Starting phenix.real_space_refine on Sun Jun 22 04:33:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sxu_25506/06_2025/7sxu_25506.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sxu_25506/06_2025/7sxu_25506.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/7sxu_25506/06_2025/7sxu_25506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sxu_25506/06_2025/7sxu_25506.map" model { file = "/net/cci-nas-00/data/ceres_data/7sxu_25506/06_2025/7sxu_25506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sxu_25506/06_2025/7sxu_25506.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= 0.001 sd= 0.029 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 111 5.16 5 C 16077 2.51 5 N 4128 2.21 5 O 4932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25248 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8136 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8136 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8136 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 14.77, per 1000 atoms: 0.58 Number of scatterers: 25248 At special positions: 0 Unit cell: (140, 145, 197, 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 111 16.00 O 4932 8.00 N 4128 7.00 C 16077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 17 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 17 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 5.74 Conformation dependent library (CDL) restraints added in 3.0 seconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 51 sheets defined 24.7% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.70 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.065A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.667A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.483A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.146A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.684A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.904A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.527A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.013A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.616A 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 337 through 343 removed outlier: 3.987A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.759A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.932A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.615A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.020A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.596A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.680A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.899A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.542A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.992A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.625A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.727A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.657A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.888A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.563A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.942A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.667A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.994A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.584A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.298A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.545A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.022A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.563A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.937A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.600A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.076A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.205A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.600A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.880A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.987A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.999A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.566A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.990A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.861A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.620A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.620A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.238A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.687A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.333A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.055A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.744A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 154 through 163 removed outlier: 5.107A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.064A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 10.290A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.913A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.627A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.566A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.929A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.695A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.982A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.686A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.583A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.583A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.253A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.281A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.114A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.915A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 154 through 163 removed outlier: 9.790A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.834A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 10.228A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.780A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS C 136 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.205A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.731A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.796A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.728A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.172A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.173A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 1095 hydrogen bonds defined for protein. 3009 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: 11.40 Time building geometry restraints manager: 6.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7418 1.34 - 1.46: 6223 1.46 - 1.58: 12039 1.58 - 1.70: 0 1.70 - 1.83: 138 Bond restraints: 25818 Sorted by residual: bond pdb=" C LEU C 560 " pdb=" N PRO C 561 " ideal model delta sigma weight residual 1.334 1.386 -0.052 1.51e-02 4.39e+03 1.17e+01 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.88e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.42e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.04e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.68e+00 ... (remaining 25813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 34049 2.01 - 4.03: 983 4.03 - 6.04: 80 6.04 - 8.05: 22 8.05 - 10.07: 8 Bond angle restraints: 35142 Sorted by residual: angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.23 -5.53 1.22e+00 6.72e-01 2.05e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.11 -5.41 1.22e+00 6.72e-01 1.97e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.90 -5.20 1.22e+00 6.72e-01 1.82e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 122.01 -7.91 2.00e+00 2.50e-01 1.56e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.57 -4.64 1.20e+00 6.94e-01 1.50e+01 ... (remaining 35137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14916 17.99 - 35.98: 1016 35.98 - 53.97: 156 53.97 - 71.96: 59 71.96 - 89.95: 29 Dihedral angle restraints: 16176 sinusoidal: 7095 harmonic: 9081 Sorted by residual: dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 154.25 25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA LEU B 517 " pdb=" C LEU B 517 " pdb=" N LEU B 518 " pdb=" CA LEU B 518 " ideal model delta harmonic sigma weight residual 180.00 154.30 25.70 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA PHE C 515 " pdb=" C PHE C 515 " pdb=" N GLU C 516 " pdb=" CA GLU C 516 " ideal model delta harmonic sigma weight residual 180.00 157.21 22.79 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 16173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3354 0.067 - 0.135: 742 0.135 - 0.202: 54 0.202 - 0.270: 5 0.270 - 0.337: 3 Chirality restraints: 4158 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 4155 not shown) Planarity restraints: 4515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 902 " -0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C MET C 902 " 0.058 2.00e-02 2.50e+03 pdb=" O MET C 902 " -0.022 2.00e-02 2.50e+03 pdb=" N ALA C 903 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 920 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.02e+00 pdb=" C GLN C 920 " 0.049 2.00e-02 2.50e+03 pdb=" O GLN C 920 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS C 921 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A1029 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.80e+00 pdb=" C MET A1029 " 0.048 2.00e-02 2.50e+03 pdb=" O MET A1029 " -0.018 2.00e-02 2.50e+03 pdb=" N SER A1030 " -0.016 2.00e-02 2.50e+03 ... (remaining 4512 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 6631 2.81 - 3.33: 20888 3.33 - 3.85: 42695 3.85 - 4.38: 48962 4.38 - 4.90: 84078 Nonbonded interactions: 203254 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.284 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.294 3.040 nonbonded pdb=" O ASP B 80 " pdb=" OH TYR B 265 " model vdw 2.304 3.040 nonbonded pdb=" O ASP A 80 " pdb=" OH TYR A 265 " model vdw 2.307 3.040 nonbonded pdb=" OD1 ASN B 394 " pdb=" OH TYR B 396 " model vdw 2.307 3.040 ... (remaining 203249 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 4.310 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: 0.910 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 57.130 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 25920 Z= 0.223 Angle : 0.793 15.258 35406 Z= 0.409 Chirality : 0.053 0.337 4158 Planarity : 0.007 0.067 4473 Dihedral : 12.884 89.952 10206 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 3072 helix: 0.20 (0.18), residues: 647 sheet: 0.18 (0.19), residues: 679 loop : -0.89 (0.13), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 886 HIS 0.003 0.001 HIS B 655 PHE 0.034 0.002 PHE B 135 TYR 0.026 0.002 TYR A 200 ARG 0.015 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00776 ( 42) link_NAG-ASN : angle 3.42284 ( 126) link_BETA1-4 : bond 0.00682 ( 18) link_BETA1-4 : angle 1.27439 ( 54) hydrogen bonds : bond 0.16944 ( 1030) hydrogen bonds : angle 8.03069 ( 3009) SS BOND : bond 0.00249 ( 42) SS BOND : angle 1.33171 ( 84) covalent geometry : bond 0.00464 (25818) covalent geometry : angle 0.76460 (35142) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 985 ASP cc_start: 0.8072 (m-30) cc_final: 0.7417 (m-30) REVERT: A 1002 GLN cc_start: 0.8560 (tt0) cc_final: 0.8301 (tm-30) REVERT: B 54 LEU cc_start: 0.8850 (mm) cc_final: 0.8618 (mm) REVERT: B 104 TRP cc_start: 0.7332 (m-90) cc_final: 0.6994 (m-90) REVERT: B 304 LYS cc_start: 0.9372 (mmtm) cc_final: 0.9105 (mmmm) REVERT: B 779 GLN cc_start: 0.8615 (tp40) cc_final: 0.8301 (tm-30) REVERT: B 858 LEU cc_start: 0.8629 (mt) cc_final: 0.8296 (pt) REVERT: B 985 ASP cc_start: 0.7916 (p0) cc_final: 0.7565 (p0) REVERT: C 189 LEU cc_start: 0.7531 (tp) cc_final: 0.6897 (tt) REVERT: C 217 PRO cc_start: 0.8010 (Cg_endo) cc_final: 0.7688 (Cg_exo) REVERT: C 277 LEU cc_start: 0.7898 (mm) cc_final: 0.7657 (mp) REVERT: C 279 TYR cc_start: 0.6049 (m-80) cc_final: 0.5617 (m-10) REVERT: C 378 LYS cc_start: 0.8905 (ttmt) cc_final: 0.8684 (ptmm) REVERT: C 453 TYR cc_start: 0.7437 (p90) cc_final: 0.7207 (p90) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 1.3124 time to fit residues: 374.3435 Evaluate side-chains 113 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.8980 chunk 236 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 148 optimal weight: 20.0000 chunk 182 optimal weight: 2.9990 chunk 283 optimal weight: 0.0070 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 188 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN B1005 GLN C 49 HIS C 388 ASN C 394 ASN C 762 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.131171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.083340 restraints weight = 70180.679| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 4.35 r_work: 0.3122 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25920 Z= 0.185 Angle : 0.621 12.666 35406 Z= 0.312 Chirality : 0.046 0.286 4158 Planarity : 0.005 0.051 4473 Dihedral : 6.423 55.556 4605 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.99 % Allowed : 6.22 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.14), residues: 3072 helix: 1.49 (0.20), residues: 688 sheet: 0.16 (0.20), residues: 656 loop : -0.65 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 104 HIS 0.004 0.001 HIS C 49 PHE 0.019 0.001 PHE A 275 TYR 0.018 0.001 TYR C1067 ARG 0.007 0.001 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00548 ( 42) link_NAG-ASN : angle 2.97355 ( 126) link_BETA1-4 : bond 0.00242 ( 18) link_BETA1-4 : angle 1.14912 ( 54) hydrogen bonds : bond 0.04460 ( 1030) hydrogen bonds : angle 6.11060 ( 3009) SS BOND : bond 0.00197 ( 42) SS BOND : angle 0.76780 ( 84) covalent geometry : bond 0.00410 (25818) covalent geometry : angle 0.59424 (35142) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 2.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 950 ASP cc_start: 0.8768 (m-30) cc_final: 0.8546 (m-30) REVERT: A 979 ASP cc_start: 0.8965 (m-30) cc_final: 0.8726 (t0) REVERT: A 985 ASP cc_start: 0.8331 (m-30) cc_final: 0.7700 (m-30) REVERT: A 988 GLU cc_start: 0.8590 (pm20) cc_final: 0.8188 (pm20) REVERT: A 1002 GLN cc_start: 0.9150 (tt0) cc_final: 0.8690 (tm-30) REVERT: B 104 TRP cc_start: 0.7747 (m-90) cc_final: 0.7531 (m-90) REVERT: B 567 ARG cc_start: 0.3100 (pmt-80) cc_final: 0.2686 (pmt-80) REVERT: B 725 GLU cc_start: 0.8959 (tt0) cc_final: 0.8732 (tt0) REVERT: B 780 GLU cc_start: 0.8793 (mp0) cc_final: 0.8591 (mp0) REVERT: B 858 LEU cc_start: 0.9021 (mt) cc_final: 0.8462 (pt) REVERT: C 258 TRP cc_start: 0.1483 (p-90) cc_final: 0.1182 (p90) REVERT: C 392 PHE cc_start: 0.8096 (m-10) cc_final: 0.7800 (m-10) REVERT: C 400 PHE cc_start: 0.8828 (p90) cc_final: 0.8550 (OUTLIER) REVERT: C 453 TYR cc_start: 0.6742 (p90) cc_final: 0.6503 (p90) REVERT: C 512 VAL cc_start: 0.8061 (t) cc_final: 0.7827 (p) outliers start: 27 outliers final: 7 residues processed: 157 average time/residue: 1.1896 time to fit residues: 224.3943 Evaluate side-chains 113 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 194 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 chunk 309 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 166 optimal weight: 0.3980 chunk 123 optimal weight: 10.0000 chunk 281 optimal weight: 4.9990 chunk 172 optimal weight: 0.5980 chunk 245 optimal weight: 0.0670 chunk 175 optimal weight: 0.0170 chunk 163 optimal weight: 3.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.131484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.082211 restraints weight = 71392.212| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 5.14 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25920 Z= 0.112 Angle : 0.551 11.656 35406 Z= 0.277 Chirality : 0.045 0.330 4158 Planarity : 0.004 0.053 4473 Dihedral : 5.806 53.958 4605 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.21 % Allowed : 7.98 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 3072 helix: 1.92 (0.20), residues: 696 sheet: 0.40 (0.19), residues: 677 loop : -0.58 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 104 HIS 0.002 0.000 HIS B1048 PHE 0.021 0.001 PHE B 140 TYR 0.020 0.001 TYR B1067 ARG 0.004 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00665 ( 42) link_NAG-ASN : angle 2.76926 ( 126) link_BETA1-4 : bond 0.00332 ( 18) link_BETA1-4 : angle 1.03709 ( 54) hydrogen bonds : bond 0.03985 ( 1030) hydrogen bonds : angle 5.68766 ( 3009) SS BOND : bond 0.00129 ( 42) SS BOND : angle 0.63271 ( 84) covalent geometry : bond 0.00242 (25818) covalent geometry : angle 0.52533 (35142) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 4.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.6968 (m-10) REVERT: A 950 ASP cc_start: 0.8529 (m-30) cc_final: 0.8187 (m-30) REVERT: A 985 ASP cc_start: 0.8195 (m-30) cc_final: 0.7541 (m-30) REVERT: A 988 GLU cc_start: 0.8583 (pm20) cc_final: 0.8177 (pm20) REVERT: A 1002 GLN cc_start: 0.8723 (tt0) cc_final: 0.8422 (tm-30) REVERT: B 118 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8244 (pt) REVERT: B 567 ARG cc_start: 0.2634 (pmt-80) cc_final: 0.2378 (pmt-80) REVERT: B 725 GLU cc_start: 0.8336 (tt0) cc_final: 0.8092 (tt0) REVERT: B 780 GLU cc_start: 0.8147 (mp0) cc_final: 0.7890 (mp0) REVERT: B 858 LEU cc_start: 0.9044 (mt) cc_final: 0.8494 (pt) REVERT: C 204 TYR cc_start: 0.6641 (m-80) cc_final: 0.5759 (m-80) REVERT: C 285 ILE cc_start: 0.7642 (mt) cc_final: 0.7434 (mp) REVERT: C 400 PHE cc_start: 0.8932 (p90) cc_final: 0.8582 (p90) REVERT: C 512 VAL cc_start: 0.8547 (t) cc_final: 0.8316 (m) REVERT: C 773 GLU cc_start: 0.8595 (tt0) cc_final: 0.8379 (tt0) REVERT: C 950 ASP cc_start: 0.8943 (m-30) cc_final: 0.8681 (m-30) outliers start: 33 outliers final: 10 residues processed: 144 average time/residue: 2.0179 time to fit residues: 353.0920 Evaluate side-chains 118 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 4.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 163 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 148 optimal weight: 0.2980 chunk 156 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 284 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN B 787 GLN B 824 ASN B1005 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 872 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.128006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.080751 restraints weight = 71603.389| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 4.22 r_work: 0.3046 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25920 Z= 0.226 Angle : 0.605 11.671 35406 Z= 0.304 Chirality : 0.046 0.317 4158 Planarity : 0.004 0.064 4473 Dihedral : 5.529 54.626 4605 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.24 % Allowed : 8.49 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 3072 helix: 1.94 (0.20), residues: 700 sheet: 0.12 (0.19), residues: 681 loop : -0.57 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 104 HIS 0.008 0.001 HIS C 49 PHE 0.022 0.002 PHE B 140 TYR 0.028 0.001 TYR C 453 ARG 0.007 0.001 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00653 ( 42) link_NAG-ASN : angle 2.81501 ( 126) link_BETA1-4 : bond 0.00222 ( 18) link_BETA1-4 : angle 1.25177 ( 54) hydrogen bonds : bond 0.04392 ( 1030) hydrogen bonds : angle 5.64468 ( 3009) SS BOND : bond 0.00182 ( 42) SS BOND : angle 0.70360 ( 84) covalent geometry : bond 0.00505 (25818) covalent geometry : angle 0.58058 (35142) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 2.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.7206 (m-10) REVERT: A 762 GLN cc_start: 0.8942 (mt0) cc_final: 0.8679 (mt0) REVERT: A 950 ASP cc_start: 0.8911 (m-30) cc_final: 0.8558 (m-30) REVERT: A 985 ASP cc_start: 0.8373 (m-30) cc_final: 0.7664 (m-30) REVERT: A 988 GLU cc_start: 0.8811 (pm20) cc_final: 0.8405 (pm20) REVERT: A 1002 GLN cc_start: 0.9124 (tt0) cc_final: 0.8788 (tm-30) REVERT: A 1010 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8385 (mp10) REVERT: B 240 THR cc_start: 0.6509 (m) cc_final: 0.6175 (t) REVERT: B 304 LYS cc_start: 0.9428 (mmmm) cc_final: 0.9215 (mmmm) REVERT: B 779 GLN cc_start: 0.9155 (tp40) cc_final: 0.8659 (tm-30) REVERT: B 780 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8625 (mp0) REVERT: C 204 TYR cc_start: 0.6879 (m-80) cc_final: 0.6033 (m-80) REVERT: C 258 TRP cc_start: 0.1815 (p-90) cc_final: 0.1388 (p90) REVERT: C 378 LYS cc_start: 0.8576 (ttmm) cc_final: 0.8282 (tmtm) REVERT: C 400 PHE cc_start: 0.9139 (p90) cc_final: 0.8747 (p90) outliers start: 34 outliers final: 11 residues processed: 142 average time/residue: 1.2175 time to fit residues: 206.7591 Evaluate side-chains 120 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 246 optimal weight: 5.9990 chunk 162 optimal weight: 0.0970 chunk 78 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 277 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 46 optimal weight: 50.0000 chunk 152 optimal weight: 0.9990 chunk 254 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.128117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.083008 restraints weight = 72891.498| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.84 r_work: 0.3080 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25920 Z= 0.160 Angle : 0.563 11.421 35406 Z= 0.282 Chirality : 0.045 0.317 4158 Planarity : 0.004 0.059 4473 Dihedral : 5.191 53.002 4605 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.24 % Allowed : 9.11 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 3072 helix: 2.12 (0.20), residues: 698 sheet: 0.15 (0.19), residues: 680 loop : -0.55 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 104 HIS 0.009 0.001 HIS C 49 PHE 0.024 0.001 PHE B 140 TYR 0.020 0.001 TYR B1067 ARG 0.006 0.000 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 42) link_NAG-ASN : angle 2.69571 ( 126) link_BETA1-4 : bond 0.00266 ( 18) link_BETA1-4 : angle 1.02998 ( 54) hydrogen bonds : bond 0.04004 ( 1030) hydrogen bonds : angle 5.48036 ( 3009) SS BOND : bond 0.00124 ( 42) SS BOND : angle 0.60020 ( 84) covalent geometry : bond 0.00357 (25818) covalent geometry : angle 0.53965 (35142) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 2.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7432 (OUTLIER) cc_final: 0.7219 (m-10) REVERT: A 762 GLN cc_start: 0.8888 (mt0) cc_final: 0.8594 (mt0) REVERT: A 950 ASP cc_start: 0.8969 (m-30) cc_final: 0.8585 (m-30) REVERT: A 985 ASP cc_start: 0.8174 (m-30) cc_final: 0.7481 (m-30) REVERT: A 988 GLU cc_start: 0.8659 (pm20) cc_final: 0.8266 (pm20) REVERT: A 1002 GLN cc_start: 0.9164 (tt0) cc_final: 0.8672 (tm-30) REVERT: A 1010 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8374 (mp10) REVERT: B 118 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8272 (pt) REVERT: B 240 THR cc_start: 0.6496 (m) cc_final: 0.6080 (t) REVERT: B 304 LYS cc_start: 0.9324 (mmmm) cc_final: 0.9112 (mmmm) REVERT: B 697 MET cc_start: 0.8985 (ttm) cc_final: 0.8757 (ttm) REVERT: B 725 GLU cc_start: 0.9013 (tt0) cc_final: 0.8800 (tt0) REVERT: B 779 GLN cc_start: 0.9101 (tp40) cc_final: 0.8537 (tm-30) REVERT: B 780 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8492 (mp0) REVERT: C 204 TYR cc_start: 0.6697 (m-80) cc_final: 0.5893 (m-80) REVERT: C 258 TRP cc_start: 0.1707 (p-90) cc_final: 0.1334 (p90) REVERT: C 400 PHE cc_start: 0.9079 (p90) cc_final: 0.8854 (p90) REVERT: C 755 GLN cc_start: 0.8948 (mm110) cc_final: 0.8640 (mm-40) outliers start: 34 outliers final: 8 residues processed: 131 average time/residue: 1.6258 time to fit residues: 252.4571 Evaluate side-chains 112 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 2.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 993 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 42 optimal weight: 40.0000 chunk 135 optimal weight: 4.9990 chunk 144 optimal weight: 0.0010 chunk 140 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 chunk 306 optimal weight: 0.8980 chunk 255 optimal weight: 10.0000 chunk 196 optimal weight: 0.8980 chunk 227 optimal weight: 0.5980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN B1005 GLN C 121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.129992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.084316 restraints weight = 71609.272| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 4.02 r_work: 0.3097 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25920 Z= 0.113 Angle : 0.540 11.283 35406 Z= 0.270 Chirality : 0.044 0.321 4158 Planarity : 0.004 0.063 4473 Dihedral : 4.800 53.662 4605 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.10 % Allowed : 10.10 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.15), residues: 3072 helix: 2.21 (0.20), residues: 699 sheet: 0.20 (0.19), residues: 691 loop : -0.47 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 104 HIS 0.001 0.000 HIS A 655 PHE 0.025 0.001 PHE B 140 TYR 0.020 0.001 TYR B1067 ARG 0.004 0.000 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00558 ( 42) link_NAG-ASN : angle 2.58417 ( 126) link_BETA1-4 : bond 0.00283 ( 18) link_BETA1-4 : angle 0.95523 ( 54) hydrogen bonds : bond 0.03707 ( 1030) hydrogen bonds : angle 5.26134 ( 3009) SS BOND : bond 0.00112 ( 42) SS BOND : angle 0.54762 ( 84) covalent geometry : bond 0.00248 (25818) covalent geometry : angle 0.51754 (35142) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 2.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 GLN cc_start: 0.8884 (mt0) cc_final: 0.8536 (mt0) REVERT: A 950 ASP cc_start: 0.9020 (m-30) cc_final: 0.8687 (m-30) REVERT: A 957 GLN cc_start: 0.8797 (tm-30) cc_final: 0.8594 (tm-30) REVERT: A 985 ASP cc_start: 0.8183 (m-30) cc_final: 0.7454 (m-30) REVERT: A 988 GLU cc_start: 0.8657 (pm20) cc_final: 0.8208 (pm20) REVERT: A 1002 GLN cc_start: 0.9136 (tt0) cc_final: 0.8621 (tm-30) REVERT: A 1010 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8379 (mp10) REVERT: B 118 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8274 (pt) REVERT: B 240 THR cc_start: 0.6373 (m) cc_final: 0.6044 (t) REVERT: B 304 LYS cc_start: 0.9374 (mmmm) cc_final: 0.9148 (mmmm) REVERT: B 776 LYS cc_start: 0.9168 (tttm) cc_final: 0.8811 (tmmt) REVERT: B 779 GLN cc_start: 0.9108 (tp40) cc_final: 0.8418 (tm-30) REVERT: B 780 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: C 49 HIS cc_start: 0.7986 (m-70) cc_final: 0.7662 (m-70) REVERT: C 204 TYR cc_start: 0.6685 (m-80) cc_final: 0.5944 (m-80) REVERT: C 258 TRP cc_start: 0.1856 (p-90) cc_final: 0.1399 (p90) REVERT: C 400 PHE cc_start: 0.9165 (p90) cc_final: 0.8946 (p90) REVERT: C 584 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8519 (mm) REVERT: C 755 GLN cc_start: 0.8915 (mm110) cc_final: 0.8647 (mm-40) REVERT: C 773 GLU cc_start: 0.8933 (tt0) cc_final: 0.8686 (tt0) outliers start: 30 outliers final: 5 residues processed: 130 average time/residue: 1.3268 time to fit residues: 203.5522 Evaluate side-chains 115 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 155 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 286 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 267 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 35 optimal weight: 50.0000 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.127977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.081861 restraints weight = 73035.065| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.87 r_work: 0.3053 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25920 Z= 0.196 Angle : 0.578 10.791 35406 Z= 0.290 Chirality : 0.045 0.302 4158 Planarity : 0.004 0.059 4473 Dihedral : 4.802 52.688 4605 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.84 % Allowed : 10.94 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 3072 helix: 2.24 (0.20), residues: 700 sheet: 0.18 (0.19), residues: 673 loop : -0.53 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 104 HIS 0.004 0.001 HIS C 49 PHE 0.018 0.001 PHE C 392 TYR 0.024 0.001 TYR A 200 ARG 0.005 0.000 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00611 ( 42) link_NAG-ASN : angle 2.62697 ( 126) link_BETA1-4 : bond 0.00223 ( 18) link_BETA1-4 : angle 1.09573 ( 54) hydrogen bonds : bond 0.03997 ( 1030) hydrogen bonds : angle 5.33616 ( 3009) SS BOND : bond 0.00131 ( 42) SS BOND : angle 0.60455 ( 84) covalent geometry : bond 0.00439 (25818) covalent geometry : angle 0.55637 (35142) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 GLN cc_start: 0.8925 (mt0) cc_final: 0.8622 (mt0) REVERT: A 950 ASP cc_start: 0.8978 (m-30) cc_final: 0.8585 (m-30) REVERT: A 957 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8590 (tm-30) REVERT: A 985 ASP cc_start: 0.8173 (m-30) cc_final: 0.7459 (m-30) REVERT: A 988 GLU cc_start: 0.8674 (pm20) cc_final: 0.8237 (pm20) REVERT: A 1002 GLN cc_start: 0.9163 (tt0) cc_final: 0.8695 (tm-30) REVERT: A 1010 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8379 (mp10) REVERT: B 118 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8297 (pt) REVERT: B 240 THR cc_start: 0.6336 (m) cc_final: 0.5968 (t) REVERT: B 304 LYS cc_start: 0.9357 (mmmm) cc_final: 0.9126 (mmmm) REVERT: B 776 LYS cc_start: 0.9149 (tttm) cc_final: 0.8815 (tmmt) REVERT: B 779 GLN cc_start: 0.9103 (tp40) cc_final: 0.8405 (tm-30) REVERT: B 780 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8440 (mp0) REVERT: C 400 PHE cc_start: 0.9208 (p90) cc_final: 0.8967 (p90) REVERT: C 505 TYR cc_start: 0.7949 (t80) cc_final: 0.7618 (t80) REVERT: C 773 GLU cc_start: 0.8951 (tt0) cc_final: 0.8750 (tt0) outliers start: 23 outliers final: 11 residues processed: 119 average time/residue: 1.2156 time to fit residues: 173.3397 Evaluate side-chains 110 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 48 optimal weight: 9.9990 chunk 297 optimal weight: 0.6980 chunk 219 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 280 optimal weight: 0.8980 chunk 204 optimal weight: 1.9990 chunk 146 optimal weight: 0.0000 chunk 184 optimal weight: 0.7980 chunk 78 optimal weight: 0.3980 chunk 272 optimal weight: 2.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.129508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.083750 restraints weight = 71223.847| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.98 r_work: 0.3090 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25920 Z= 0.108 Angle : 0.544 12.294 35406 Z= 0.273 Chirality : 0.044 0.308 4158 Planarity : 0.004 0.062 4473 Dihedral : 4.646 53.638 4605 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.70 % Allowed : 11.45 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.15), residues: 3072 helix: 2.39 (0.20), residues: 691 sheet: 0.32 (0.19), residues: 694 loop : -0.47 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 258 HIS 0.003 0.000 HIS C 49 PHE 0.028 0.001 PHE B 238 TYR 0.029 0.001 TYR C 501 ARG 0.005 0.000 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00531 ( 42) link_NAG-ASN : angle 2.50770 ( 126) link_BETA1-4 : bond 0.00301 ( 18) link_BETA1-4 : angle 0.90429 ( 54) hydrogen bonds : bond 0.03641 ( 1030) hydrogen bonds : angle 5.15876 ( 3009) SS BOND : bond 0.00111 ( 42) SS BOND : angle 0.50273 ( 84) covalent geometry : bond 0.00236 (25818) covalent geometry : angle 0.52312 (35142) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 2.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.7228 (m-80) REVERT: A 762 GLN cc_start: 0.8883 (mt0) cc_final: 0.8531 (mt0) REVERT: A 950 ASP cc_start: 0.9003 (m-30) cc_final: 0.8663 (m-30) REVERT: A 957 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8534 (tm-30) REVERT: A 985 ASP cc_start: 0.8167 (m-30) cc_final: 0.7412 (m-30) REVERT: A 988 GLU cc_start: 0.8721 (pm20) cc_final: 0.8302 (pm20) REVERT: A 1002 GLN cc_start: 0.9125 (tt0) cc_final: 0.8615 (tm-30) REVERT: A 1010 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8350 (mp10) REVERT: A 1050 MET cc_start: 0.9205 (ptp) cc_final: 0.8873 (ptm) REVERT: B 118 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8277 (pt) REVERT: B 240 THR cc_start: 0.6237 (m) cc_final: 0.5830 (t) REVERT: B 304 LYS cc_start: 0.9336 (mmmm) cc_final: 0.9113 (mmmm) REVERT: B 697 MET cc_start: 0.8877 (mtm) cc_final: 0.8640 (mtp) REVERT: B 776 LYS cc_start: 0.9184 (tttm) cc_final: 0.8806 (tmmt) REVERT: B 779 GLN cc_start: 0.9118 (tp40) cc_final: 0.8464 (tm-30) REVERT: B 780 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: C 204 TYR cc_start: 0.6559 (m-80) cc_final: 0.6242 (m-80) REVERT: C 773 GLU cc_start: 0.8951 (tt0) cc_final: 0.8709 (tt0) REVERT: C 934 ILE cc_start: 0.9131 (tt) cc_final: 0.8854 (pp) outliers start: 19 outliers final: 7 residues processed: 120 average time/residue: 1.1849 time to fit residues: 170.5587 Evaluate side-chains 113 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 160 optimal weight: 2.9990 chunk 305 optimal weight: 0.5980 chunk 113 optimal weight: 6.9990 chunk 302 optimal weight: 0.3980 chunk 93 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 chunk 153 optimal weight: 7.9990 chunk 264 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 872 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.128632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.082694 restraints weight = 71706.212| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 4.06 r_work: 0.3053 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25920 Z= 0.154 Angle : 0.571 18.227 35406 Z= 0.284 Chirality : 0.045 0.294 4158 Planarity : 0.004 0.062 4473 Dihedral : 4.595 52.775 4605 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.70 % Allowed : 11.75 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.15), residues: 3072 helix: 2.43 (0.20), residues: 692 sheet: 0.36 (0.19), residues: 684 loop : -0.49 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 258 HIS 0.003 0.001 HIS C 49 PHE 0.022 0.001 PHE B 238 TYR 0.025 0.001 TYR B 200 ARG 0.006 0.000 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 42) link_NAG-ASN : angle 2.53336 ( 126) link_BETA1-4 : bond 0.00221 ( 18) link_BETA1-4 : angle 1.03546 ( 54) hydrogen bonds : bond 0.03830 ( 1030) hydrogen bonds : angle 5.17736 ( 3009) SS BOND : bond 0.00114 ( 42) SS BOND : angle 0.54584 ( 84) covalent geometry : bond 0.00346 (25818) covalent geometry : angle 0.55037 (35142) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 2.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7757 (OUTLIER) cc_final: 0.7309 (m-80) REVERT: A 762 GLN cc_start: 0.8931 (mt0) cc_final: 0.8561 (mt0) REVERT: A 790 LYS cc_start: 0.9421 (mtpt) cc_final: 0.9060 (mtmm) REVERT: A 950 ASP cc_start: 0.8996 (m-30) cc_final: 0.8645 (m-30) REVERT: A 957 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8536 (tm-30) REVERT: A 979 ASP cc_start: 0.8960 (m-30) cc_final: 0.8748 (t0) REVERT: A 985 ASP cc_start: 0.8236 (m-30) cc_final: 0.7569 (m-30) REVERT: A 988 GLU cc_start: 0.8761 (pm20) cc_final: 0.8404 (pm20) REVERT: A 1002 GLN cc_start: 0.9149 (tt0) cc_final: 0.8654 (tm-30) REVERT: A 1010 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8365 (mp10) REVERT: A 1050 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8896 (ptm) REVERT: B 118 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8301 (pt) REVERT: B 240 THR cc_start: 0.6177 (m) cc_final: 0.5841 (t) REVERT: B 304 LYS cc_start: 0.9385 (mmmm) cc_final: 0.9169 (mmmm) REVERT: B 762 GLN cc_start: 0.8680 (mt0) cc_final: 0.8466 (mt0) REVERT: B 776 LYS cc_start: 0.9197 (tttm) cc_final: 0.8819 (tmmt) REVERT: B 779 GLN cc_start: 0.9106 (tp40) cc_final: 0.8450 (tm-30) REVERT: B 780 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8225 (mp0) REVERT: C 153 MET cc_start: 0.5703 (pmm) cc_final: 0.5341 (ppp) REVERT: C 204 TYR cc_start: 0.6735 (m-80) cc_final: 0.6392 (m-80) REVERT: C 584 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8625 (pp) REVERT: C 773 GLU cc_start: 0.8950 (tt0) cc_final: 0.8725 (tt0) outliers start: 19 outliers final: 8 residues processed: 123 average time/residue: 1.2576 time to fit residues: 184.8638 Evaluate side-chains 116 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 220 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 78 optimal weight: 0.0870 chunk 264 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.128006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.082329 restraints weight = 71473.755| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.95 r_work: 0.3062 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25920 Z= 0.147 Angle : 0.563 15.528 35406 Z= 0.281 Chirality : 0.045 0.286 4158 Planarity : 0.004 0.063 4473 Dihedral : 4.619 52.823 4605 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.66 % Allowed : 11.82 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.15), residues: 3072 helix: 2.45 (0.20), residues: 691 sheet: 0.33 (0.19), residues: 691 loop : -0.47 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 258 HIS 0.003 0.001 HIS A 519 PHE 0.027 0.001 PHE C 392 TYR 0.019 0.001 TYR B1067 ARG 0.007 0.000 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00533 ( 42) link_NAG-ASN : angle 2.49079 ( 126) link_BETA1-4 : bond 0.00247 ( 18) link_BETA1-4 : angle 0.93440 ( 54) hydrogen bonds : bond 0.03735 ( 1030) hydrogen bonds : angle 5.13867 ( 3009) SS BOND : bond 0.00119 ( 42) SS BOND : angle 0.53888 ( 84) covalent geometry : bond 0.00331 (25818) covalent geometry : angle 0.54312 (35142) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.8177 (t80) cc_final: 0.7619 (t80) REVERT: A 762 GLN cc_start: 0.8905 (mt0) cc_final: 0.8554 (mt0) REVERT: A 790 LYS cc_start: 0.9378 (mtpt) cc_final: 0.9032 (mtmm) REVERT: A 950 ASP cc_start: 0.8986 (m-30) cc_final: 0.8688 (p0) REVERT: A 957 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8528 (tm-30) REVERT: A 985 ASP cc_start: 0.8151 (m-30) cc_final: 0.7396 (m-30) REVERT: A 988 GLU cc_start: 0.8705 (pm20) cc_final: 0.8249 (pm20) REVERT: A 1002 GLN cc_start: 0.9157 (tt0) cc_final: 0.8646 (tm-30) REVERT: A 1010 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8357 (mp10) REVERT: A 1050 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8903 (ptm) REVERT: B 118 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8269 (pt) REVERT: B 240 THR cc_start: 0.6136 (m) cc_final: 0.5717 (t) REVERT: B 304 LYS cc_start: 0.9351 (mmmm) cc_final: 0.9112 (mmmm) REVERT: B 347 PHE cc_start: 0.2105 (OUTLIER) cc_final: 0.1647 (m-10) REVERT: B 762 GLN cc_start: 0.8655 (mt0) cc_final: 0.8432 (mt0) REVERT: B 776 LYS cc_start: 0.9182 (tttm) cc_final: 0.8785 (tmmt) REVERT: B 779 GLN cc_start: 0.9121 (tp40) cc_final: 0.8478 (tm-30) REVERT: B 780 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8190 (mp0) REVERT: C 204 TYR cc_start: 0.6552 (m-80) cc_final: 0.6268 (m-80) REVERT: C 258 TRP cc_start: 0.2095 (p-90) cc_final: 0.1867 (p-90) REVERT: C 773 GLU cc_start: 0.8949 (tt0) cc_final: 0.8712 (tt0) outliers start: 18 outliers final: 9 residues processed: 119 average time/residue: 1.3571 time to fit residues: 189.8422 Evaluate side-chains 115 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 311 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 chunk 144 optimal weight: 30.0000 chunk 156 optimal weight: 8.9990 chunk 281 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 170 optimal weight: 0.0980 chunk 280 optimal weight: 0.6980 chunk 48 optimal weight: 20.0000 chunk 299 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.127247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.081504 restraints weight = 71537.721| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.99 r_work: 0.3036 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25920 Z= 0.181 Angle : 0.583 13.492 35406 Z= 0.293 Chirality : 0.045 0.275 4158 Planarity : 0.004 0.064 4473 Dihedral : 4.667 52.471 4605 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.51 % Allowed : 12.07 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.15), residues: 3072 helix: 2.45 (0.20), residues: 693 sheet: 0.24 (0.19), residues: 697 loop : -0.47 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 258 HIS 0.003 0.001 HIS B 69 PHE 0.019 0.001 PHE B 238 TYR 0.023 0.001 TYR C 453 ARG 0.009 0.000 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00529 ( 42) link_NAG-ASN : angle 2.52116 ( 126) link_BETA1-4 : bond 0.00224 ( 18) link_BETA1-4 : angle 1.01830 ( 54) hydrogen bonds : bond 0.03900 ( 1030) hydrogen bonds : angle 5.19426 ( 3009) SS BOND : bond 0.00137 ( 42) SS BOND : angle 0.59014 ( 84) covalent geometry : bond 0.00407 (25818) covalent geometry : angle 0.56313 (35142) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21161.01 seconds wall clock time: 368 minutes 44.98 seconds (22124.98 seconds total)