7590 (t0) cc_final: 0.7380 (t0) REVERT: A 444 LYS cc_start: 0.4952 (pttt) cc_final: 0.3796 (tmtm) REVERT: A 452 ARG cc_start: 0.5889 (OUTLIER) cc_final: 0.4495 (mtp85) REVERT: A 480 CYS cc_start: 0.1463 (OUTLIER) cc_final: 0.0921 (t) REVERT: A 529 LYS cc_start: 0.7104 (OUTLIER) cc_final: 0.6133 (mtpt) REVERT: A 787 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8873 (mt0) REVERT: A 869 MET cc_start: 0.9188 (mtt) cc_final: 0.8951 (mtt) REVERT: B 324 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7779 (pm20) REVERT: B 331 ASN cc_start: 0.6879 (OUTLIER) cc_final: 0.6195 (m-40) REVERT: B 421 TYR cc_start: 0.7781 (p90) cc_final: 0.7548 (p90) REVERT: B 787 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8306 (mt0) REVERT: B 811 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6651 (mttt) REVERT: B 1113 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8505 (mt0) REVERT: C 95 THR cc_start: 0.8677 (p) cc_final: 0.8393 (p) REVERT: C 200 TYR cc_start: 0.7101 (OUTLIER) cc_final: 0.6724 (t80) REVERT: C 325 SER cc_start: 0.9058 (OUTLIER) cc_final: 0.8814 (p) REVERT: C 340 GLU cc_start: 0.8716 (mp0) cc_final: 0.8120 (pm20) REVERT: C 402 ILE cc_start: 0.8750 (pt) cc_final: 0.8548 (pp) REVERT: C 487 ASN cc_start: 0.6614 (m-40) cc_final: 0.5664 (p0) REVERT: C 523 THR cc_start: 0.5271 (OUTLIER) cc_final: 0.4976 (p) REVERT: C 529 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8087 (ttpt) REVERT: C 995 ARG cc_start: 0.8552 (mtp180) cc_final: 0.8286 (mtt-85) REVERT: H 11 LEU cc_start: 0.6425 (tm) cc_final: 0.5837 (mm) REVERT: H 19 ARG cc_start: 0.7922 (ttt180) cc_final: 0.6809 (ttt90) REVERT: H 82 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6594 (tp40) REVERT: L 18 ARG cc_start: 0.8024 (mmm160) cc_final: 0.7803 (mtp-110) REVERT: L 38 GLN cc_start: 0.8348 (tp-100) cc_final: 0.7986 (tm-30) REVERT: L 81 GLU cc_start: 0.7297 (pt0) cc_final: 0.6892 (pp20) REVERT: I 39 GLN cc_start: 0.2481 (tt0) cc_final: 0.1991 (mp-120) REVERT: M 31 ASN cc_start: 0.6342 (t0) cc_final: 0.5976 (t0) REVERT: J 67 ARG cc_start: 0.6724 (ttp-170) cc_final: 0.6316 (ttt-90) REVERT: J 83 MET cc_start: 0.5892 (pmm) cc_final: 0.5287 (mpp) REVERT: J 84 ASN cc_start: 0.5855 (m-40) cc_final: 0.4928 (p0) outliers start: 93 outliers final: 60 residues processed: 298 average time/residue: 1.1061 time to fit residues: 404.8262 Evaluate side-chains 279 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 203 time to evaluate : 3.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 120 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 355 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 299 optimal weight: 3.9990 chunk 329 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 190 optimal weight: 0.9980 chunk 152 optimal weight: 9.9990 chunk 269 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN A1142 GLN B 81 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B1005 GLN C 99 ASN C1002 GLN H 82 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.162822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.109843 restraints weight = 44927.566| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.49 r_work: 0.3109 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30480 Z= 0.123 Angle : 0.681 13.780 41599 Z= 0.331 Chirality : 0.048 0.503 4844 Planarity : 0.004 0.053 5256 Dihedral : 6.691 59.405 5455 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.91 % Favored : 93.96 % Rotamer: Outliers : 2.75 % Allowed : 26.20 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.14), residues: 3607 helix: 1.65 (0.21), residues: 648 sheet: -0.28 (0.16), residues: 1073 loop : -1.71 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 33 HIS 0.002 0.001 HIS B1064 PHE 0.016 0.001 PHE I 68 TYR 0.022 0.001 TYR B 396 ARG 0.010 0.000 ARG B 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 48) link_NAG-ASN : angle 2.37850 ( 144) link_BETA1-4 : bond 0.00480 ( 23) link_BETA1-4 : angle 1.99928 ( 69) hydrogen bonds : bond 0.03990 ( 1002) hydrogen bonds : angle 5.10333 ( 2805) SS BOND : bond 0.00419 ( 45) SS BOND : angle 1.83869 ( 90) covalent geometry : bond 0.00277 (30364) covalent geometry : angle 0.65862 (41296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28194.59 seconds wall clock time: 492 minutes 39.93 seconds (29559.93 seconds total)