Starting phenix.real_space_refine on Sun Jun 22 04:22:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sxv_25507/06_2025/7sxv_25507.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sxv_25507/06_2025/7sxv_25507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sxv_25507/06_2025/7sxv_25507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sxv_25507/06_2025/7sxv_25507.map" model { file = "/net/cci-nas-00/data/ceres_data/7sxv_25507/06_2025/7sxv_25507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sxv_25507/06_2025/7sxv_25507.cif" } resolution = 2.79 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= 0.028 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 16071 2.51 5 N 4128 2.21 5 O 4935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25245 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "D" Number of atoms: 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: 15.03, per 1000 atoms: 0.60 Number of scatterers: 25245 At special positions: 0 Unit cell: (141, 145, 198, 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 4935 8.00 N 4128 7.00 C 16071 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 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=2.04 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: 6.03 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 24.6% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.65 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: 4.063A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.654A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.465A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.510A 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: 4.114A 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: 3.659A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.900A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.016A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.587A 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: 3.936A 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: 3.685A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.912A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.644A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.981A 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: 3.619A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.514A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.580A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.867A 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: 3.535A 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: 3.937A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.565A 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: 3.823A 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 387 removed outlier: 3.694A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.903A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.579A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.913A 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: 3.692A 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: 3.951A 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: 3.606A 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: 4.301A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.561A 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: 8.237A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.855A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.844A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 163 removed outlier: 5.233A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.264A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 10.197A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.824A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.074A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.109A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.569A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.030A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.603A 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=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.854A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.633A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.633A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.328A 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: 4.508A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.217A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.698A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC2, 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: 6.305A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.033A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.342A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.494A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.995A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.784A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 9.931A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.555A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.274A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.615A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.907A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.532A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.014A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.748A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.567A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.567A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.294A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.249A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.095A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.818A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 154 through 163 removed outlier: 9.781A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.879A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.770A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS C 136 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.166A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.080A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.841A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.389A 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: 6.711A 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: 3.510A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.211A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.469A 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: 6.552A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.069A 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: 6.552A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.547A 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: 4.198A 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 1075 hydrogen bonds defined for protein. 2958 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: 11.10 Time building geometry restraints manager: 7.17 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: 7599 1.34 - 1.46: 6290 1.46 - 1.58: 11788 1.58 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 25815 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 1.16e+01 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.55e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.13e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.89e+00 ... (remaining 25810 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 34031 2.01 - 4.02: 997 4.02 - 6.03: 79 6.03 - 8.04: 27 8.04 - 10.05: 8 Bond angle restraints: 35142 Sorted by residual: angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.40 -5.70 1.22e+00 6.72e-01 2.18e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.29 -5.59 1.22e+00 6.72e-01 2.10e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.98 -5.28 1.22e+00 6.72e-01 1.87e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 122.19 -8.09 2.00e+00 2.50e-01 1.64e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.61 -4.68 1.20e+00 6.94e-01 1.52e+01 ... (remaining 35137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14898 17.99 - 35.98: 1026 35.98 - 53.97: 150 53.97 - 71.97: 67 71.97 - 89.96: 29 Dihedral angle restraints: 16170 sinusoidal: 7089 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 180.00 154.23 25.77 0 5.00e+00 4.00e-02 2.66e+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 180.00 154.29 25.71 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 180.00 157.32 22.68 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 16167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3344 0.067 - 0.133: 743 0.133 - 0.200: 62 0.200 - 0.267: 5 0.267 - 0.333: 4 Chirality restraints: 4158 Sorted by residual: 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 -2.07 -0.33 2.00e-01 2.50e+01 2.78e+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 -2.08 -0.32 2.00e-01 2.50e+01 2.54e+00 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 -2.09 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 4155 not shown) Planarity restraints: 4518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 902 " -0.016 2.00e-02 2.50e+03 3.31e-02 1.09e+01 pdb=" C MET C 902 " 0.057 2.00e-02 2.50e+03 pdb=" O MET C 902 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA C 903 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 135 " 0.016 2.00e-02 2.50e+03 2.42e-02 1.03e+01 pdb=" CG PHE B 135 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE B 135 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 PHE B 135 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 135 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE B 135 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE B 135 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 920 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.09e+00 pdb=" C GLN C 920 " 0.052 2.00e-02 2.50e+03 pdb=" O GLN C 920 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS C 921 " -0.018 2.00e-02 2.50e+03 ... (remaining 4515 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6876 2.81 - 3.33: 20880 3.33 - 3.86: 42755 3.86 - 4.38: 48858 4.38 - 4.90: 84223 Nonbonded interactions: 203592 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.315 3.040 nonbonded pdb=" OE1 GLN B 115 " pdb=" OG1 THR B 167 " model vdw 2.318 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.318 3.040 nonbonded pdb=" O ASP B 80 " pdb=" OH TYR B 265 " model vdw 2.329 3.040 ... (remaining 203587 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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: 2.650 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: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 57.150 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.140 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:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 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 0.068 25917 Z= 0.226 Angle : 0.804 15.057 35406 Z= 0.416 Chirality : 0.053 0.333 4158 Planarity : 0.007 0.067 4476 Dihedral : 12.942 89.958 10200 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: -0.65 (0.13), residues: 3072 helix: 0.18 (0.18), residues: 648 sheet: 0.19 (0.19), residues: 682 loop : -0.92 (0.13), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 886 HIS 0.004 0.001 HIS A 66 PHE 0.048 0.002 PHE B 135 TYR 0.023 0.002 TYR C1067 ARG 0.016 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00896 ( 42) link_NAG-ASN : angle 3.37016 ( 126) link_BETA1-4 : bond 0.00724 ( 18) link_BETA1-4 : angle 1.29723 ( 54) hydrogen bonds : bond 0.16971 ( 1025) hydrogen bonds : angle 7.99738 ( 2958) SS BOND : bond 0.00250 ( 42) SS BOND : angle 1.40080 ( 84) covalent geometry : bond 0.00472 (25815) covalent geometry : angle 0.77623 (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 280 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 2.675 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 99 ASN cc_start: 0.7566 (m-40) cc_final: 0.7136 (p0) REVERT: A 304 LYS cc_start: 0.9230 (mmmm) cc_final: 0.8989 (mmmm) REVERT: A 869 MET cc_start: 0.8443 (mtm) cc_final: 0.8170 (mtp) REVERT: A 950 ASP cc_start: 0.8096 (t0) cc_final: 0.7787 (t0) REVERT: A 954 GLN cc_start: 0.8536 (mt0) cc_final: 0.8074 (mt0) REVERT: B 214 ARG cc_start: 0.6653 (ttt90) cc_final: 0.6441 (pmm150) REVERT: B 353 TRP cc_start: 0.7328 (p-90) cc_final: 0.7066 (p-90) REVERT: B 386 LYS cc_start: 0.8972 (mmtt) cc_final: 0.8334 (mmtp) REVERT: B 565 PHE cc_start: 0.8151 (p90) cc_final: 0.6792 (m-80) REVERT: B 858 LEU cc_start: 0.8785 (mt) cc_final: 0.8395 (pt) REVERT: B 985 ASP cc_start: 0.7368 (p0) cc_final: 0.6978 (p0) REVERT: C 41 LYS cc_start: 0.7010 (mmtp) cc_final: 0.6259 (tttt) REVERT: C 85 PRO cc_start: 0.8353 (Cg_exo) cc_final: 0.8031 (Cg_endo) REVERT: C 140 PHE cc_start: 0.7664 (p90) cc_final: 0.6972 (OUTLIER) REVERT: C 175 PHE cc_start: 0.6216 (m-10) cc_final: 0.5722 (m-80) REVERT: C 298 GLU cc_start: 0.8408 (tt0) cc_final: 0.8149 (mt-10) REVERT: C 353 TRP cc_start: 0.6271 (p-90) cc_final: 0.5717 (p-90) REVERT: C 532 ASN cc_start: 0.8747 (t0) cc_final: 0.8419 (t0) REVERT: C 582 LEU cc_start: 0.9167 (mp) cc_final: 0.8915 (pp) REVERT: C 902 MET cc_start: 0.8626 (tpt) cc_final: 0.8365 (tpt) outliers start: 0 outliers final: 1 residues processed: 280 average time/residue: 1.3760 time to fit residues: 445.9171 Evaluate side-chains 139 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 2.749 ------------------------------------------------------------------------------- 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: 2.9990 chunk 236 optimal weight: 5.9990 chunk 131 optimal weight: 0.0270 chunk 80 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 94 optimal weight: 0.5980 chunk 148 optimal weight: 4.9990 chunk 182 optimal weight: 0.5980 chunk 283 optimal weight: 0.9980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 957 GLN A1002 GLN B 66 HIS B 787 GLN B 901 GLN B 957 GLN B1002 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.127703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.083420 restraints weight = 70015.760| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.87 r_work: 0.3224 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25917 Z= 0.124 Angle : 0.591 12.316 35406 Z= 0.298 Chirality : 0.045 0.255 4158 Planarity : 0.005 0.150 4476 Dihedral : 6.613 58.983 4605 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.39 % Allowed : 6.00 % Favored : 92.61 % 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: -0.02 (0.14), residues: 3072 helix: 1.43 (0.20), residues: 676 sheet: 0.27 (0.19), residues: 689 loop : -0.71 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.004 0.001 HIS A 66 PHE 0.021 0.001 PHE B 135 TYR 0.019 0.001 TYR C 265 ARG 0.018 0.001 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00558 ( 42) link_NAG-ASN : angle 2.61137 ( 126) link_BETA1-4 : bond 0.00283 ( 18) link_BETA1-4 : angle 1.11596 ( 54) hydrogen bonds : bond 0.04291 ( 1025) hydrogen bonds : angle 6.14238 ( 2958) SS BOND : bond 0.00172 ( 42) SS BOND : angle 0.78299 ( 84) covalent geometry : bond 0.00264 (25815) covalent geometry : angle 0.56884 (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 202 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 164 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9152 (tm-30) cc_final: 0.8653 (tm-30) REVERT: A 88 ASP cc_start: 0.8631 (m-30) cc_final: 0.8165 (p0) REVERT: A 99 ASN cc_start: 0.7859 (m-40) cc_final: 0.7265 (p0) REVERT: A 188 ASN cc_start: 0.7004 (m-40) cc_final: 0.6301 (p0) REVERT: A 304 LYS cc_start: 0.9303 (mmmm) cc_final: 0.8905 (mmmm) REVERT: A 950 ASP cc_start: 0.9019 (t0) cc_final: 0.8708 (t0) REVERT: A 954 GLN cc_start: 0.9151 (mt0) cc_final: 0.8646 (mt0) REVERT: A 984 LEU cc_start: 0.7764 (mp) cc_final: 0.7519 (mm) REVERT: A 985 ASP cc_start: 0.8470 (m-30) cc_final: 0.8021 (m-30) REVERT: A 1010 GLN cc_start: 0.8971 (mp10) cc_final: 0.8552 (mp10) REVERT: A 1029 MET cc_start: 0.9483 (OUTLIER) cc_final: 0.9246 (tpp) REVERT: B 52 GLN cc_start: 0.8858 (tp40) cc_final: 0.8628 (tp-100) REVERT: B 386 LYS cc_start: 0.8543 (mmtt) cc_final: 0.7857 (mmtp) REVERT: B 858 LEU cc_start: 0.8991 (mt) cc_final: 0.8466 (pt) REVERT: B 985 ASP cc_start: 0.7660 (p0) cc_final: 0.7318 (p0) REVERT: B 1138 TYR cc_start: 0.8608 (t80) cc_final: 0.8392 (t80) REVERT: B 1144 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7223 (tm-30) REVERT: C 140 PHE cc_start: 0.7838 (p90) cc_final: 0.7121 (OUTLIER) REVERT: C 189 LEU cc_start: 0.8506 (tp) cc_final: 0.8271 (mt) REVERT: C 269 TYR cc_start: 0.7040 (m-80) cc_final: 0.6399 (m-80) REVERT: C 298 GLU cc_start: 0.8724 (tt0) cc_final: 0.8215 (mt-10) REVERT: C 532 ASN cc_start: 0.9176 (t0) cc_final: 0.8766 (t0) REVERT: C 582 LEU cc_start: 0.9249 (mp) cc_final: 0.9001 (pp) REVERT: C 902 MET cc_start: 0.9315 (tpt) cc_final: 0.9102 (tpt) REVERT: C 957 GLN cc_start: 0.8388 (tm-30) cc_final: 0.8158 (tm-30) REVERT: C 1002 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8107 (tp-100) REVERT: C 1010 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8752 (mp10) outliers start: 38 outliers final: 11 residues processed: 186 average time/residue: 1.2525 time to fit residues: 274.1847 Evaluate side-chains 138 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 148 optimal weight: 7.9990 chunk 135 optimal weight: 20.0000 chunk 133 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 309 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 281 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A1002 GLN B 66 HIS B 787 GLN B 957 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.125531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.081706 restraints weight = 70175.330| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.71 r_work: 0.3140 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25917 Z= 0.195 Angle : 0.599 12.763 35406 Z= 0.301 Chirality : 0.045 0.272 4158 Planarity : 0.004 0.090 4476 Dihedral : 5.991 59.612 4605 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.76 % Allowed : 7.17 % Favored : 91.07 % 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: 0.11 (0.14), residues: 3072 helix: 1.67 (0.20), residues: 697 sheet: 0.21 (0.19), residues: 700 loop : -0.66 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 104 HIS 0.003 0.001 HIS A 207 PHE 0.019 0.001 PHE B 135 TYR 0.022 0.001 TYR A1067 ARG 0.017 0.001 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 42) link_NAG-ASN : angle 2.55690 ( 126) link_BETA1-4 : bond 0.00253 ( 18) link_BETA1-4 : angle 1.13445 ( 54) hydrogen bonds : bond 0.04494 ( 1025) hydrogen bonds : angle 5.81845 ( 2958) SS BOND : bond 0.00458 ( 42) SS BOND : angle 0.82576 ( 84) covalent geometry : bond 0.00433 (25815) covalent geometry : angle 0.57861 (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 185 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 137 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.8637 (t-90) cc_final: 0.8299 (t70) REVERT: A 52 GLN cc_start: 0.8989 (tm-30) cc_final: 0.8651 (tm-30) REVERT: A 88 ASP cc_start: 0.8713 (m-30) cc_final: 0.8164 (p0) REVERT: A 99 ASN cc_start: 0.7691 (m-40) cc_final: 0.7059 (p0) REVERT: A 188 ASN cc_start: 0.7079 (m-40) cc_final: 0.6448 (p0) REVERT: A 304 LYS cc_start: 0.9296 (mmmm) cc_final: 0.8974 (mmmm) REVERT: A 950 ASP cc_start: 0.9054 (t0) cc_final: 0.8789 (t0) REVERT: A 954 GLN cc_start: 0.9013 (mt0) cc_final: 0.8635 (mt0) REVERT: A 964 LYS cc_start: 0.9515 (tppt) cc_final: 0.9293 (mppt) REVERT: A 1010 GLN cc_start: 0.9047 (mp10) cc_final: 0.8633 (mp10) REVERT: A 1050 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.8599 (ppp) REVERT: B 309 GLU cc_start: 0.8495 (mp0) cc_final: 0.8133 (pm20) REVERT: B 434 ILE cc_start: 0.6787 (OUTLIER) cc_final: 0.6180 (pp) REVERT: B 1002 GLN cc_start: 0.9015 (tp40) cc_final: 0.8283 (tp-100) REVERT: B 1138 TYR cc_start: 0.8617 (t80) cc_final: 0.8257 (t80) REVERT: B 1142 GLN cc_start: 0.8133 (tp40) cc_final: 0.7921 (tm-30) REVERT: B 1144 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7390 (tm-30) REVERT: C 140 PHE cc_start: 0.7849 (p90) cc_final: 0.7195 (p90) REVERT: C 269 TYR cc_start: 0.7155 (m-80) cc_final: 0.6044 (m-80) REVERT: C 532 ASN cc_start: 0.9154 (t0) cc_final: 0.8841 (t0) REVERT: C 582 LEU cc_start: 0.9247 (mp) cc_final: 0.8968 (pp) REVERT: C 745 ASP cc_start: 0.8984 (OUTLIER) cc_final: 0.8602 (p0) REVERT: C 957 GLN cc_start: 0.8362 (tm-30) cc_final: 0.8057 (tm-30) REVERT: C 1002 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8393 (tm-30) REVERT: C 1010 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8863 (mp10) outliers start: 48 outliers final: 13 residues processed: 168 average time/residue: 1.7990 time to fit residues: 364.9339 Evaluate side-chains 134 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 6.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 190 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 185 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 156 optimal weight: 0.0870 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN B 66 HIS B 957 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.123800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.079673 restraints weight = 70333.647| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.74 r_work: 0.3129 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25917 Z= 0.195 Angle : 0.575 10.397 35406 Z= 0.287 Chirality : 0.045 0.270 4158 Planarity : 0.004 0.037 4476 Dihedral : 5.633 59.981 4605 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.72 % Allowed : 8.31 % Favored : 89.97 % 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: 0.17 (0.15), residues: 3072 helix: 1.80 (0.20), residues: 708 sheet: 0.10 (0.19), residues: 694 loop : -0.61 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 104 HIS 0.004 0.001 HIS A 207 PHE 0.023 0.001 PHE B 238 TYR 0.021 0.001 TYR A1067 ARG 0.003 0.000 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00581 ( 42) link_NAG-ASN : angle 2.43142 ( 126) link_BETA1-4 : bond 0.00283 ( 18) link_BETA1-4 : angle 1.03104 ( 54) hydrogen bonds : bond 0.04257 ( 1025) hydrogen bonds : angle 5.69517 ( 2958) SS BOND : bond 0.00487 ( 42) SS BOND : angle 0.75509 ( 84) covalent geometry : bond 0.00435 (25815) covalent geometry : angle 0.55532 (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 185 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 138 time to evaluate : 2.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9043 (tm-30) cc_final: 0.8714 (tm-30) REVERT: A 79 PHE cc_start: 0.5963 (t80) cc_final: 0.5682 (t80) REVERT: A 88 ASP cc_start: 0.8791 (m-30) cc_final: 0.8146 (p0) REVERT: A 188 ASN cc_start: 0.7224 (m-40) cc_final: 0.6519 (p0) REVERT: A 304 LYS cc_start: 0.9330 (mmmm) cc_final: 0.9047 (mmmm) REVERT: A 950 ASP cc_start: 0.9037 (t0) cc_final: 0.8782 (t0) REVERT: A 954 GLN cc_start: 0.9066 (mt0) cc_final: 0.8668 (mt0) REVERT: A 957 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8311 (tm-30) REVERT: A 964 LYS cc_start: 0.9509 (tppt) cc_final: 0.9236 (mppt) REVERT: A 1050 MET cc_start: 0.9332 (OUTLIER) cc_final: 0.8738 (ppp) REVERT: B 52 GLN cc_start: 0.9123 (tm-30) cc_final: 0.8830 (tp-100) REVERT: B 309 GLU cc_start: 0.8634 (mp0) cc_final: 0.8198 (pm20) REVERT: B 434 ILE cc_start: 0.6979 (OUTLIER) cc_final: 0.6359 (pp) REVERT: B 773 GLU cc_start: 0.8979 (tt0) cc_final: 0.8639 (tt0) REVERT: B 1001 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9452 (tm) REVERT: B 1002 GLN cc_start: 0.9027 (tp40) cc_final: 0.8326 (tp-100) REVERT: B 1138 TYR cc_start: 0.8683 (t80) cc_final: 0.8378 (t80) REVERT: B 1142 GLN cc_start: 0.8216 (tp40) cc_final: 0.7993 (tm-30) REVERT: B 1144 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7348 (tm-30) REVERT: C 45 SER cc_start: 0.7903 (OUTLIER) cc_final: 0.7636 (t) REVERT: C 140 PHE cc_start: 0.7844 (p90) cc_final: 0.7185 (p90) REVERT: C 189 LEU cc_start: 0.8713 (tp) cc_final: 0.8479 (mt) REVERT: C 237 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6878 (ttp-110) REVERT: C 269 TYR cc_start: 0.7254 (m-80) cc_final: 0.5980 (m-80) REVERT: C 532 ASN cc_start: 0.9196 (t0) cc_final: 0.8922 (t0) REVERT: C 582 LEU cc_start: 0.9287 (mp) cc_final: 0.9007 (pp) REVERT: C 957 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8072 (tm-30) REVERT: C 964 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.9075 (mppt) REVERT: C 1002 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8445 (tm-30) REVERT: C 1010 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8714 (mp10) outliers start: 47 outliers final: 14 residues processed: 169 average time/residue: 1.2821 time to fit residues: 257.3224 Evaluate side-chains 135 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 13 optimal weight: 0.0770 chunk 59 optimal weight: 4.9990 chunk 97 optimal weight: 0.4980 chunk 204 optimal weight: 0.8980 chunk 171 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 275 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 246 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 487 ASN A 907 ASN B 957 GLN B1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.124161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.080638 restraints weight = 69545.193| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.68 r_work: 0.3143 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25917 Z= 0.138 Angle : 0.537 10.320 35406 Z= 0.269 Chirality : 0.044 0.265 4158 Planarity : 0.003 0.038 4476 Dihedral : 5.336 59.580 4605 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.68 % Allowed : 9.07 % Favored : 89.24 % 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: 0.27 (0.15), residues: 3072 helix: 1.86 (0.20), residues: 721 sheet: 0.04 (0.19), residues: 679 loop : -0.49 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 104 HIS 0.004 0.001 HIS A 207 PHE 0.015 0.001 PHE B 238 TYR 0.021 0.001 TYR A1067 ARG 0.004 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 42) link_NAG-ASN : angle 2.33630 ( 126) link_BETA1-4 : bond 0.00316 ( 18) link_BETA1-4 : angle 0.93869 ( 54) hydrogen bonds : bond 0.03977 ( 1025) hydrogen bonds : angle 5.50804 ( 2958) SS BOND : bond 0.00160 ( 42) SS BOND : angle 0.65434 ( 84) covalent geometry : bond 0.00304 (25815) covalent geometry : angle 0.51872 (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 176 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 130 time to evaluate : 2.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8755 (tm-30) REVERT: A 79 PHE cc_start: 0.5969 (t80) cc_final: 0.5694 (t80) REVERT: A 88 ASP cc_start: 0.8818 (m-30) cc_final: 0.8108 (p0) REVERT: A 188 ASN cc_start: 0.7137 (m110) cc_final: 0.6445 (p0) REVERT: A 304 LYS cc_start: 0.9308 (mmmm) cc_final: 0.9033 (mmmm) REVERT: A 950 ASP cc_start: 0.8999 (t0) cc_final: 0.8795 (t0) REVERT: A 954 GLN cc_start: 0.9068 (mt0) cc_final: 0.8682 (mt0) REVERT: A 964 LYS cc_start: 0.9512 (tppt) cc_final: 0.9269 (mppt) REVERT: A 1010 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8427 (mp10) REVERT: A 1050 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.8640 (ppp) REVERT: A 1144 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7427 (tm-30) REVERT: B 309 GLU cc_start: 0.8661 (mp0) cc_final: 0.8252 (pm20) REVERT: B 434 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6513 (pp) REVERT: B 955 ASN cc_start: 0.9306 (m-40) cc_final: 0.9093 (m-40) REVERT: B 1001 LEU cc_start: 0.9674 (OUTLIER) cc_final: 0.9415 (tm) REVERT: B 1002 GLN cc_start: 0.8987 (tp40) cc_final: 0.8261 (tp-100) REVERT: B 1010 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8367 (pp30) REVERT: B 1138 TYR cc_start: 0.8689 (t80) cc_final: 0.8374 (t80) REVERT: B 1142 GLN cc_start: 0.8198 (tp40) cc_final: 0.7989 (tm-30) REVERT: B 1144 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7293 (pp20) REVERT: C 140 PHE cc_start: 0.7919 (p90) cc_final: 0.7289 (p90) REVERT: C 532 ASN cc_start: 0.9233 (t0) cc_final: 0.8978 (t0) REVERT: C 582 LEU cc_start: 0.9235 (mp) cc_final: 0.8998 (pp) REVERT: C 957 GLN cc_start: 0.8379 (tm-30) cc_final: 0.8049 (tm-30) REVERT: C 964 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.9000 (mppt) REVERT: C 1002 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8437 (tm-30) REVERT: C 1010 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8688 (mp10) outliers start: 46 outliers final: 15 residues processed: 163 average time/residue: 1.7156 time to fit residues: 337.8774 Evaluate side-chains 139 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 301 optimal weight: 2.9990 chunk 217 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 chunk 156 optimal weight: 0.9980 chunk 276 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 134 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 chunk 274 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 957 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.123186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.079525 restraints weight = 69256.507| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.66 r_work: 0.3123 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25917 Z= 0.183 Angle : 0.563 10.289 35406 Z= 0.281 Chirality : 0.045 0.268 4158 Planarity : 0.004 0.045 4476 Dihedral : 5.234 56.563 4605 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.35 % Allowed : 9.95 % Favored : 88.69 % 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: 0.26 (0.15), residues: 3072 helix: 1.92 (0.20), residues: 717 sheet: -0.07 (0.19), residues: 681 loop : -0.46 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 104 HIS 0.003 0.001 HIS A 207 PHE 0.021 0.001 PHE C 135 TYR 0.020 0.001 TYR A1067 ARG 0.007 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00569 ( 42) link_NAG-ASN : angle 2.32510 ( 126) link_BETA1-4 : bond 0.00261 ( 18) link_BETA1-4 : angle 0.97625 ( 54) hydrogen bonds : bond 0.04076 ( 1025) hydrogen bonds : angle 5.51473 ( 2958) SS BOND : bond 0.00131 ( 42) SS BOND : angle 0.67312 ( 84) covalent geometry : bond 0.00411 (25815) covalent geometry : angle 0.54577 (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 166 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 2.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8784 (tm-30) REVERT: A 79 PHE cc_start: 0.6150 (t80) cc_final: 0.5897 (t80) REVERT: A 88 ASP cc_start: 0.8756 (m-30) cc_final: 0.8088 (p0) REVERT: A 188 ASN cc_start: 0.7150 (m110) cc_final: 0.6487 (p0) REVERT: A 304 LYS cc_start: 0.9333 (mmmm) cc_final: 0.9037 (mmmm) REVERT: A 950 ASP cc_start: 0.8991 (t0) cc_final: 0.8743 (t0) REVERT: A 954 GLN cc_start: 0.9079 (mt0) cc_final: 0.8624 (mt0) REVERT: A 964 LYS cc_start: 0.9517 (tppt) cc_final: 0.9286 (mppt) REVERT: A 1010 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8447 (mp10) REVERT: A 1050 MET cc_start: 0.9366 (OUTLIER) cc_final: 0.8705 (ppp) REVERT: A 1144 GLU cc_start: 0.8555 (mm-30) cc_final: 0.7799 (tm-30) REVERT: B 200 TYR cc_start: 0.8830 (m-80) cc_final: 0.8227 (t80) REVERT: B 309 GLU cc_start: 0.8658 (mp0) cc_final: 0.8288 (pm20) REVERT: B 434 ILE cc_start: 0.7231 (OUTLIER) cc_final: 0.6644 (pp) REVERT: B 740 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8659 (ttt) REVERT: B 773 GLU cc_start: 0.8970 (tt0) cc_final: 0.8662 (tt0) REVERT: B 955 ASN cc_start: 0.9307 (m-40) cc_final: 0.9095 (m-40) REVERT: B 1001 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9437 (tm) REVERT: B 1002 GLN cc_start: 0.9008 (tp40) cc_final: 0.8261 (tp-100) REVERT: B 1138 TYR cc_start: 0.8674 (t80) cc_final: 0.8372 (t80) REVERT: B 1144 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7516 (tm-30) REVERT: C 45 SER cc_start: 0.8028 (OUTLIER) cc_final: 0.7819 (t) REVERT: C 140 PHE cc_start: 0.7744 (p90) cc_final: 0.7164 (p90) REVERT: C 532 ASN cc_start: 0.9274 (t0) cc_final: 0.9006 (t0) REVERT: C 582 LEU cc_start: 0.9238 (mp) cc_final: 0.9023 (pp) REVERT: C 762 GLN cc_start: 0.8898 (mt0) cc_final: 0.8608 (mt0) REVERT: C 957 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8061 (tm-30) REVERT: C 1002 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8466 (tm-30) REVERT: C 1010 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8699 (mp10) outliers start: 37 outliers final: 17 residues processed: 156 average time/residue: 1.2420 time to fit residues: 230.3723 Evaluate side-chains 144 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 260 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 270 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 133 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 chunk 288 optimal weight: 0.9990 chunk 251 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 196 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1010 GLN C 314 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.124972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.082058 restraints weight = 70184.673| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.62 r_work: 0.3142 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25917 Z= 0.120 Angle : 0.539 10.232 35406 Z= 0.269 Chirality : 0.044 0.266 4158 Planarity : 0.004 0.080 4476 Dihedral : 5.040 53.039 4605 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.28 % Allowed : 10.14 % Favored : 88.58 % 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: 0.38 (0.15), residues: 3072 helix: 2.04 (0.20), residues: 712 sheet: 0.01 (0.19), residues: 676 loop : -0.39 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 104 HIS 0.003 0.001 HIS A 207 PHE 0.018 0.001 PHE C 135 TYR 0.020 0.001 TYR A1067 ARG 0.014 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 42) link_NAG-ASN : angle 2.25154 ( 126) link_BETA1-4 : bond 0.00313 ( 18) link_BETA1-4 : angle 0.89434 ( 54) hydrogen bonds : bond 0.03840 ( 1025) hydrogen bonds : angle 5.38926 ( 2958) SS BOND : bond 0.00126 ( 42) SS BOND : angle 0.60284 ( 84) covalent geometry : bond 0.00266 (25815) covalent geometry : angle 0.52145 (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 164 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9089 (tm-30) cc_final: 0.8806 (tm-30) REVERT: A 88 ASP cc_start: 0.8729 (m-30) cc_final: 0.7976 (p0) REVERT: A 188 ASN cc_start: 0.7127 (m110) cc_final: 0.6475 (p0) REVERT: A 304 LYS cc_start: 0.9336 (mmmm) cc_final: 0.9049 (mmmm) REVERT: A 950 ASP cc_start: 0.8972 (t0) cc_final: 0.8767 (t0) REVERT: A 954 GLN cc_start: 0.9079 (mt0) cc_final: 0.8677 (mt0) REVERT: A 964 LYS cc_start: 0.9522 (tppt) cc_final: 0.9279 (mppt) REVERT: A 1050 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.8652 (ppp) REVERT: A 1144 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7775 (tm-30) REVERT: B 200 TYR cc_start: 0.8759 (m-80) cc_final: 0.8244 (t80) REVERT: B 309 GLU cc_start: 0.8666 (mp0) cc_final: 0.8321 (pm20) REVERT: B 434 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.6792 (pp) REVERT: B 955 ASN cc_start: 0.9287 (m-40) cc_final: 0.9070 (m-40) REVERT: B 1001 LEU cc_start: 0.9675 (OUTLIER) cc_final: 0.9436 (tm) REVERT: B 1002 GLN cc_start: 0.8978 (tp40) cc_final: 0.8252 (tp-100) REVERT: B 1010 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8489 (pp30) REVERT: C 45 SER cc_start: 0.8126 (OUTLIER) cc_final: 0.7918 (t) REVERT: C 140 PHE cc_start: 0.7779 (p90) cc_final: 0.7192 (p90) REVERT: C 532 ASN cc_start: 0.9258 (t0) cc_final: 0.9004 (t0) REVERT: C 582 LEU cc_start: 0.9240 (mp) cc_final: 0.9009 (pp) REVERT: C 762 GLN cc_start: 0.8889 (mt0) cc_final: 0.8584 (mt0) REVERT: C 957 GLN cc_start: 0.8381 (tm-30) cc_final: 0.8024 (tm-30) REVERT: C 1002 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8440 (tm-30) REVERT: C 1010 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8744 (mp10) outliers start: 35 outliers final: 15 residues processed: 153 average time/residue: 1.2092 time to fit residues: 221.3006 Evaluate side-chains 142 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 252 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 230 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 291 optimal weight: 0.9980 chunk 266 optimal weight: 2.9990 chunk 267 optimal weight: 0.6980 chunk 177 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1010 GLN C1011 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.123534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.079710 restraints weight = 69986.621| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.72 r_work: 0.3140 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25917 Z= 0.144 Angle : 0.547 10.219 35406 Z= 0.272 Chirality : 0.044 0.267 4158 Planarity : 0.004 0.056 4476 Dihedral : 4.927 52.944 4605 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.24 % Allowed : 10.61 % Favored : 88.14 % 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: 0.41 (0.15), residues: 3072 helix: 2.07 (0.20), residues: 712 sheet: 0.04 (0.19), residues: 671 loop : -0.38 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 104 HIS 0.003 0.001 HIS A 207 PHE 0.013 0.001 PHE B 898 TYR 0.020 0.001 TYR A1067 ARG 0.007 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00531 ( 42) link_NAG-ASN : angle 2.23501 ( 126) link_BETA1-4 : bond 0.00296 ( 18) link_BETA1-4 : angle 0.92446 ( 54) hydrogen bonds : bond 0.03855 ( 1025) hydrogen bonds : angle 5.36816 ( 2958) SS BOND : bond 0.00119 ( 42) SS BOND : angle 0.61303 ( 84) covalent geometry : bond 0.00323 (25815) covalent geometry : angle 0.53022 (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 158 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9091 (tm-30) cc_final: 0.8809 (tm-30) REVERT: A 88 ASP cc_start: 0.8750 (m-30) cc_final: 0.7975 (p0) REVERT: A 104 TRP cc_start: 0.7417 (m-90) cc_final: 0.7109 (m-90) REVERT: A 188 ASN cc_start: 0.7154 (m110) cc_final: 0.6521 (p0) REVERT: A 304 LYS cc_start: 0.9340 (mmmm) cc_final: 0.9057 (mmmm) REVERT: A 950 ASP cc_start: 0.8982 (t0) cc_final: 0.8767 (t0) REVERT: A 954 GLN cc_start: 0.9118 (mt0) cc_final: 0.8710 (mt0) REVERT: A 964 LYS cc_start: 0.9515 (tppt) cc_final: 0.9264 (mppt) REVERT: A 1010 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8429 (mp10) REVERT: A 1050 MET cc_start: 0.9373 (OUTLIER) cc_final: 0.8677 (ppp) REVERT: A 1144 GLU cc_start: 0.8530 (mm-30) cc_final: 0.7800 (tm-30) REVERT: B 135 PHE cc_start: 0.8388 (m-80) cc_final: 0.8064 (m-80) REVERT: B 200 TYR cc_start: 0.8750 (m-80) cc_final: 0.8251 (t80) REVERT: B 309 GLU cc_start: 0.8690 (mp0) cc_final: 0.8346 (pm20) REVERT: B 434 ILE cc_start: 0.7442 (OUTLIER) cc_final: 0.6838 (pp) REVERT: B 773 GLU cc_start: 0.8965 (tt0) cc_final: 0.8736 (tt0) REVERT: B 955 ASN cc_start: 0.9283 (m-40) cc_final: 0.9057 (m-40) REVERT: B 1001 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9446 (tm) REVERT: B 1002 GLN cc_start: 0.8998 (tp40) cc_final: 0.8189 (tp-100) REVERT: C 140 PHE cc_start: 0.7772 (p90) cc_final: 0.7190 (p90) REVERT: C 532 ASN cc_start: 0.9197 (t0) cc_final: 0.8973 (t0) REVERT: C 762 GLN cc_start: 0.8901 (mt0) cc_final: 0.8597 (mt0) REVERT: C 957 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8047 (tm-30) REVERT: C 1002 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8460 (tm-30) REVERT: C 1010 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8771 (mp10) outliers start: 34 outliers final: 15 residues processed: 148 average time/residue: 1.2753 time to fit residues: 223.2542 Evaluate side-chains 140 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 181 optimal weight: 0.2980 chunk 191 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 30 optimal weight: 20.0000 chunk 62 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 310 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** B 196 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.124475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.081311 restraints weight = 70578.115| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.63 r_work: 0.3158 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25917 Z= 0.127 Angle : 0.547 13.573 35406 Z= 0.271 Chirality : 0.044 0.269 4158 Planarity : 0.003 0.044 4476 Dihedral : 4.701 52.924 4605 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.06 % Allowed : 10.87 % Favored : 88.07 % 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: 0.45 (0.15), residues: 3072 helix: 2.11 (0.20), residues: 718 sheet: -0.05 (0.19), residues: 677 loop : -0.30 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 104 HIS 0.002 0.001 HIS C 66 PHE 0.018 0.001 PHE B 392 TYR 0.020 0.001 TYR A1067 ARG 0.006 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 42) link_NAG-ASN : angle 2.19663 ( 126) link_BETA1-4 : bond 0.00312 ( 18) link_BETA1-4 : angle 0.88126 ( 54) hydrogen bonds : bond 0.03709 ( 1025) hydrogen bonds : angle 5.26078 ( 2958) SS BOND : bond 0.00131 ( 42) SS BOND : angle 0.61214 ( 84) covalent geometry : bond 0.00283 (25815) covalent geometry : angle 0.53076 (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 153 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8824 (tm-30) REVERT: A 104 TRP cc_start: 0.7397 (m-90) cc_final: 0.6778 (m-90) REVERT: A 188 ASN cc_start: 0.7225 (m110) cc_final: 0.6604 (p0) REVERT: A 304 LYS cc_start: 0.9308 (mmmm) cc_final: 0.9017 (mmmm) REVERT: A 867 ASP cc_start: 0.8953 (m-30) cc_final: 0.8732 (p0) REVERT: A 950 ASP cc_start: 0.8963 (t0) cc_final: 0.8727 (t0) REVERT: A 954 GLN cc_start: 0.9093 (mt0) cc_final: 0.8671 (mt0) REVERT: A 1010 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8428 (mp10) REVERT: A 1050 MET cc_start: 0.9363 (OUTLIER) cc_final: 0.8697 (ppp) REVERT: A 1111 GLU cc_start: 0.8495 (pp20) cc_final: 0.7990 (pp20) REVERT: A 1144 GLU cc_start: 0.8569 (mm-30) cc_final: 0.7878 (tm-30) REVERT: B 135 PHE cc_start: 0.8416 (m-80) cc_final: 0.8091 (m-80) REVERT: B 200 TYR cc_start: 0.8741 (m-80) cc_final: 0.8264 (t80) REVERT: B 309 GLU cc_start: 0.8675 (mp0) cc_final: 0.8323 (pm20) REVERT: B 434 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.6907 (pp) REVERT: B 740 MET cc_start: 0.9138 (tpt) cc_final: 0.8906 (tpt) REVERT: B 1001 LEU cc_start: 0.9649 (OUTLIER) cc_final: 0.9415 (tm) REVERT: B 1002 GLN cc_start: 0.8986 (tp40) cc_final: 0.8161 (tp-100) REVERT: B 1010 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8322 (pp30) REVERT: C 140 PHE cc_start: 0.7798 (p90) cc_final: 0.7221 (p90) REVERT: C 532 ASN cc_start: 0.9284 (t0) cc_final: 0.9072 (t0) REVERT: C 582 LEU cc_start: 0.8975 (pp) cc_final: 0.8676 (mm) REVERT: C 762 GLN cc_start: 0.8929 (mt0) cc_final: 0.8605 (mt0) REVERT: C 957 GLN cc_start: 0.8386 (tm-30) cc_final: 0.8016 (tm-30) REVERT: C 1002 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8483 (tm-30) REVERT: C 1010 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8755 (mp10) outliers start: 29 outliers final: 14 residues processed: 148 average time/residue: 1.2603 time to fit residues: 222.7080 Evaluate side-chains 139 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 234 optimal weight: 1.9990 chunk 307 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 chunk 179 optimal weight: 0.9990 chunk 281 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 310 optimal weight: 0.4980 chunk 30 optimal weight: 20.0000 chunk 280 optimal weight: 0.5980 chunk 180 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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** B 196 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.123459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.079813 restraints weight = 70199.237| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.68 r_work: 0.3136 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 25917 Z= 0.135 Angle : 0.553 11.642 35406 Z= 0.274 Chirality : 0.044 0.270 4158 Planarity : 0.004 0.040 4476 Dihedral : 4.656 52.889 4605 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.91 % Allowed : 11.23 % Favored : 87.85 % 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: 0.49 (0.15), residues: 3072 helix: 2.14 (0.20), residues: 718 sheet: 0.01 (0.19), residues: 659 loop : -0.30 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C 104 HIS 0.002 0.001 HIS A 207 PHE 0.019 0.001 PHE B 392 TYR 0.020 0.001 TYR A1067 ARG 0.004 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 42) link_NAG-ASN : angle 2.19880 ( 126) link_BETA1-4 : bond 0.00302 ( 18) link_BETA1-4 : angle 0.90765 ( 54) hydrogen bonds : bond 0.03706 ( 1025) hydrogen bonds : angle 5.27247 ( 2958) SS BOND : bond 0.00111 ( 42) SS BOND : angle 0.60418 ( 84) covalent geometry : bond 0.00305 (25815) covalent geometry : angle 0.53704 (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 149 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9119 (tm-30) cc_final: 0.8864 (tm-30) REVERT: A 104 TRP cc_start: 0.7453 (m-90) cc_final: 0.6835 (m-90) REVERT: A 188 ASN cc_start: 0.7153 (m110) cc_final: 0.6529 (p0) REVERT: A 304 LYS cc_start: 0.9313 (mmmm) cc_final: 0.9026 (mmmm) REVERT: A 950 ASP cc_start: 0.8937 (t0) cc_final: 0.8731 (t0) REVERT: A 954 GLN cc_start: 0.9097 (mt0) cc_final: 0.8682 (mt0) REVERT: A 1010 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8434 (mp10) REVERT: A 1050 MET cc_start: 0.9385 (OUTLIER) cc_final: 0.8739 (ppp) REVERT: A 1111 GLU cc_start: 0.8502 (pp20) cc_final: 0.8004 (pp20) REVERT: A 1144 GLU cc_start: 0.8587 (mm-30) cc_final: 0.7907 (tm-30) REVERT: B 135 PHE cc_start: 0.8367 (m-80) cc_final: 0.8029 (m-80) REVERT: B 200 TYR cc_start: 0.8765 (m-80) cc_final: 0.8276 (t80) REVERT: B 309 GLU cc_start: 0.8713 (mp0) cc_final: 0.8371 (pm20) REVERT: B 434 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.6946 (pp) REVERT: B 773 GLU cc_start: 0.8972 (tt0) cc_final: 0.8687 (tt0) REVERT: B 1001 LEU cc_start: 0.9654 (OUTLIER) cc_final: 0.9414 (tm) REVERT: B 1002 GLN cc_start: 0.8992 (tp40) cc_final: 0.8189 (tp-100) REVERT: B 1010 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8390 (pp30) REVERT: C 140 PHE cc_start: 0.7740 (p90) cc_final: 0.7182 (p90) REVERT: C 565 PHE cc_start: 0.8153 (p90) cc_final: 0.7223 (m-10) REVERT: C 582 LEU cc_start: 0.8845 (pp) cc_final: 0.8536 (mm) REVERT: C 762 GLN cc_start: 0.8926 (mt0) cc_final: 0.8604 (mt0) REVERT: C 957 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8060 (tm-30) REVERT: C 1002 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8493 (tm-30) REVERT: C 1010 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8785 (mp10) outliers start: 25 outliers final: 14 residues processed: 143 average time/residue: 1.2782 time to fit residues: 217.5291 Evaluate side-chains 140 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 8 optimal weight: 7.9990 chunk 282 optimal weight: 5.9990 chunk 304 optimal weight: 0.9990 chunk 276 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 177 optimal weight: 0.0570 chunk 75 optimal weight: 0.3980 chunk 87 optimal weight: 0.9980 chunk 264 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 overall best weight: 0.8902 ------------------------------------------------------------------------------- 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** B 196 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.123570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.079985 restraints weight = 70116.719| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.68 r_work: 0.3140 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 25917 Z= 0.127 Angle : 0.552 11.563 35406 Z= 0.274 Chirality : 0.044 0.270 4158 Planarity : 0.003 0.040 4476 Dihedral : 4.608 52.977 4605 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.91 % Allowed : 11.34 % Favored : 87.74 % 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: 0.50 (0.15), residues: 3072 helix: 2.16 (0.20), residues: 718 sheet: 0.01 (0.19), residues: 666 loop : -0.29 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP C 104 HIS 0.002 0.001 HIS A 66 PHE 0.030 0.001 PHE C 175 TYR 0.020 0.001 TYR A1067 ARG 0.004 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 42) link_NAG-ASN : angle 2.18325 ( 126) link_BETA1-4 : bond 0.00339 ( 18) link_BETA1-4 : angle 0.89952 ( 54) hydrogen bonds : bond 0.03696 ( 1025) hydrogen bonds : angle 5.25019 ( 2958) SS BOND : bond 0.00104 ( 42) SS BOND : angle 0.56880 ( 84) covalent geometry : bond 0.00293 (25815) covalent geometry : angle 0.53627 (35142) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23671.81 seconds wall clock time: 410 minutes 42.04 seconds (24642.04 seconds total)