Starting phenix.real_space_refine on Thu Mar 5 21:35:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sxw_25508/03_2026/7sxw_25508.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sxw_25508/03_2026/7sxw_25508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sxw_25508/03_2026/7sxw_25508.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sxw_25508/03_2026/7sxw_25508.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sxw_25508/03_2026/7sxw_25508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sxw_25508/03_2026/7sxw_25508.map" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.035 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 4125 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25242 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8134 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8134 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8134 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: 6.71, per 1000 atoms: 0.27 Number of scatterers: 25242 At special positions: 0 Unit cell: (140, 145, 197, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 4935 8.00 N 4125 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 17 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 17 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.1 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 24.8% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 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: 4.033A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.682A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.466A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.529A 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: 4.111A 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: 3.636A 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: 3.896A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.503A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.022A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.606A 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: 3.988A 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 390 removed outlier: 3.706A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.923A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.614A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.987A 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: 3.605A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.589A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.897A 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: 3.512A 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: 3.953A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.597A 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: 3.792A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.683A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.895A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.584A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.949A 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: 3.670A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.503A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) 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: 3.976A 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: 3.586A 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: 4.309A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.643A 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: 8.129A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.845A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.953A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.803A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 163 removed outlier: 5.370A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.157A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 10.019A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.816A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.907A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.983A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.636A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.971A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.879A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.580A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.580A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.188A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.717A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.261A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.144A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.686A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 154 through 163 removed outlier: 5.216A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.022A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 10.261A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.255A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.693A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.511A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.919A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.660A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.001A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.694A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.551A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.551A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.209A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.222A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.233A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.902A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 154 through 163 removed outlier: 9.752A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.824A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 10.196A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.739A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.196A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.782A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.796A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.510A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.742A 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: 6.212A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.451A 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: 6.576A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.033A 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: 6.576A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.541A 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: 4.158A 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 1073 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: 6.72 Time building geometry restraints manager: 3.33 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: 7495 1.34 - 1.46: 6152 1.46 - 1.58: 12027 1.58 - 1.70: 0 1.70 - 1.83: 138 Bond restraints: 25812 Sorted by residual: bond pdb=" C LEU C 560 " pdb=" N PRO C 561 " ideal model delta sigma weight residual 1.334 1.387 -0.053 1.51e-02 4.39e+03 1.24e+01 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.70e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.05e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.05e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.98e+00 ... (remaining 25807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 34068 2.01 - 4.01: 959 4.01 - 6.02: 78 6.02 - 8.02: 27 8.02 - 10.03: 7 Bond angle restraints: 35139 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 110.70 116.36 -5.66 1.22e+00 6.72e-01 2.15e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.36 -5.66 1.22e+00 6.72e-01 2.15e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.81 -5.11 1.22e+00 6.72e-01 1.76e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 122.05 -7.95 2.00e+00 2.50e-01 1.58e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.62 -4.69 1.20e+00 6.94e-01 1.53e+01 ... (remaining 35134 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14909 17.99 - 35.97: 1032 35.97 - 53.96: 137 53.96 - 71.95: 60 71.95 - 89.93: 29 Dihedral angle restraints: 16167 sinusoidal: 7086 harmonic: 9081 Sorted by residual: 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 180.00 154.06 25.94 0 5.00e+00 4.00e-02 2.69e+01 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 180.00 154.31 25.69 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 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 16164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3378 0.068 - 0.136: 726 0.136 - 0.205: 50 0.205 - 0.273: 4 0.273 - 0.341: 3 Chirality restraints: 4161 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 -2.06 -0.34 2.00e-01 2.50e+01 2.91e+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 -2.06 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 4158 not shown) Planarity restraints: 4515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 902 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C MET C 902 " 0.055 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=" CA MET A1029 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" C MET A1029 " 0.049 2.00e-02 2.50e+03 pdb=" O MET A1029 " -0.018 2.00e-02 2.50e+03 pdb=" N SER A1030 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 920 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.91e+00 pdb=" C GLN C 920 " 0.049 2.00e-02 2.50e+03 pdb=" O GLN C 920 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS C 921 " -0.016 2.00e-02 2.50e+03 ... (remaining 4512 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6876 2.81 - 3.33: 21020 3.33 - 3.86: 43039 3.86 - 4.38: 49366 4.38 - 4.90: 84432 Nonbonded interactions: 204733 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.290 3.040 nonbonded pdb=" O ASP A 80 " pdb=" OH TYR A 265 " model vdw 2.323 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.329 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.333 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.334 3.040 ... (remaining 204728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' 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: 6.440 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: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 28.020 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 25914 Z= 0.219 Angle : 0.786 15.040 35403 Z= 0.404 Chirality : 0.053 0.341 4161 Planarity : 0.007 0.067 4473 Dihedral : 12.799 89.933 10197 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.13), residues: 3072 helix: 0.22 (0.18), residues: 637 sheet: 0.10 (0.19), residues: 690 loop : -0.85 (0.13), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 357 TYR 0.026 0.002 TYR C1067 PHE 0.040 0.002 PHE B 135 TRP 0.021 0.002 TRP A 886 HIS 0.005 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00455 (25812) covalent geometry : angle 0.75828 (35139) SS BOND : bond 0.00256 ( 42) SS BOND : angle 1.32867 ( 84) hydrogen bonds : bond 0.16549 ( 1025) hydrogen bonds : angle 8.10249 ( 2958) link_BETA1-4 : bond 0.00681 ( 18) link_BETA1-4 : angle 1.24488 ( 54) link_NAG-ASN : bond 0.00760 ( 42) link_NAG-ASN : angle 3.40282 ( 126) *********************** 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 224 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.957 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 79 PHE cc_start: 0.6826 (t80) cc_final: 0.6547 (t80) REVERT: A 88 ASP cc_start: 0.8254 (m-30) cc_final: 0.7372 (p0) REVERT: A 104 TRP cc_start: 0.7208 (m-90) cc_final: 0.6896 (m-90) REVERT: A 229 LEU cc_start: 0.8787 (mt) cc_final: 0.8552 (tt) REVERT: A 755 GLN cc_start: 0.8523 (mm110) cc_final: 0.7882 (mm-40) REVERT: B 104 TRP cc_start: 0.7124 (m-90) cc_final: 0.6134 (m-90) REVERT: B 203 ILE cc_start: 0.8831 (mt) cc_final: 0.8611 (mp) REVERT: B 318 PHE cc_start: 0.7933 (t80) cc_final: 0.7686 (t80) REVERT: B 342 PHE cc_start: 0.8182 (m-80) cc_final: 0.7849 (m-10) REVERT: B 858 LEU cc_start: 0.8635 (mt) cc_final: 0.8124 (pt) REVERT: B 985 ASP cc_start: 0.8195 (p0) cc_final: 0.7762 (p0) REVERT: C 54 LEU cc_start: 0.8678 (mm) cc_final: 0.8295 (mt) REVERT: C 386 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8161 (mmmm) REVERT: C 582 LEU cc_start: 0.8967 (mp) cc_final: 0.8424 (tm) REVERT: C 981 LEU cc_start: 0.8956 (mm) cc_final: 0.8628 (pp) REVERT: C 985 ASP cc_start: 0.7764 (p0) cc_final: 0.7533 (p0) REVERT: C 1145 LEU cc_start: 0.7513 (pt) cc_final: 0.7222 (tm) outliers start: 0 outliers final: 3 residues processed: 224 average time/residue: 0.7297 time to fit residues: 186.9663 Evaluate side-chains 105 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 321 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN B 901 GLN B 907 ASN B 957 GLN C 49 HIS C 540 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.110910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.067572 restraints weight = 82761.689| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 4.37 r_work: 0.3055 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 25914 Z= 0.243 Angle : 0.662 11.149 35403 Z= 0.331 Chirality : 0.047 0.291 4161 Planarity : 0.005 0.054 4473 Dihedral : 6.269 57.557 4612 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.95 % Allowed : 6.04 % Favored : 93.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.14), residues: 3072 helix: 1.37 (0.20), residues: 680 sheet: 0.26 (0.19), residues: 699 loop : -0.66 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 454 TYR 0.026 0.002 TYR C1067 PHE 0.021 0.002 PHE B 238 TRP 0.017 0.002 TRP C 886 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00542 (25812) covalent geometry : angle 0.63626 (35139) SS BOND : bond 0.00223 ( 42) SS BOND : angle 0.81003 ( 84) hydrogen bonds : bond 0.04549 ( 1025) hydrogen bonds : angle 6.24060 ( 2958) link_BETA1-4 : bond 0.00297 ( 18) link_BETA1-4 : angle 1.32591 ( 54) link_NAG-ASN : bond 0.00869 ( 42) link_NAG-ASN : angle 2.99691 ( 126) *********************** 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 142 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.6882 (t80) cc_final: 0.6485 (t80) REVERT: A 755 GLN cc_start: 0.8997 (mm110) cc_final: 0.8676 (mm110) REVERT: A 979 ASP cc_start: 0.9128 (m-30) cc_final: 0.8897 (p0) REVERT: A 981 LEU cc_start: 0.8926 (mt) cc_final: 0.8623 (pp) REVERT: A 990 GLU cc_start: 0.8832 (pp20) cc_final: 0.8632 (pp20) REVERT: B 85 PRO cc_start: 0.8999 (Cg_exo) cc_final: 0.8783 (Cg_endo) REVERT: B 104 TRP cc_start: 0.8023 (m-90) cc_final: 0.7575 (m100) REVERT: B 269 TYR cc_start: 0.9121 (m-80) cc_final: 0.8560 (m-10) REVERT: B 318 PHE cc_start: 0.8432 (t80) cc_final: 0.8065 (t80) REVERT: B 342 PHE cc_start: 0.8589 (m-80) cc_final: 0.8248 (m-80) REVERT: B 985 ASP cc_start: 0.8558 (p0) cc_final: 0.8244 (p0) REVERT: C 237 ARG cc_start: 0.8217 (ttp-110) cc_final: 0.7846 (ppp80) REVERT: C 387 LEU cc_start: 0.8040 (mt) cc_final: 0.7795 (mp) REVERT: C 957 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8543 (tm-30) REVERT: C 964 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.9078 (mtmm) REVERT: C 981 LEU cc_start: 0.9246 (mm) cc_final: 0.8962 (pp) REVERT: C 988 GLU cc_start: 0.9089 (mp0) cc_final: 0.8749 (mp0) outliers start: 26 outliers final: 9 residues processed: 136 average time/residue: 0.6619 time to fit residues: 105.3671 Evaluate side-chains 95 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 154 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 305 optimal weight: 4.9990 chunk 234 optimal weight: 5.9990 chunk 273 optimal weight: 3.9990 chunk 187 optimal weight: 0.0980 chunk 111 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 chunk 175 optimal weight: 0.9990 chunk 205 optimal weight: 0.8980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 314 GLN A 907 ASN A 955 ASN B 907 ASN B 957 GLN C 121 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.110684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.069063 restraints weight = 82426.861| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.77 r_work: 0.3069 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25914 Z= 0.164 Angle : 0.567 10.979 35403 Z= 0.285 Chirality : 0.044 0.261 4161 Planarity : 0.004 0.054 4473 Dihedral : 5.822 58.001 4607 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.28 % Allowed : 7.35 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.15), residues: 3072 helix: 1.68 (0.20), residues: 696 sheet: 0.26 (0.19), residues: 699 loop : -0.61 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1091 TYR 0.023 0.001 TYR C1067 PHE 0.020 0.001 PHE C 392 TRP 0.027 0.002 TRP A 104 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00362 (25812) covalent geometry : angle 0.54046 (35139) SS BOND : bond 0.00179 ( 42) SS BOND : angle 0.74647 ( 84) hydrogen bonds : bond 0.04174 ( 1025) hydrogen bonds : angle 5.94068 ( 2958) link_BETA1-4 : bond 0.00271 ( 18) link_BETA1-4 : angle 1.06977 ( 54) link_NAG-ASN : bond 0.00678 ( 42) link_NAG-ASN : angle 2.81408 ( 126) *********************** 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 129 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.9199 (OUTLIER) cc_final: 0.8955 (m110) REVERT: A 755 GLN cc_start: 0.8975 (mm110) cc_final: 0.8712 (mm110) REVERT: A 981 LEU cc_start: 0.8973 (mt) cc_final: 0.8642 (pp) REVERT: B 104 TRP cc_start: 0.8013 (m-90) cc_final: 0.7755 (m100) REVERT: B 1002 GLN cc_start: 0.9352 (tp40) cc_final: 0.9128 (tp40) REVERT: C 237 ARG cc_start: 0.8286 (ttp-110) cc_final: 0.7969 (ppp80) REVERT: C 351 TYR cc_start: 0.7303 (p90) cc_final: 0.7094 (p90) REVERT: C 387 LEU cc_start: 0.7998 (mt) cc_final: 0.7778 (mp) REVERT: C 957 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8419 (tm-30) REVERT: C 988 GLU cc_start: 0.9084 (mp0) cc_final: 0.8767 (mp0) outliers start: 35 outliers final: 11 residues processed: 119 average time/residue: 0.6316 time to fit residues: 88.7109 Evaluate side-chains 93 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 745 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 14 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 150 optimal weight: 30.0000 chunk 63 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 47 optimal weight: 30.0000 chunk 53 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 955 ASN B 824 ASN B 907 ASN B 957 GLN C 207 HIS C 779 GLN C1011 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.115707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.073638 restraints weight = 80118.120| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 4.04 r_work: 0.3004 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 25914 Z= 0.271 Angle : 0.647 10.016 35403 Z= 0.323 Chirality : 0.047 0.255 4161 Planarity : 0.004 0.052 4473 Dihedral : 5.872 59.118 4607 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.76 % Allowed : 7.68 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 3072 helix: 1.57 (0.20), residues: 698 sheet: -0.06 (0.19), residues: 694 loop : -0.61 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 102 TYR 0.026 0.002 TYR C 756 PHE 0.028 0.002 PHE B 106 TRP 0.040 0.002 TRP A 104 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00607 (25812) covalent geometry : angle 0.62389 (35139) SS BOND : bond 0.00233 ( 42) SS BOND : angle 0.82601 ( 84) hydrogen bonds : bond 0.04532 ( 1025) hydrogen bonds : angle 5.96578 ( 2958) link_BETA1-4 : bond 0.00298 ( 18) link_BETA1-4 : angle 1.35216 ( 54) link_NAG-ASN : bond 0.00807 ( 42) link_NAG-ASN : angle 2.80803 ( 126) *********************** 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 134 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 86 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.9174 (OUTLIER) cc_final: 0.8928 (m110) REVERT: A 229 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7531 (tm) REVERT: A 588 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8485 (p) REVERT: A 981 LEU cc_start: 0.8968 (mt) cc_final: 0.8723 (pp) REVERT: A 1002 GLN cc_start: 0.8947 (tm-30) cc_final: 0.8566 (tm-30) REVERT: B 104 TRP cc_start: 0.8025 (m-90) cc_final: 0.7683 (m100) REVERT: B 1002 GLN cc_start: 0.9439 (tp40) cc_final: 0.9236 (tp40) REVERT: C 63 THR cc_start: 0.5772 (OUTLIER) cc_final: 0.5570 (t) REVERT: C 351 TYR cc_start: 0.7080 (p90) cc_final: 0.6864 (p90) REVERT: C 368 LEU cc_start: 0.8352 (mp) cc_final: 0.7933 (tp) REVERT: C 434 ILE cc_start: 0.1827 (OUTLIER) cc_final: 0.1183 (mp) REVERT: C 957 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8397 (tm-30) REVERT: C 981 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8986 (pp) REVERT: C 988 GLU cc_start: 0.9168 (mp0) cc_final: 0.8748 (mp0) outliers start: 48 outliers final: 20 residues processed: 127 average time/residue: 0.6018 time to fit residues: 90.4847 Evaluate side-chains 100 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 981 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 132 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 302 optimal weight: 0.6980 chunk 190 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 280 optimal weight: 0.9980 chunk 263 optimal weight: 0.0070 chunk 295 optimal weight: 0.5980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 755 GLN B 907 ASN B 957 GLN C 188 ASN C 613 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.110521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.069553 restraints weight = 82442.578| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.67 r_work: 0.3066 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25914 Z= 0.108 Angle : 0.532 9.517 35403 Z= 0.268 Chirality : 0.044 0.266 4161 Planarity : 0.004 0.055 4473 Dihedral : 5.383 58.574 4607 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.17 % Allowed : 9.11 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.15), residues: 3072 helix: 1.83 (0.20), residues: 701 sheet: -0.01 (0.19), residues: 701 loop : -0.51 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 237 TYR 0.021 0.001 TYR C1067 PHE 0.013 0.001 PHE B 238 TRP 0.021 0.001 TRP A 104 HIS 0.002 0.000 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00235 (25812) covalent geometry : angle 0.51083 (35139) SS BOND : bond 0.00142 ( 42) SS BOND : angle 0.60372 ( 84) hydrogen bonds : bond 0.03850 ( 1025) hydrogen bonds : angle 5.62195 ( 2958) link_BETA1-4 : bond 0.00339 ( 18) link_BETA1-4 : angle 0.90969 ( 54) link_NAG-ASN : bond 0.00584 ( 42) link_NAG-ASN : angle 2.49843 ( 126) *********************** 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 121 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7558 (tm) REVERT: A 957 GLN cc_start: 0.9047 (tt0) cc_final: 0.8680 (tm-30) REVERT: A 981 LEU cc_start: 0.8931 (mt) cc_final: 0.8681 (pp) REVERT: B 104 TRP cc_start: 0.8043 (m-90) cc_final: 0.7732 (m100) REVERT: B 342 PHE cc_start: 0.8595 (m-80) cc_final: 0.8262 (m-80) REVERT: C 63 THR cc_start: 0.5895 (OUTLIER) cc_final: 0.5690 (t) REVERT: C 351 TYR cc_start: 0.7069 (p90) cc_final: 0.6805 (p90) REVERT: C 368 LEU cc_start: 0.8395 (mp) cc_final: 0.7735 (tm) REVERT: C 957 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8346 (tm-30) REVERT: C 981 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.9002 (pp) REVERT: C 988 GLU cc_start: 0.9162 (mp0) cc_final: 0.8697 (mp0) outliers start: 32 outliers final: 15 residues processed: 114 average time/residue: 0.6399 time to fit residues: 85.6428 Evaluate side-chains 97 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 981 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 153 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 242 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 271 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 213 optimal weight: 6.9990 chunk 134 optimal weight: 30.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN B 907 ASN B 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.107927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.067712 restraints weight = 84637.798| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.39 r_work: 0.3006 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 25914 Z= 0.242 Angle : 0.613 9.778 35403 Z= 0.306 Chirality : 0.046 0.257 4161 Planarity : 0.004 0.053 4473 Dihedral : 5.474 58.850 4607 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.57 % Allowed : 9.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.15), residues: 3072 helix: 1.67 (0.20), residues: 707 sheet: -0.15 (0.19), residues: 679 loop : -0.55 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 995 TYR 0.021 0.002 TYR B1067 PHE 0.017 0.001 PHE C 898 TRP 0.018 0.002 TRP A 104 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00546 (25812) covalent geometry : angle 0.59140 (35139) SS BOND : bond 0.00197 ( 42) SS BOND : angle 0.74926 ( 84) hydrogen bonds : bond 0.04369 ( 1025) hydrogen bonds : angle 5.82274 ( 2958) link_BETA1-4 : bond 0.00347 ( 18) link_BETA1-4 : angle 1.33241 ( 54) link_NAG-ASN : bond 0.00712 ( 42) link_NAG-ASN : angle 2.63840 ( 126) *********************** 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 133 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 90 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7666 (tm) REVERT: A 755 GLN cc_start: 0.8969 (mm-40) cc_final: 0.8732 (mm110) REVERT: A 981 LEU cc_start: 0.8909 (mt) cc_final: 0.8695 (pp) REVERT: B 41 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7863 (mmpt) REVERT: B 104 TRP cc_start: 0.7998 (m-90) cc_final: 0.7675 (m100) REVERT: B 342 PHE cc_start: 0.8577 (m-80) cc_final: 0.8247 (m-80) REVERT: C 351 TYR cc_start: 0.7152 (p90) cc_final: 0.6916 (p90) REVERT: C 368 LEU cc_start: 0.8320 (mp) cc_final: 0.7724 (tm) REVERT: C 516 GLU cc_start: 0.4704 (OUTLIER) cc_final: 0.4398 (pp20) REVERT: C 957 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8368 (tm-30) REVERT: C 964 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.9049 (mtmm) REVERT: C 981 LEU cc_start: 0.9264 (mm) cc_final: 0.9017 (pp) REVERT: C 988 GLU cc_start: 0.9192 (mp0) cc_final: 0.8758 (mp0) outliers start: 43 outliers final: 20 residues processed: 123 average time/residue: 0.5795 time to fit residues: 84.5208 Evaluate side-chains 101 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 201 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 227 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 37 optimal weight: 7.9990 chunk 113 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN B 957 GLN C 314 GLN C 334 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.109216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.068641 restraints weight = 82390.886| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.59 r_work: 0.3048 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25914 Z= 0.127 Angle : 0.549 9.702 35403 Z= 0.276 Chirality : 0.044 0.269 4161 Planarity : 0.004 0.059 4473 Dihedral : 5.187 59.498 4607 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.46 % Allowed : 9.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.15), residues: 3072 helix: 1.80 (0.20), residues: 706 sheet: -0.08 (0.19), residues: 704 loop : -0.49 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 995 TYR 0.021 0.001 TYR C1067 PHE 0.021 0.001 PHE B 135 TRP 0.023 0.001 TRP A 104 HIS 0.002 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00281 (25812) covalent geometry : angle 0.52931 (35139) SS BOND : bond 0.00143 ( 42) SS BOND : angle 0.59311 ( 84) hydrogen bonds : bond 0.03856 ( 1025) hydrogen bonds : angle 5.58250 ( 2958) link_BETA1-4 : bond 0.00309 ( 18) link_BETA1-4 : angle 1.00186 ( 54) link_NAG-ASN : bond 0.00546 ( 42) link_NAG-ASN : angle 2.44037 ( 126) *********************** 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 128 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 88 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7607 (tm) REVERT: A 957 GLN cc_start: 0.9065 (tt0) cc_final: 0.8679 (tm-30) REVERT: A 981 LEU cc_start: 0.8928 (mt) cc_final: 0.8635 (pp) REVERT: B 104 TRP cc_start: 0.7995 (m-90) cc_final: 0.7785 (m100) REVERT: B 342 PHE cc_start: 0.8558 (m-80) cc_final: 0.8220 (m-10) REVERT: B 505 TYR cc_start: 0.6993 (OUTLIER) cc_final: 0.6692 (m-80) REVERT: C 63 THR cc_start: 0.5904 (OUTLIER) cc_final: 0.5672 (t) REVERT: C 351 TYR cc_start: 0.7125 (p90) cc_final: 0.6879 (p90) REVERT: C 368 LEU cc_start: 0.8285 (mp) cc_final: 0.7677 (tm) REVERT: C 516 GLU cc_start: 0.4834 (OUTLIER) cc_final: 0.4482 (pp20) REVERT: C 957 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8319 (tm-30) REVERT: C 981 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.9024 (pp) REVERT: C 988 GLU cc_start: 0.9267 (mp0) cc_final: 0.8781 (mp0) outliers start: 40 outliers final: 18 residues processed: 120 average time/residue: 0.5999 time to fit residues: 85.3292 Evaluate side-chains 102 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 981 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 163 optimal weight: 8.9990 chunk 289 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 229 optimal weight: 30.0000 chunk 119 optimal weight: 9.9990 chunk 307 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 203 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN B 957 GLN C 334 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.108632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.067769 restraints weight = 82971.157| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.63 r_work: 0.3029 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 25914 Z= 0.176 Angle : 0.567 9.647 35403 Z= 0.285 Chirality : 0.044 0.264 4161 Planarity : 0.004 0.055 4473 Dihedral : 5.132 59.878 4607 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.24 % Allowed : 10.54 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.15), residues: 3072 helix: 1.76 (0.20), residues: 712 sheet: -0.10 (0.19), residues: 703 loop : -0.51 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 319 TYR 0.021 0.001 TYR C1067 PHE 0.023 0.001 PHE B 135 TRP 0.025 0.001 TRP A 104 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00395 (25812) covalent geometry : angle 0.54709 (35139) SS BOND : bond 0.00160 ( 42) SS BOND : angle 0.69620 ( 84) hydrogen bonds : bond 0.03997 ( 1025) hydrogen bonds : angle 5.61059 ( 2958) link_BETA1-4 : bond 0.00245 ( 18) link_BETA1-4 : angle 1.09901 ( 54) link_NAG-ASN : bond 0.00592 ( 42) link_NAG-ASN : angle 2.45545 ( 126) *********************** 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 116 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 82 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7813 (tm) REVERT: A 957 GLN cc_start: 0.9063 (tt0) cc_final: 0.8645 (tm-30) REVERT: A 981 LEU cc_start: 0.8978 (mt) cc_final: 0.8660 (pp) REVERT: B 41 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7838 (mmpt) REVERT: B 104 TRP cc_start: 0.8041 (m-90) cc_final: 0.7750 (m100) REVERT: B 214 ARG cc_start: 0.8474 (ttt90) cc_final: 0.8101 (pmt170) REVERT: B 342 PHE cc_start: 0.8559 (m-80) cc_final: 0.8204 (m-10) REVERT: B 505 TYR cc_start: 0.6965 (OUTLIER) cc_final: 0.6645 (m-80) REVERT: C 63 THR cc_start: 0.5930 (OUTLIER) cc_final: 0.5687 (t) REVERT: C 351 TYR cc_start: 0.7169 (p90) cc_final: 0.6911 (p90) REVERT: C 368 LEU cc_start: 0.8275 (mp) cc_final: 0.7649 (tm) REVERT: C 516 GLU cc_start: 0.4897 (OUTLIER) cc_final: 0.4543 (pp20) REVERT: C 957 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8335 (tm-30) REVERT: C 988 GLU cc_start: 0.9279 (mp0) cc_final: 0.8874 (mp0) outliers start: 34 outliers final: 20 residues processed: 108 average time/residue: 0.6357 time to fit residues: 81.4257 Evaluate side-chains 100 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 745 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 95 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 304 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 197 optimal weight: 0.0470 chunk 208 optimal weight: 9.9990 chunk 308 optimal weight: 1.9990 chunk 141 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 225 optimal weight: 20.0000 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 762 GLN B 907 ASN B 957 GLN C 334 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.109370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.068731 restraints weight = 83223.284| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.61 r_work: 0.3054 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 25914 Z= 0.115 Angle : 0.547 9.581 35403 Z= 0.274 Chirality : 0.044 0.269 4161 Planarity : 0.004 0.059 4473 Dihedral : 4.914 58.161 4607 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.24 % Allowed : 10.57 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 3072 helix: 1.92 (0.20), residues: 703 sheet: -0.03 (0.19), residues: 704 loop : -0.45 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 995 TYR 0.020 0.001 TYR C1067 PHE 0.029 0.001 PHE B 201 TRP 0.030 0.001 TRP A 104 HIS 0.002 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00260 (25812) covalent geometry : angle 0.52824 (35139) SS BOND : bond 0.00129 ( 42) SS BOND : angle 0.61245 ( 84) hydrogen bonds : bond 0.03755 ( 1025) hydrogen bonds : angle 5.46660 ( 2958) link_BETA1-4 : bond 0.00309 ( 18) link_BETA1-4 : angle 0.95356 ( 54) link_NAG-ASN : bond 0.00524 ( 42) link_NAG-ASN : angle 2.34422 ( 126) *********************** 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 118 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 84 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7788 (tm) REVERT: A 957 GLN cc_start: 0.9064 (tt0) cc_final: 0.8655 (tm-30) REVERT: B 104 TRP cc_start: 0.8021 (m-90) cc_final: 0.7704 (m100) REVERT: B 153 MET cc_start: 0.5320 (ppp) cc_final: 0.4691 (tpp) REVERT: B 214 ARG cc_start: 0.8482 (ttt90) cc_final: 0.8099 (pmt170) REVERT: B 342 PHE cc_start: 0.8537 (m-80) cc_final: 0.8176 (m-10) REVERT: B 505 TYR cc_start: 0.6945 (OUTLIER) cc_final: 0.6629 (m-80) REVERT: C 368 LEU cc_start: 0.8226 (mp) cc_final: 0.7587 (tm) REVERT: C 516 GLU cc_start: 0.4998 (OUTLIER) cc_final: 0.4578 (pp20) REVERT: C 957 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8340 (tm-30) REVERT: C 988 GLU cc_start: 0.9267 (mp0) cc_final: 0.8850 (pm20) outliers start: 34 outliers final: 18 residues processed: 111 average time/residue: 0.6433 time to fit residues: 83.9132 Evaluate side-chains 97 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 745 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 203 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 299 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 201 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 303 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 ASN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.108736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.068172 restraints weight = 83372.512| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.62 r_work: 0.3042 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 25914 Z= 0.163 Angle : 0.569 9.617 35403 Z= 0.285 Chirality : 0.044 0.268 4161 Planarity : 0.004 0.060 4473 Dihedral : 4.922 58.613 4607 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.38 % Favored : 97.59 % Rotamer: Outliers : 0.73 % Allowed : 11.23 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 3072 helix: 1.83 (0.20), residues: 709 sheet: -0.02 (0.19), residues: 704 loop : -0.46 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 357 TYR 0.021 0.001 TYR C1067 PHE 0.026 0.001 PHE A 374 TRP 0.029 0.001 TRP A 104 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00375 (25812) covalent geometry : angle 0.55106 (35139) SS BOND : bond 0.00150 ( 42) SS BOND : angle 0.59972 ( 84) hydrogen bonds : bond 0.03872 ( 1025) hydrogen bonds : angle 5.48694 ( 2958) link_BETA1-4 : bond 0.00249 ( 18) link_BETA1-4 : angle 1.00460 ( 54) link_NAG-ASN : bond 0.00548 ( 42) link_NAG-ASN : angle 2.36762 ( 126) ********************** 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 103 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7706 (tm) REVERT: A 957 GLN cc_start: 0.9043 (tt0) cc_final: 0.8639 (tm-30) REVERT: B 104 TRP cc_start: 0.8006 (m-90) cc_final: 0.7698 (m100) REVERT: B 214 ARG cc_start: 0.8273 (ttt90) cc_final: 0.8010 (pmt170) REVERT: B 342 PHE cc_start: 0.8554 (m-80) cc_final: 0.8213 (m-10) REVERT: B 505 TYR cc_start: 0.6863 (OUTLIER) cc_final: 0.6608 (m-80) REVERT: C 368 LEU cc_start: 0.8251 (mp) cc_final: 0.7610 (tm) REVERT: C 516 GLU cc_start: 0.5001 (OUTLIER) cc_final: 0.4592 (pp20) REVERT: C 957 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8326 (tm-30) REVERT: C 988 GLU cc_start: 0.9299 (mp0) cc_final: 0.8879 (mp0) outliers start: 20 outliers final: 16 residues processed: 100 average time/residue: 0.6567 time to fit residues: 77.4958 Evaluate side-chains 96 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 745 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 73 optimal weight: 0.7980 chunk 277 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 116 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 231 optimal weight: 0.8980 chunk 281 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 0.0370 chunk 290 optimal weight: 1.9990 chunk 21 optimal weight: 30.0000 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 762 GLN C 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.108825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.068973 restraints weight = 83627.993| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.47 r_work: 0.3057 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 25914 Z= 0.123 Angle : 0.561 9.697 35403 Z= 0.281 Chirality : 0.044 0.270 4161 Planarity : 0.004 0.070 4473 Dihedral : 4.826 57.976 4607 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.84 % Allowed : 11.34 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.15), residues: 3072 helix: 1.96 (0.20), residues: 695 sheet: 0.02 (0.19), residues: 707 loop : -0.41 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 357 TYR 0.020 0.001 TYR C1067 PHE 0.031 0.001 PHE B 201 TRP 0.030 0.001 TRP A 104 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00284 (25812) covalent geometry : angle 0.54371 (35139) SS BOND : bond 0.00126 ( 42) SS BOND : angle 0.58329 ( 84) hydrogen bonds : bond 0.03817 ( 1025) hydrogen bonds : angle 5.42845 ( 2958) link_BETA1-4 : bond 0.00278 ( 18) link_BETA1-4 : angle 0.97047 ( 54) link_NAG-ASN : bond 0.00519 ( 42) link_NAG-ASN : angle 2.31745 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10531.78 seconds wall clock time: 179 minutes 42.96 seconds (10782.96 seconds total)