Starting phenix.real_space_refine on Sun Jul 5 04:16:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sxs_25504/07_2026/7sxs_25504.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sxs_25504/07_2026/7sxs_25504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sxs_25504/07_2026/7sxs_25504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sxs_25504/07_2026/7sxs_25504.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sxs_25504/07_2026/7sxs_25504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sxs_25504/07_2026/7sxs_25504.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7sxs_25504/07_2026/7sxs_25504.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sxs_25504/07_2026/7sxs_25504.cif" } resolution = 2.64 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= 0.038 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 16059 2.51 5 N 4137 2.21 5 O 4938 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-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25245 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 8 Time building chain proxies: 6.05, per 1000 atoms: 0.24 Number of scatterers: 25245 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 4938 8.00 N 4137 7.00 C 16059 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: 2.32 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, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 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: 4.087A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.653A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.489A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.523A 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: 4.123A 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: 3.673A 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: 3.903A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.025A 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: 3.968A 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: 3.695A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.922A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.563A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.986A 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: 3.609A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.500A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.557A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.924A 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: 3.574A 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 1033 removed outlier: 3.948A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.602A 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: 3.747A 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 389 removed outlier: 3.648A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.869A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.576A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.917A 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: 3.694A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.991A 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: 3.576A 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: 4.303A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.567A 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: 8.092A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.960A 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: 3.622A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.251A 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: 3.962A 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: 3.691A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.076A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.214A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.691A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.726A 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: 6.847A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.088A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.449A 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: 3.967A 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: 3.503A 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: 6.021A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.410A 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: 6.848A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.875A 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: 6.565A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.041A 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: 6.565A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.576A 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: 4.155A 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: 3.709A 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: 8.359A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.075A 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: 3.672A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.502A 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: 5.081A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.072A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.237A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.713A 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: 3.671A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.289A 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) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.526A 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: 6.847A 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: 3.621A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.930A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.434A 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: 3.606A 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: 6.485A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.085A 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: 6.485A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.494A 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: 4.263A 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: 8.177A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.716A 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: 4.212A 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: 3.932A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.544A 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: 9.823A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.880A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 10.252A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.768A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS C 136 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.923A 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: 5.174A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.861A 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: 3.669A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.669A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) 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: 3.635A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.210A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.473A 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: 6.474A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.057A 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: 6.474A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.583A 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: 4.136A 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 1098 hydrogen bonds defined for protein. 3015 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: 7.64 Time building geometry restraints manager: 3.11 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: 7529 1.34 - 1.46: 6242 1.46 - 1.58: 11903 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 -0.052 1.51e-02 4.39e+03 1.20e+01 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.45e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.41e+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 6.05e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.66e+00 ... (remaining 25807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 34002 1.99 - 3.98: 1006 3.98 - 5.97: 95 5.97 - 7.96: 21 7.96 - 9.95: 9 Bond angle restraints: 35133 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 110.70 116.39 -5.69 1.22e+00 6.72e-01 2.18e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.34 -5.64 1.22e+00 6.72e-01 2.14e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.07 -5.37 1.22e+00 6.72e-01 1.94e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 122.33 -8.23 2.00e+00 2.50e-01 1.69e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.67 -4.74 1.20e+00 6.94e-01 1.56e+01 ... (remaining 35128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 13762 17.98 - 35.96: 964 35.96 - 53.94: 114 53.94 - 71.93: 50 71.93 - 89.91: 29 Dihedral angle restraints: 14919 sinusoidal: 5841 harmonic: 9078 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 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+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 180.00 157.35 22.65 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 14916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3283 0.063 - 0.127: 778 0.127 - 0.190: 84 0.190 - 0.253: 5 0.253 - 0.317: 5 Chirality restraints: 4155 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 -2.08 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.43e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 4152 not shown) Planarity restraints: 4521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 902 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.56e+00 pdb=" C MET C 902 " 0.053 2.00e-02 2.50e+03 pdb=" O MET C 902 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA C 903 " -0.018 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 2.89e-02 8.33e+00 pdb=" C GLN C 920 " 0.050 2.00e-02 2.50e+03 pdb=" O GLN C 920 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS C 921 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 135 " 0.014 2.00e-02 2.50e+03 2.17e-02 8.27e+00 pdb=" CG PHE B 135 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE B 135 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE B 135 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 135 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE B 135 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE B 135 " 0.001 2.00e-02 2.50e+03 ... (remaining 4518 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6164 2.80 - 3.32: 21113 3.32 - 3.85: 43056 3.85 - 4.37: 49720 4.37 - 4.90: 85023 Nonbonded interactions: 205076 Sorted by model distance: nonbonded pdb=" OH TYR A 369 " pdb=" O ALA C 475 " model vdw 2.272 3.040 nonbonded pdb=" OE1 GLN B 115 " pdb=" OG1 THR B 167 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.287 3.040 nonbonded pdb=" OD1 ASN B 394 " pdb=" OH TYR B 396 " model vdw 2.289 3.040 nonbonded pdb=" O ASP A 80 " pdb=" OH TYR A 265 " model vdw 2.316 3.040 ... (remaining 205071 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: 0.02 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 27.900 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 0.070 25914 Z= 0.226 Angle : 0.805 14.982 35397 Z= 0.415 Chirality : 0.053 0.317 4155 Planarity : 0.007 0.066 4479 Dihedral : 13.045 89.907 8949 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: 0.21 (0.18), residues: 639 sheet: 0.21 (0.19), residues: 684 loop : -0.90 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 357 TYR 0.025 0.002 TYR C1067 PHE 0.043 0.002 PHE B 135 TRP 0.023 0.002 TRP A 886 HIS 0.006 0.001 HIS B 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.23 (25812) covalent geometry : angle 0.77616 / 0.41 (35133) SS BOND : bond 0.00240 / 0.17 ( 42) SS BOND : angle 1.29507 / 0.88 ( 84) hydrogen bonds : bond 0.16762 / 11.37 ( 1028) hydrogen bonds : angle 8.04409 / 5.63 ( 3015) link_BETA1-4 : bond 0.00667 / 0.43 ( 18) link_BETA1-4 : angle 1.41482 / 0.99 ( 54) link_NAG-ASN : bond 0.00801 / 0.41 ( 42) link_NAG-ASN : angle 3.49438 / 2.91 ( 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 219 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PRO cc_start: 0.8970 (Cg_exo) cc_final: 0.8722 (Cg_endo) REVERT: A 153 MET cc_start: 0.3575 (ptt) cc_final: 0.3367 (tpt) REVERT: A 175 PHE cc_start: 0.5143 (m-10) cc_final: 0.4891 (m-10) REVERT: B 140 PHE cc_start: 0.7854 (p90) cc_final: 0.7472 (OUTLIER) REVERT: B 244 LEU cc_start: 0.6402 (mt) cc_final: 0.6059 (tm) REVERT: C 85 PRO cc_start: 0.8669 (Cg_exo) cc_final: 0.8144 (Cg_endo) REVERT: C 218 GLN cc_start: 0.7911 (tt0) cc_final: 0.7661 (tp-100) REVERT: C 226 LEU cc_start: 0.5896 (tp) cc_final: 0.5196 (mm) REVERT: C 403 ARG cc_start: 0.8140 (mtp180) cc_final: 0.7709 (mtp85) REVERT: C 421 TYR cc_start: 0.9113 (m-10) cc_final: 0.8751 (m-10) outliers start: 0 outliers final: 2 residues processed: 219 average time/residue: 0.6808 time to fit residues: 171.0758 Evaluate side-chains 102 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN A1005 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.104351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.063187 restraints weight = 71519.941| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.25 r_work: 0.2957 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25914 Z= 0.218 Angle : 0.639 12.500 35397 Z= 0.320 Chirality : 0.047 0.702 4155 Planarity : 0.005 0.061 4479 Dihedral : 4.652 24.501 3347 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.73 % Allowed : 5.53 % Favored : 93.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.04 (0.14), residues: 3072 helix: 1.49 (0.20), residues: 675 sheet: 0.28 (0.19), residues: 661 loop : -0.65 (0.13), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 190 TYR 0.021 0.001 TYR C1067 PHE 0.019 0.002 PHE B 135 TRP 0.022 0.002 TRP A 353 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.22 (25812) covalent geometry : angle 0.61193 / 0.31 (35133) SS BOND : bond 0.00197 / 0.13 ( 42) SS BOND : angle 0.78103 / 0.54 ( 84) hydrogen bonds : bond 0.04691 / 3.14 ( 1028) hydrogen bonds : angle 6.23420 / 4.39 ( 3015) link_BETA1-4 : bond 0.00191 / 0.13 ( 18) link_BETA1-4 : angle 1.11392 / 0.79 ( 54) link_NAG-ASN : bond 0.00567 / 0.32 ( 42) link_NAG-ASN : angle 3.04714 / 2.34 ( 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 127 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3865 (ptt) cc_final: 0.3519 (tpt) REVERT: A 304 LYS cc_start: 0.9417 (mmmm) cc_final: 0.9180 (mmmm) REVERT: B 140 PHE cc_start: 0.8293 (p90) cc_final: 0.8025 (OUTLIER) REVERT: B 858 LEU cc_start: 0.9042 (mt) cc_final: 0.8563 (pt) REVERT: C 218 GLN cc_start: 0.8082 (tt0) cc_final: 0.7657 (tp-100) REVERT: C 403 ARG cc_start: 0.8026 (mtp180) cc_final: 0.7570 (mmm-85) REVERT: C 417 LYS cc_start: 0.8988 (tptt) cc_final: 0.8492 (tptp) REVERT: C 421 TYR cc_start: 0.9091 (m-10) cc_final: 0.8787 (m-10) outliers start: 20 outliers final: 8 residues processed: 121 average time/residue: 0.6223 time to fit residues: 88.3458 Evaluate side-chains 92 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 305 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 chunk 273 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 216 optimal weight: 20.0000 chunk 175 optimal weight: 0.6980 chunk 205 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN B 245 HIS B 354 ASN B 824 ASN B 901 GLN C 121 ASN C 580 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.103789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.062455 restraints weight = 71487.067| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.29 r_work: 0.2926 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25914 Z= 0.178 Angle : 0.587 11.075 35397 Z= 0.292 Chirality : 0.046 0.561 4155 Planarity : 0.004 0.042 4479 Dihedral : 4.466 23.622 3347 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.99 % Allowed : 6.62 % Favored : 92.39 % 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: 0.26 (0.15), residues: 3072 helix: 1.95 (0.20), residues: 682 sheet: 0.17 (0.19), residues: 674 loop : -0.54 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 995 TYR 0.021 0.001 TYR C1067 PHE 0.024 0.001 PHE B 565 TRP 0.017 0.001 TRP A 353 HIS 0.003 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (25812) covalent geometry : angle 0.56083 / 0.29 (35133) SS BOND : bond 0.00188 / 0.13 ( 42) SS BOND : angle 0.70103 / 0.47 ( 84) hydrogen bonds : bond 0.04349 / 2.92 ( 1028) hydrogen bonds : angle 5.85079 / 4.10 ( 3015) link_BETA1-4 : bond 0.00245 / 0.16 ( 18) link_BETA1-4 : angle 0.99476 / 0.69 ( 54) link_NAG-ASN : bond 0.00972 / 0.55 ( 42) link_NAG-ASN : angle 2.86578 / 2.27 ( 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 123 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3706 (ptt) cc_final: 0.3346 (tpt) REVERT: A 304 LYS cc_start: 0.9408 (mmmm) cc_final: 0.9183 (mmmm) REVERT: A 1010 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8540 (mp10) REVERT: A 1029 MET cc_start: 0.9667 (OUTLIER) cc_final: 0.9325 (tpp) REVERT: B 140 PHE cc_start: 0.8419 (p90) cc_final: 0.8188 (OUTLIER) REVERT: B 434 ILE cc_start: 0.5607 (OUTLIER) cc_final: 0.5177 (pp) REVERT: C 144 TYR cc_start: 0.5361 (m-10) cc_final: 0.5031 (m-80) REVERT: C 218 GLN cc_start: 0.8138 (tt0) cc_final: 0.7629 (tp-100) REVERT: C 403 ARG cc_start: 0.7967 (mtp180) cc_final: 0.7535 (mtp85) REVERT: C 417 LYS cc_start: 0.9117 (tptt) cc_final: 0.8792 (tptp) REVERT: C 421 TYR cc_start: 0.9104 (m-10) cc_final: 0.8749 (m-10) REVERT: C 584 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8063 (mm) outliers start: 27 outliers final: 11 residues processed: 117 average time/residue: 0.5529 time to fit residues: 76.8995 Evaluate side-chains 104 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 584 ILE 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 214 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 153 optimal weight: 8.9990 chunk 38 optimal weight: 20.0000 chunk 243 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 270 optimal weight: 5.9990 chunk 192 optimal weight: 0.8980 chunk 147 optimal weight: 40.0000 chunk 107 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 907 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 907 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.102167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.060605 restraints weight = 71359.702| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.30 r_work: 0.2894 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 25914 Z= 0.254 Angle : 0.631 16.621 35397 Z= 0.311 Chirality : 0.047 0.434 4155 Planarity : 0.004 0.040 4479 Dihedral : 4.559 22.431 3347 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.39 % Allowed : 7.43 % Favored : 91.18 % 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: 0.28 (0.15), residues: 3072 helix: 2.06 (0.20), residues: 700 sheet: -0.02 (0.19), residues: 673 loop : -0.50 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 995 TYR 0.021 0.002 TYR C1067 PHE 0.028 0.002 PHE B 565 TRP 0.015 0.002 TRP A 886 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.25 (25812) covalent geometry : angle 0.60527 / 0.31 (35133) SS BOND : bond 0.00216 / 0.15 ( 42) SS BOND : angle 0.68383 / 0.45 ( 84) hydrogen bonds : bond 0.04619 / 3.10 ( 1028) hydrogen bonds : angle 5.80706 / 4.07 ( 3015) link_BETA1-4 : bond 0.00170 / 0.10 ( 18) link_BETA1-4 : angle 1.06827 / 0.74 ( 54) link_NAG-ASN : bond 0.00812 / 0.50 ( 42) link_NAG-ASN : angle 2.96450 / 2.26 ( 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 132 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3874 (ptt) cc_final: 0.3438 (tpp) REVERT: A 323 THR cc_start: 0.9058 (OUTLIER) cc_final: 0.8762 (p) REVERT: A 365 TYR cc_start: 0.8172 (m-80) cc_final: 0.7921 (m-80) REVERT: A 1010 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8882 (mp10) REVERT: B 140 PHE cc_start: 0.8529 (p90) cc_final: 0.8292 (OUTLIER) REVERT: B 392 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7421 (m-80) REVERT: B 858 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8729 (pt) REVERT: B 985 ASP cc_start: 0.8692 (p0) cc_final: 0.8452 (p0) REVERT: C 101 ILE cc_start: 0.6342 (mm) cc_final: 0.5854 (OUTLIER) REVERT: C 218 GLN cc_start: 0.8197 (tt0) cc_final: 0.7705 (tp-100) REVERT: C 403 ARG cc_start: 0.7965 (mtp180) cc_final: 0.7563 (mtp-110) REVERT: C 417 LYS cc_start: 0.9143 (tptt) cc_final: 0.8854 (tptp) REVERT: C 421 TYR cc_start: 0.9082 (m-10) cc_final: 0.8687 (m-10) REVERT: C 584 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8222 (mm) REVERT: C 995 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8769 (mtp-110) outliers start: 38 outliers final: 17 residues processed: 124 average time/residue: 0.4957 time to fit residues: 74.3878 Evaluate side-chains 108 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 295 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 279 optimal weight: 0.2980 chunk 100 optimal weight: 0.9990 chunk 246 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 254 optimal weight: 0.8980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 762 GLN B 907 ASN C 955 ASN C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.103128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.062785 restraints weight = 70909.301| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.19 r_work: 0.2929 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25914 Z= 0.136 Angle : 0.550 10.997 35397 Z= 0.273 Chirality : 0.045 0.406 4155 Planarity : 0.004 0.039 4479 Dihedral : 4.328 23.095 3345 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.17 % Allowed : 8.05 % Favored : 90.78 % 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: 0.43 (0.15), residues: 3072 helix: 2.25 (0.20), residues: 700 sheet: 0.05 (0.19), residues: 672 loop : -0.42 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.020 0.001 TYR C1067 PHE 0.024 0.001 PHE B 565 TRP 0.021 0.001 TRP C 104 HIS 0.002 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (25812) covalent geometry : angle 0.52666 / 0.27 (35133) SS BOND : bond 0.00126 / 0.09 ( 42) SS BOND : angle 0.57798 / 0.39 ( 84) hydrogen bonds : bond 0.04045 / 2.72 ( 1028) hydrogen bonds : angle 5.57435 / 3.91 ( 3015) link_BETA1-4 : bond 0.00286 / 0.18 ( 18) link_BETA1-4 : angle 0.88857 / 0.60 ( 54) link_NAG-ASN : bond 0.00649 / 0.40 ( 42) link_NAG-ASN : angle 2.65819 / 2.14 ( 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 119 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3881 (ptt) cc_final: 0.3438 (tpp) REVERT: A 323 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8750 (p) REVERT: A 365 TYR cc_start: 0.8148 (m-80) cc_final: 0.7898 (m-80) REVERT: B 140 PHE cc_start: 0.8554 (p90) cc_final: 0.8277 (OUTLIER) REVERT: B 434 ILE cc_start: 0.5803 (OUTLIER) cc_final: 0.5374 (pp) REVERT: B 858 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8649 (pt) REVERT: C 378 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8121 (tmmm) REVERT: C 403 ARG cc_start: 0.7928 (mtp180) cc_final: 0.7484 (mtp85) REVERT: C 417 LYS cc_start: 0.9174 (tptt) cc_final: 0.8888 (tptp) REVERT: C 421 TYR cc_start: 0.9096 (m-10) cc_final: 0.8698 (m-10) REVERT: C 584 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8261 (mm) REVERT: C 995 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8915 (mtp-110) outliers start: 32 outliers final: 10 residues processed: 113 average time/residue: 0.5837 time to fit residues: 78.7576 Evaluate side-chains 98 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 292 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 269 optimal weight: 3.9990 chunk 201 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 255 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 1 optimal weight: 0.0670 chunk 257 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.102717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.061857 restraints weight = 71374.339| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.19 r_work: 0.2918 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25914 Z= 0.157 Angle : 0.554 10.772 35397 Z= 0.275 Chirality : 0.045 0.391 4155 Planarity : 0.004 0.038 4479 Dihedral : 4.271 22.284 3345 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.24 % Allowed : 8.71 % Favored : 90.05 % 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: 0.47 (0.15), residues: 3072 helix: 2.29 (0.20), residues: 700 sheet: -0.01 (0.20), residues: 661 loop : -0.37 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 995 TYR 0.020 0.001 TYR C1067 PHE 0.025 0.001 PHE B 565 TRP 0.012 0.001 TRP C 104 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (25812) covalent geometry : angle 0.53115 / 0.27 (35133) SS BOND : bond 0.00139 / 0.10 ( 42) SS BOND : angle 0.60385 / 0.40 ( 84) hydrogen bonds : bond 0.04063 / 2.74 ( 1028) hydrogen bonds : angle 5.50983 / 3.86 ( 3015) link_BETA1-4 : bond 0.00229 / 0.15 ( 18) link_BETA1-4 : angle 0.95351 / 0.66 ( 54) link_NAG-ASN : bond 0.00643 / 0.39 ( 42) link_NAG-ASN : angle 2.61882 / 2.10 ( 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 124 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3772 (ptt) cc_final: 0.3391 (tpp) REVERT: A 323 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8732 (p) REVERT: A 365 TYR cc_start: 0.8158 (m-80) cc_final: 0.7914 (m-80) REVERT: B 140 PHE cc_start: 0.8517 (p90) cc_final: 0.8219 (OUTLIER) REVERT: B 392 PHE cc_start: 0.7918 (OUTLIER) cc_final: 0.7351 (m-80) REVERT: B 434 ILE cc_start: 0.5930 (OUTLIER) cc_final: 0.5536 (pp) REVERT: B 858 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8696 (pt) REVERT: C 237 ARG cc_start: 0.6991 (ttp80) cc_final: 0.6647 (tmm-80) REVERT: C 324 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8900 (pm20) REVERT: C 403 ARG cc_start: 0.7969 (mtp180) cc_final: 0.7629 (mtp-110) REVERT: C 417 LYS cc_start: 0.9185 (tptt) cc_final: 0.8881 (tptm) REVERT: C 421 TYR cc_start: 0.9071 (m-10) cc_final: 0.8699 (m-10) REVERT: C 584 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8201 (mm) REVERT: C 995 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8879 (mtp-110) outliers start: 34 outliers final: 12 residues processed: 116 average time/residue: 0.5840 time to fit residues: 80.7338 Evaluate side-chains 103 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 29 optimal weight: 30.0000 chunk 9 optimal weight: 9.9990 chunk 249 optimal weight: 0.3980 chunk 160 optimal weight: 4.9990 chunk 230 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 271 optimal weight: 0.8980 chunk 247 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 284 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN A1005 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.102699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.061939 restraints weight = 71225.790| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.16 r_work: 0.2924 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25914 Z= 0.146 Angle : 0.541 10.858 35397 Z= 0.269 Chirality : 0.044 0.378 4155 Planarity : 0.004 0.037 4479 Dihedral : 4.203 21.788 3345 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.21 % Allowed : 9.44 % Favored : 89.35 % 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: 0.51 (0.15), residues: 3072 helix: 2.34 (0.20), residues: 700 sheet: -0.02 (0.20), residues: 664 loop : -0.34 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 765 TYR 0.020 0.001 TYR C1067 PHE 0.026 0.001 PHE B 565 TRP 0.011 0.001 TRP C 104 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (25812) covalent geometry : angle 0.51846 / 0.26 (35133) SS BOND : bond 0.00124 / 0.09 ( 42) SS BOND : angle 0.56535 / 0.38 ( 84) hydrogen bonds : bond 0.03957 / 2.66 ( 1028) hydrogen bonds : angle 5.43633 / 3.80 ( 3015) link_BETA1-4 : bond 0.00254 / 0.16 ( 18) link_BETA1-4 : angle 0.89937 / 0.62 ( 54) link_NAG-ASN : bond 0.00620 / 0.38 ( 42) link_NAG-ASN : angle 2.56360 / 2.07 ( 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 121 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3470 (ptt) cc_final: 0.3205 (tpp) REVERT: A 323 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8743 (p) REVERT: A 365 TYR cc_start: 0.8106 (m-80) cc_final: 0.7846 (m-80) REVERT: B 140 PHE cc_start: 0.8522 (p90) cc_final: 0.8234 (OUTLIER) REVERT: B 392 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7345 (m-80) REVERT: B 434 ILE cc_start: 0.6110 (OUTLIER) cc_final: 0.5728 (pp) REVERT: B 858 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8671 (pt) REVERT: C 218 GLN cc_start: 0.8382 (tt0) cc_final: 0.7811 (tp-100) REVERT: C 237 ARG cc_start: 0.7052 (ttp80) cc_final: 0.6624 (tmm-80) REVERT: C 324 GLU cc_start: 0.9237 (OUTLIER) cc_final: 0.8879 (pm20) REVERT: C 403 ARG cc_start: 0.7966 (mtp180) cc_final: 0.7694 (mtp-110) REVERT: C 417 LYS cc_start: 0.9193 (tptt) cc_final: 0.8924 (tptm) REVERT: C 421 TYR cc_start: 0.9081 (m-10) cc_final: 0.8667 (m-10) REVERT: C 584 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8238 (mm) REVERT: C 995 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8857 (mtp-110) outliers start: 33 outliers final: 13 residues processed: 115 average time/residue: 0.6103 time to fit residues: 82.5378 Evaluate side-chains 103 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 116 optimal weight: 1.9990 chunk 243 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 259 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 258 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.102199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.061208 restraints weight = 71452.535| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.19 r_work: 0.2900 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25914 Z= 0.178 Angle : 0.554 10.631 35397 Z= 0.276 Chirality : 0.045 0.373 4155 Planarity : 0.004 0.040 4479 Dihedral : 4.269 31.724 3345 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.88 % Allowed : 10.10 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.49 (0.15), residues: 3072 helix: 2.35 (0.20), residues: 700 sheet: -0.06 (0.20), residues: 664 loop : -0.34 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 567 TYR 0.020 0.001 TYR C 380 PHE 0.028 0.001 PHE C 497 TRP 0.008 0.001 TRP B 436 HIS 0.002 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (25812) covalent geometry : angle 0.53239 / 0.27 (35133) SS BOND : bond 0.00130 / 0.09 ( 42) SS BOND : angle 0.57198 / 0.38 ( 84) hydrogen bonds : bond 0.04067 / 2.73 ( 1028) hydrogen bonds : angle 5.48794 / 3.85 ( 3015) link_BETA1-4 : bond 0.00204 / 0.13 ( 18) link_BETA1-4 : angle 0.92787 / 0.64 ( 54) link_NAG-ASN : bond 0.00625 / 0.38 ( 42) link_NAG-ASN : angle 2.56521 / 2.07 ( 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 111 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3337 (ptt) cc_final: 0.3029 (tpp) REVERT: A 323 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8757 (p) REVERT: A 365 TYR cc_start: 0.8128 (m-80) cc_final: 0.7847 (m-80) REVERT: B 140 PHE cc_start: 0.8532 (p90) cc_final: 0.8250 (OUTLIER) REVERT: B 392 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7395 (m-80) REVERT: B 434 ILE cc_start: 0.6236 (OUTLIER) cc_final: 0.5841 (pp) REVERT: B 858 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8689 (pt) REVERT: C 237 ARG cc_start: 0.7104 (ttp80) cc_final: 0.6635 (tmm-80) REVERT: C 324 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8872 (pm20) REVERT: C 403 ARG cc_start: 0.7967 (mtp180) cc_final: 0.7653 (mtp85) REVERT: C 421 TYR cc_start: 0.9072 (m-10) cc_final: 0.8667 (m-10) REVERT: C 995 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8855 (mtp-110) outliers start: 24 outliers final: 14 residues processed: 105 average time/residue: 0.6005 time to fit residues: 74.4415 Evaluate side-chains 103 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 254 optimal weight: 10.0000 chunk 311 optimal weight: 0.0050 chunk 212 optimal weight: 1.9990 chunk 267 optimal weight: 0.7980 chunk 292 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 270 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 242 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 195 optimal weight: 0.5980 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 354 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.102555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.061915 restraints weight = 71043.757| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.23 r_work: 0.2908 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3142 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= 0.136 Angle : 0.541 12.146 35397 Z= 0.269 Chirality : 0.044 0.364 4155 Planarity : 0.004 0.037 4479 Dihedral : 4.150 21.665 3345 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.95 % Allowed : 10.21 % Favored : 88.84 % 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: 0.56 (0.15), residues: 3072 helix: 2.46 (0.20), residues: 693 sheet: -0.03 (0.20), residues: 657 loop : -0.30 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 319 TYR 0.020 0.001 TYR C 380 PHE 0.028 0.001 PHE C 497 TRP 0.029 0.001 TRP C 104 HIS 0.002 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (25812) covalent geometry : angle 0.52035 / 0.26 (35133) SS BOND : bond 0.00112 / 0.08 ( 42) SS BOND : angle 0.55283 / 0.37 ( 84) hydrogen bonds : bond 0.03850 / 2.59 ( 1028) hydrogen bonds : angle 5.39023 / 3.77 ( 3015) link_BETA1-4 : bond 0.00266 / 0.17 ( 18) link_BETA1-4 : angle 0.86596 / 0.59 ( 54) link_NAG-ASN : bond 0.00605 / 0.36 ( 42) link_NAG-ASN : angle 2.51150 / 2.04 ( 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 115 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3400 (ptt) cc_final: 0.3033 (tpp) REVERT: A 323 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8758 (p) REVERT: A 365 TYR cc_start: 0.8151 (m-80) cc_final: 0.7856 (m-80) REVERT: B 140 PHE cc_start: 0.8530 (p90) cc_final: 0.8234 (OUTLIER) REVERT: B 392 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: B 434 ILE cc_start: 0.6377 (OUTLIER) cc_final: 0.5965 (pp) REVERT: B 858 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8674 (pt) REVERT: C 69 HIS cc_start: 0.5421 (t-90) cc_final: 0.5220 (t-90) REVERT: C 218 GLN cc_start: 0.8536 (tt0) cc_final: 0.8004 (tp-100) REVERT: C 237 ARG cc_start: 0.7094 (ttp80) cc_final: 0.6664 (tmm-80) REVERT: C 324 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.8863 (pm20) REVERT: C 403 ARG cc_start: 0.7998 (mtp180) cc_final: 0.7696 (mtp85) REVERT: C 421 TYR cc_start: 0.9030 (m-10) cc_final: 0.8659 (m-10) REVERT: C 495 TYR cc_start: 0.5382 (m-80) cc_final: 0.4689 (m-80) REVERT: C 497 PHE cc_start: 0.4160 (m-10) cc_final: 0.3171 (m-80) REVERT: C 584 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8183 (mm) REVERT: C 995 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8859 (mtp-110) outliers start: 26 outliers final: 14 residues processed: 109 average time/residue: 0.4945 time to fit residues: 65.3289 Evaluate side-chains 106 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 159 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 93 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 213 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 239 optimal weight: 10.0000 chunk 222 optimal weight: 8.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** 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 = 0.3981 r_free = 0.3981 target = 0.101581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.060744 restraints weight = 71248.255| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.21 r_work: 0.2877 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 25914 Z= 0.199 Angle : 0.569 10.723 35397 Z= 0.283 Chirality : 0.045 0.358 4155 Planarity : 0.004 0.050 4479 Dihedral : 4.252 21.076 3345 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.88 % Allowed : 10.32 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.48 (0.15), residues: 3072 helix: 2.40 (0.20), residues: 692 sheet: -0.16 (0.20), residues: 669 loop : -0.32 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 319 TYR 0.019 0.001 TYR C1067 PHE 0.026 0.001 PHE B 565 TRP 0.039 0.002 TRP C 104 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (25812) covalent geometry : angle 0.54770 / 0.28 (35133) SS BOND : bond 0.00163 / 0.11 ( 42) SS BOND : angle 0.57908 / 0.39 ( 84) hydrogen bonds : bond 0.04194 / 2.82 ( 1028) hydrogen bonds : angle 5.52273 / 3.87 ( 3015) link_BETA1-4 : bond 0.00183 / 0.11 ( 18) link_BETA1-4 : angle 0.97588 / 0.67 ( 54) link_NAG-ASN : bond 0.00630 / 0.39 ( 42) link_NAG-ASN : angle 2.57466 / 2.07 ( 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 110 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3551 (ptt) cc_final: 0.2998 (tpp) REVERT: A 323 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8601 (p) REVERT: A 365 TYR cc_start: 0.8217 (m-80) cc_final: 0.7912 (m-80) REVERT: B 140 PHE cc_start: 0.8584 (p90) cc_final: 0.8298 (p90) REVERT: B 392 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7530 (m-80) REVERT: B 434 ILE cc_start: 0.6523 (OUTLIER) cc_final: 0.6122 (pp) REVERT: B 858 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8756 (pt) REVERT: C 194 PHE cc_start: 0.7216 (m-10) cc_final: 0.6965 (m-10) REVERT: C 218 GLN cc_start: 0.8556 (tt0) cc_final: 0.8039 (tp-100) REVERT: C 324 GLU cc_start: 0.9254 (OUTLIER) cc_final: 0.8869 (pm20) REVERT: C 403 ARG cc_start: 0.7946 (mtp180) cc_final: 0.7625 (mtp85) REVERT: C 495 TYR cc_start: 0.5421 (m-80) cc_final: 0.4854 (m-80) REVERT: C 497 PHE cc_start: 0.4132 (m-10) cc_final: 0.3198 (m-80) REVERT: C 584 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8094 (mm) REVERT: C 995 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.8839 (mtp-110) REVERT: C 1092 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8687 (pm20) outliers start: 24 outliers final: 12 residues processed: 105 average time/residue: 0.5464 time to fit residues: 69.4114 Evaluate side-chains 104 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 68 optimal weight: 0.8980 chunk 287 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 chunk 273 optimal weight: 5.9990 chunk 223 optimal weight: 7.9990 chunk 305 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 241 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 354 ASN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.102336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.061586 restraints weight = 71095.268| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.29 r_work: 0.2906 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25914 Z= 0.125 Angle : 0.536 10.784 35397 Z= 0.268 Chirality : 0.044 0.359 4155 Planarity : 0.004 0.041 4479 Dihedral : 4.132 21.506 3345 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.73 % Allowed : 10.57 % 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: 0.57 (0.15), residues: 3072 helix: 2.53 (0.20), residues: 685 sheet: -0.13 (0.20), residues: 669 loop : -0.26 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 319 TYR 0.020 0.001 TYR C1067 PHE 0.025 0.001 PHE B 565 TRP 0.047 0.001 TRP C 104 HIS 0.002 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (25812) covalent geometry : angle 0.51497 / 0.26 (35133) SS BOND : bond 0.00120 / 0.08 ( 42) SS BOND : angle 0.54485 / 0.37 ( 84) hydrogen bonds : bond 0.03873 / 2.61 ( 1028) hydrogen bonds : angle 5.40040 / 3.78 ( 3015) link_BETA1-4 : bond 0.00276 / 0.18 ( 18) link_BETA1-4 : angle 0.88100 / 0.60 ( 54) link_NAG-ASN : bond 0.00597 / 0.35 ( 42) link_NAG-ASN : angle 2.51270 / 2.04 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12122.77 seconds wall clock time: 206 minutes 31.84 seconds (12391.84 seconds total)