Starting phenix.real_space_refine on Thu Mar 5 21:28:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sxt_25505/03_2026/7sxt_25505.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sxt_25505/03_2026/7sxt_25505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sxt_25505/03_2026/7sxt_25505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sxt_25505/03_2026/7sxt_25505.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sxt_25505/03_2026/7sxt_25505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sxt_25505/03_2026/7sxt_25505.map" } resolution = 2.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 16074 2.51 5 N 4125 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-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25248 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8136 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8136 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8136 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.31, per 1000 atoms: 0.25 Number of scatterers: 25248 At special positions: 0 Unit cell: (141, 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 4125 7.00 C 16074 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=2.03 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: 2.22 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, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 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: 4.046A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.682A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.461A 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: 4.104A 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: 3.680A 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: 3.920A 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: 4.030A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.562A 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: 4.002A 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: 3.674A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.910A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.570A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.978A 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: 3.633A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.575A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.902A 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: 3.521A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.968A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.550A 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: 3.810A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.670A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.886A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.530A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.907A 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: 3.715A 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: 3.964A 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: 3.601A 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 removed outlier: 3.508A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.266A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.599A 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: 7.976A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.903A 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: 3.789A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.195A 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: 3.886A 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: 3.739A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 11.581A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.259A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.442A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.739A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.703A 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: 6.824A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.982A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.518A 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: 3.993A 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: 3.559A 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: 6.060A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.406A 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: 6.829A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.867A 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: 6.528A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.082A 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: 6.528A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.206A 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: 3.685A 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: 8.341A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.075A 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: 3.985A 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: 3.623A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.500A 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: 5.078A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.192A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.704A 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: 3.677A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.823A 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: 3.645A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.041A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.636A 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: 6.499A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.047A 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: 6.499A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.479A 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: 4.228A 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: 8.190A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.676A 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: 4.190A 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: 3.951A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.642A 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: 9.704A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.790A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 10.133A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.705A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.794A 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: 5.154A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.863A 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: 3.723A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.743A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.644A 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: 6.254A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.467A 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: 6.526A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.042A 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: 6.649A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.044A 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: 6.526A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.556A 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: 4.155A 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 1087 hydrogen bonds defined for protein. 2985 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.20 Time building geometry restraints manager: 3.00 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: 7333 1.34 - 1.46: 6169 1.46 - 1.58: 12178 1.58 - 1.70: 0 1.70 - 1.83: 138 Bond restraints: 25818 Sorted by residual: bond pdb=" C LEU C 560 " pdb=" N PRO C 561 " ideal model delta sigma weight residual 1.334 1.387 -0.053 1.51e-02 4.39e+03 1.22e+01 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.65e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.12e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.94e+00 ... (remaining 25813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 34004 1.99 - 3.98: 1011 3.98 - 5.97: 96 5.97 - 7.96: 26 7.96 - 9.95: 8 Bond angle restraints: 35145 Sorted by residual: angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.36 -5.66 1.22e+00 6.72e-01 2.15e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.27 -5.57 1.22e+00 6.72e-01 2.09e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.08 -5.38 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 114.10 122.09 -7.99 2.00e+00 2.50e-01 1.60e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.60 -4.67 1.20e+00 6.94e-01 1.52e+01 ... (remaining 35140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14918 17.98 - 35.97: 1015 35.97 - 53.95: 155 53.95 - 71.93: 56 71.93 - 89.92: 29 Dihedral angle restraints: 16173 sinusoidal: 7092 harmonic: 9081 Sorted by residual: dihedral pdb=" CA LEU B 517 " pdb=" C LEU B 517 " pdb=" N LEU B 518 " pdb=" CA LEU B 518 " ideal model delta harmonic sigma weight residual 180.00 153.99 26.01 0 5.00e+00 4.00e-02 2.71e+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 180.00 154.29 25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA PHE C 515 " pdb=" C PHE C 515 " pdb=" N GLU C 516 " pdb=" CA GLU C 516 " ideal model delta harmonic sigma weight residual 180.00 157.31 22.69 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 16170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3243 0.061 - 0.122: 795 0.122 - 0.183: 103 0.183 - 0.244: 14 0.244 - 0.306: 3 Chirality restraints: 4158 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 4155 not shown) Planarity restraints: 4518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 902 " -0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C MET C 902 " 0.057 2.00e-02 2.50e+03 pdb=" O MET C 902 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA C 903 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 920 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.90e+00 pdb=" C GLN C 920 " 0.052 2.00e-02 2.50e+03 pdb=" O GLN C 920 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS C 921 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A1029 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C MET A1029 " 0.051 2.00e-02 2.50e+03 pdb=" O MET A1029 " -0.019 2.00e-02 2.50e+03 pdb=" N SER A1030 " -0.017 2.00e-02 2.50e+03 ... (remaining 4515 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6828 2.81 - 3.33: 21059 3.33 - 3.85: 43297 3.85 - 4.38: 49762 4.38 - 4.90: 84966 Nonbonded interactions: 205912 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.287 3.040 nonbonded pdb=" OE1 GLN B 115 " pdb=" OG1 THR B 167 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR A 369 " pdb=" O ALA C 475 " model vdw 2.311 3.040 nonbonded pdb=" O ASP B 80 " pdb=" OH TYR B 265 " model vdw 2.329 3.040 nonbonded pdb=" O ASP A 80 " pdb=" OH TYR A 265 " model vdw 2.334 3.040 ... (remaining 205907 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.640 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: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.010 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 0.083 25920 Z= 0.229 Angle : 0.808 15.083 35409 Z= 0.416 Chirality : 0.053 0.306 4158 Planarity : 0.007 0.065 4476 Dihedral : 12.825 89.918 10203 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.13), residues: 3072 helix: 0.10 (0.18), residues: 650 sheet: 0.11 (0.18), residues: 687 loop : -0.86 (0.13), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 357 TYR 0.029 0.002 TYR C1067 PHE 0.042 0.002 PHE B 135 TRP 0.033 0.002 TRP A 886 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00488 (25818) covalent geometry : angle 0.77876 (35145) SS BOND : bond 0.00258 ( 42) SS BOND : angle 1.30734 ( 84) hydrogen bonds : bond 0.16206 ( 1022) hydrogen bonds : angle 7.94797 ( 2985) link_BETA1-4 : bond 0.00681 ( 18) link_BETA1-4 : angle 1.38537 ( 54) link_NAG-ASN : bond 0.00806 ( 42) link_NAG-ASN : angle 3.51227 ( 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 307 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8344 (m-40) cc_final: 0.7660 (m-40) REVERT: A 153 MET cc_start: 0.4816 (ptt) cc_final: 0.3902 (tpt) REVERT: A 240 THR cc_start: 0.7417 (m) cc_final: 0.6753 (t) REVERT: A 1005 GLN cc_start: 0.8095 (mt0) cc_final: 0.7611 (mt0) REVERT: B 208 THR cc_start: 0.7675 (m) cc_final: 0.7435 (p) REVERT: B 396 TYR cc_start: 0.6611 (m-80) cc_final: 0.6355 (m-80) REVERT: B 403 ARG cc_start: 0.6496 (mtp180) cc_final: 0.6178 (ttt180) REVERT: B 408 ARG cc_start: 0.8058 (ptt90) cc_final: 0.7662 (ppt170) REVERT: B 985 ASP cc_start: 0.7729 (p0) cc_final: 0.6377 (p0) REVERT: C 54 LEU cc_start: 0.8639 (mm) cc_final: 0.8147 (mm) REVERT: C 386 LYS cc_start: 0.8952 (mmtt) cc_final: 0.8666 (mmtp) REVERT: C 453 TYR cc_start: 0.8399 (p90) cc_final: 0.8125 (p90) REVERT: C 740 MET cc_start: 0.7890 (ttt) cc_final: 0.7646 (ttm) REVERT: C 985 ASP cc_start: 0.7480 (p0) cc_final: 0.6906 (p0) outliers start: 0 outliers final: 1 residues processed: 307 average time/residue: 0.7048 time to fit residues: 248.8815 Evaluate side-chains 165 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 540 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 2.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 755 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 762 GLN B 901 GLN B1002 GLN B1011 GLN C 121 ASN C 207 HIS C 779 GLN C 957 GLN C1010 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.129307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.078183 restraints weight = 55684.040| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.73 r_work: 0.2989 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25920 Z= 0.173 Angle : 0.620 20.523 35409 Z= 0.310 Chirality : 0.046 0.454 4158 Planarity : 0.005 0.053 4476 Dihedral : 6.115 59.043 4607 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.10 % Allowed : 6.81 % Favored : 92.10 % 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: 1.46 (0.20), residues: 672 sheet: 0.35 (0.19), residues: 677 loop : -0.69 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 567 TYR 0.022 0.001 TYR C1067 PHE 0.019 0.002 PHE C 194 TRP 0.020 0.002 TRP B 886 HIS 0.007 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00388 (25818) covalent geometry : angle 0.58164 (35145) SS BOND : bond 0.00175 ( 42) SS BOND : angle 1.01380 ( 84) hydrogen bonds : bond 0.04664 ( 1022) hydrogen bonds : angle 6.12407 ( 2985) link_BETA1-4 : bond 0.00204 ( 18) link_BETA1-4 : angle 1.19581 ( 54) link_NAG-ASN : bond 0.00590 ( 42) link_NAG-ASN : angle 3.50787 ( 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 209 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8213 (m-40) cc_final: 0.7952 (m-40) REVERT: A 153 MET cc_start: 0.4625 (ptt) cc_final: 0.3496 (tmm) REVERT: A 200 TYR cc_start: 0.7749 (OUTLIER) cc_final: 0.7027 (m-10) REVERT: A 242 LEU cc_start: 0.7868 (mp) cc_final: 0.7485 (mp) REVERT: A 786 LYS cc_start: 0.8629 (pmtt) cc_final: 0.8021 (mmmt) REVERT: A 1092 GLU cc_start: 0.8481 (pm20) cc_final: 0.8043 (pp20) REVERT: B 153 MET cc_start: 0.6350 (tpp) cc_final: 0.5942 (ppp) REVERT: B 237 ARG cc_start: 0.8442 (mtp180) cc_final: 0.8074 (mtm-85) REVERT: B 400 PHE cc_start: 0.8969 (p90) cc_final: 0.8717 (p90) REVERT: B 408 ARG cc_start: 0.7924 (ptt90) cc_final: 0.7315 (ppt170) REVERT: B 1138 TYR cc_start: 0.8705 (t80) cc_final: 0.8364 (t80) REVERT: C 52 GLN cc_start: 0.7832 (tp-100) cc_final: 0.7499 (tp40) REVERT: C 420 ASP cc_start: 0.8901 (m-30) cc_final: 0.8583 (t0) REVERT: C 985 ASP cc_start: 0.7716 (p0) cc_final: 0.7471 (p0) outliers start: 30 outliers final: 10 residues processed: 200 average time/residue: 0.6131 time to fit residues: 142.4438 Evaluate side-chains 154 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 981 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 chunk 216 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 103 optimal weight: 0.1980 chunk 155 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 304 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN C 207 HIS ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.128899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.078966 restraints weight = 55624.931| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.98 r_work: 0.2963 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25920 Z= 0.141 Angle : 0.565 15.813 35409 Z= 0.282 Chirality : 0.045 0.290 4158 Planarity : 0.004 0.048 4476 Dihedral : 5.542 58.308 4607 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.39 % Allowed : 7.98 % Favored : 90.63 % 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: 0.33 (0.15), residues: 3072 helix: 2.00 (0.21), residues: 664 sheet: 0.41 (0.20), residues: 664 loop : -0.56 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 78 TYR 0.026 0.001 TYR C 453 PHE 0.020 0.001 PHE A 168 TRP 0.014 0.001 TRP B 886 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00313 (25818) covalent geometry : angle 0.53305 (35145) SS BOND : bond 0.00126 ( 42) SS BOND : angle 0.69215 ( 84) hydrogen bonds : bond 0.04317 ( 1022) hydrogen bonds : angle 5.79772 ( 2985) link_BETA1-4 : bond 0.00241 ( 18) link_BETA1-4 : angle 1.08683 ( 54) link_NAG-ASN : bond 0.00613 ( 42) link_NAG-ASN : angle 3.12647 ( 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 193 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8187 (m-40) cc_final: 0.7939 (m-40) REVERT: A 153 MET cc_start: 0.5278 (ptt) cc_final: 0.4046 (tmm) REVERT: A 200 TYR cc_start: 0.7723 (OUTLIER) cc_final: 0.6971 (m-10) REVERT: B 153 MET cc_start: 0.6457 (tpp) cc_final: 0.5971 (ppp) REVERT: B 237 ARG cc_start: 0.8526 (mtp180) cc_final: 0.8133 (mtm-85) REVERT: B 400 PHE cc_start: 0.9083 (p90) cc_final: 0.8722 (p90) REVERT: B 408 ARG cc_start: 0.8011 (ptt90) cc_final: 0.7516 (ptm-80) REVERT: B 1091 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8786 (mtm-85) REVERT: B 1138 TYR cc_start: 0.8664 (t80) cc_final: 0.8315 (t80) REVERT: C 392 PHE cc_start: 0.7749 (m-80) cc_final: 0.7318 (m-10) REVERT: C 420 ASP cc_start: 0.8943 (m-30) cc_final: 0.8624 (t0) REVERT: C 985 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7494 (p0) REVERT: C 988 GLU cc_start: 0.8957 (mp0) cc_final: 0.8668 (pm20) outliers start: 38 outliers final: 16 residues processed: 183 average time/residue: 0.6277 time to fit residues: 134.8650 Evaluate side-chains 160 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 985 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 38 optimal weight: 9.9990 chunk 243 optimal weight: 9.9990 chunk 144 optimal weight: 0.7980 chunk 270 optimal weight: 0.5980 chunk 192 optimal weight: 0.7980 chunk 147 optimal weight: 30.0000 chunk 107 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C 957 GLN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.127952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.077977 restraints weight = 55526.252| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.93 r_work: 0.2940 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25920 Z= 0.162 Angle : 0.568 14.615 35409 Z= 0.281 Chirality : 0.045 0.249 4158 Planarity : 0.004 0.046 4476 Dihedral : 5.253 56.852 4607 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.54 % Allowed : 8.71 % Favored : 89.75 % 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: 0.40 (0.15), residues: 3072 helix: 2.14 (0.20), residues: 671 sheet: 0.36 (0.20), residues: 675 loop : -0.52 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 21 TYR 0.022 0.001 TYR C1067 PHE 0.025 0.001 PHE C 140 TRP 0.017 0.001 TRP C 104 HIS 0.005 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00363 (25818) covalent geometry : angle 0.53823 (35145) SS BOND : bond 0.00127 ( 42) SS BOND : angle 0.63427 ( 84) hydrogen bonds : bond 0.04312 ( 1022) hydrogen bonds : angle 5.67050 ( 2985) link_BETA1-4 : bond 0.00215 ( 18) link_BETA1-4 : angle 1.07761 ( 54) link_NAG-ASN : bond 0.00611 ( 42) link_NAG-ASN : angle 3.02248 ( 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 192 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5469 (ptt) cc_final: 0.4053 (tmm) REVERT: A 200 TYR cc_start: 0.7678 (OUTLIER) cc_final: 0.6921 (m-10) REVERT: B 153 MET cc_start: 0.6527 (tpp) cc_final: 0.6026 (ppp) REVERT: B 237 ARG cc_start: 0.8594 (mtp180) cc_final: 0.8177 (mtm-85) REVERT: B 400 PHE cc_start: 0.9141 (p90) cc_final: 0.8711 (p90) REVERT: B 408 ARG cc_start: 0.8041 (ptt90) cc_final: 0.7548 (ptm-80) REVERT: B 512 VAL cc_start: 0.9242 (t) cc_final: 0.9019 (p) REVERT: B 985 ASP cc_start: 0.8369 (p0) cc_final: 0.8110 (p0) REVERT: C 314 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8660 (tm-30) REVERT: C 392 PHE cc_start: 0.7796 (m-80) cc_final: 0.7321 (m-10) REVERT: C 420 ASP cc_start: 0.8881 (m-30) cc_final: 0.8593 (t0) REVERT: C 453 TYR cc_start: 0.8260 (p90) cc_final: 0.7772 (p90) REVERT: C 512 VAL cc_start: 0.8780 (t) cc_final: 0.8375 (m) REVERT: C 985 ASP cc_start: 0.7946 (p0) cc_final: 0.7588 (p0) REVERT: C 988 GLU cc_start: 0.9021 (mp0) cc_final: 0.8746 (pm20) REVERT: C 990 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8497 (tm-30) REVERT: C 1141 LEU cc_start: 0.7352 (tt) cc_final: 0.7132 (tm) outliers start: 42 outliers final: 13 residues processed: 181 average time/residue: 0.6110 time to fit residues: 129.6541 Evaluate side-chains 155 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 540 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 61 optimal weight: 0.7980 chunk 190 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 141 optimal weight: 7.9990 chunk 254 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 240 optimal weight: 10.0000 chunk 133 optimal weight: 0.0980 chunk 179 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 755 GLN A 907 ASN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN C 957 GLN C1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.127671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.076588 restraints weight = 55179.421| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.71 r_work: 0.2963 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25920 Z= 0.146 Angle : 0.554 13.536 35409 Z= 0.274 Chirality : 0.045 0.243 4158 Planarity : 0.004 0.044 4476 Dihedral : 4.999 53.881 4607 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.35 % Allowed : 9.11 % Favored : 89.54 % 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: 2.25 (0.20), residues: 671 sheet: 0.30 (0.20), residues: 675 loop : -0.45 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 567 TYR 0.021 0.001 TYR B 453 PHE 0.019 0.001 PHE A 168 TRP 0.020 0.001 TRP C 104 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00323 (25818) covalent geometry : angle 0.52540 (35145) SS BOND : bond 0.00109 ( 42) SS BOND : angle 0.60353 ( 84) hydrogen bonds : bond 0.04141 ( 1022) hydrogen bonds : angle 5.53326 ( 2985) link_BETA1-4 : bond 0.00218 ( 18) link_BETA1-4 : angle 1.02643 ( 54) link_NAG-ASN : bond 0.00590 ( 42) link_NAG-ASN : angle 2.91119 ( 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 186 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5439 (ptt) cc_final: 0.3714 (mmm) REVERT: B 97 LYS cc_start: 0.6842 (OUTLIER) cc_final: 0.6533 (mtpp) REVERT: B 153 MET cc_start: 0.6591 (tpp) cc_final: 0.6135 (ppp) REVERT: B 237 ARG cc_start: 0.8541 (mtp180) cc_final: 0.8095 (mtm-85) REVERT: B 309 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8706 (mp0) REVERT: B 400 PHE cc_start: 0.9171 (p90) cc_final: 0.8663 (p90) REVERT: B 408 ARG cc_start: 0.8084 (ptt90) cc_final: 0.7562 (ptm-80) REVERT: B 512 VAL cc_start: 0.9255 (t) cc_final: 0.9045 (p) REVERT: B 646 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7314 (tpt170) REVERT: C 97 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7330 (mmmm) REVERT: C 135 PHE cc_start: 0.7422 (m-80) cc_final: 0.6975 (m-80) REVERT: C 314 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8614 (tm-30) REVERT: C 378 LYS cc_start: 0.8022 (ttmm) cc_final: 0.7549 (tmmm) REVERT: C 392 PHE cc_start: 0.7982 (m-80) cc_final: 0.7566 (m-10) REVERT: C 420 ASP cc_start: 0.8818 (m-30) cc_final: 0.8581 (t0) REVERT: C 453 TYR cc_start: 0.8176 (p90) cc_final: 0.7718 (p90) REVERT: C 512 VAL cc_start: 0.8707 (t) cc_final: 0.8405 (m) REVERT: C 661 GLU cc_start: 0.8560 (pm20) cc_final: 0.8212 (pp20) REVERT: C 985 ASP cc_start: 0.8014 (p0) cc_final: 0.7497 (p0) REVERT: C 988 GLU cc_start: 0.9010 (mp0) cc_final: 0.8749 (pm20) REVERT: C 990 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8527 (tm-30) outliers start: 37 outliers final: 12 residues processed: 176 average time/residue: 0.6540 time to fit residues: 134.1655 Evaluate side-chains 152 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 540 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 257 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 292 optimal weight: 2.9990 chunk 141 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 262 optimal weight: 5.9990 chunk 293 optimal weight: 0.8980 chunk 230 optimal weight: 0.7980 chunk 178 optimal weight: 0.5980 chunk 120 optimal weight: 4.9990 chunk 198 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN C 580 GLN C 957 GLN C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.127791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.078334 restraints weight = 55573.417| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.91 r_work: 0.2958 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25920 Z= 0.118 Angle : 0.544 12.785 35409 Z= 0.266 Chirality : 0.044 0.246 4158 Planarity : 0.003 0.045 4476 Dihedral : 4.828 53.245 4607 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.28 % Allowed : 9.40 % Favored : 89.32 % 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: 2.35 (0.20), residues: 671 sheet: 0.35 (0.20), residues: 672 loop : -0.39 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 78 TYR 0.024 0.001 TYR A 200 PHE 0.020 0.001 PHE B 168 TRP 0.026 0.001 TRP C 104 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00259 (25818) covalent geometry : angle 0.51729 (35145) SS BOND : bond 0.00100 ( 42) SS BOND : angle 0.56130 ( 84) hydrogen bonds : bond 0.03934 ( 1022) hydrogen bonds : angle 5.40922 ( 2985) link_BETA1-4 : bond 0.00254 ( 18) link_BETA1-4 : angle 0.98845 ( 54) link_NAG-ASN : bond 0.00564 ( 42) link_NAG-ASN : angle 2.78578 ( 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 181 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5357 (ptt) cc_final: 0.3573 (tmm) REVERT: A 200 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.7628 (t80) REVERT: B 97 LYS cc_start: 0.6943 (OUTLIER) cc_final: 0.6566 (mtpp) REVERT: B 153 MET cc_start: 0.6598 (tpp) cc_final: 0.6204 (ppp) REVERT: B 168 PHE cc_start: 0.6156 (t80) cc_final: 0.5897 (t80) REVERT: B 237 ARG cc_start: 0.8561 (mtp180) cc_final: 0.8116 (mtm-85) REVERT: B 309 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8698 (mp0) REVERT: B 400 PHE cc_start: 0.9193 (p90) cc_final: 0.8675 (p90) REVERT: B 408 ARG cc_start: 0.8192 (ptt90) cc_final: 0.7661 (ptm-80) REVERT: B 512 VAL cc_start: 0.9281 (t) cc_final: 0.9065 (p) REVERT: B 646 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7313 (tpt170) REVERT: C 97 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7326 (mmmm) REVERT: C 135 PHE cc_start: 0.7421 (m-80) cc_final: 0.6927 (m-80) REVERT: C 194 PHE cc_start: 0.7170 (m-10) cc_final: 0.6906 (m-10) REVERT: C 314 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8559 (tm-30) REVERT: C 378 LYS cc_start: 0.8151 (ttmm) cc_final: 0.7643 (tmmm) REVERT: C 392 PHE cc_start: 0.8012 (m-80) cc_final: 0.7764 (m-80) REVERT: C 400 PHE cc_start: 0.8587 (p90) cc_final: 0.8275 (p90) REVERT: C 403 ARG cc_start: 0.6066 (ttm110) cc_final: 0.5340 (tpp-160) REVERT: C 453 TYR cc_start: 0.8306 (p90) cc_final: 0.7789 (p90) REVERT: C 512 VAL cc_start: 0.8843 (t) cc_final: 0.8551 (m) REVERT: C 584 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7212 (mm) REVERT: C 990 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8537 (tm-30) outliers start: 35 outliers final: 11 residues processed: 169 average time/residue: 0.6724 time to fit residues: 132.2546 Evaluate side-chains 150 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 584 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 133 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 161 optimal weight: 0.0970 chunk 113 optimal weight: 10.0000 chunk 223 optimal weight: 6.9990 chunk 287 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 190 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN C 394 ASN C 957 GLN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.126831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.076610 restraints weight = 55150.061| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.96 r_work: 0.2920 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25920 Z= 0.166 Angle : 0.572 12.359 35409 Z= 0.281 Chirality : 0.045 0.237 4158 Planarity : 0.004 0.042 4476 Dihedral : 4.828 52.757 4607 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.17 % Allowed : 10.03 % 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: 2.32 (0.20), residues: 671 sheet: 0.25 (0.20), residues: 674 loop : -0.44 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 102 TYR 0.021 0.001 TYR C1067 PHE 0.016 0.001 PHE C 79 TRP 0.029 0.002 TRP C 104 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00372 (25818) covalent geometry : angle 0.54658 (35145) SS BOND : bond 0.00128 ( 42) SS BOND : angle 0.60717 ( 84) hydrogen bonds : bond 0.04275 ( 1022) hydrogen bonds : angle 5.49871 ( 2985) link_BETA1-4 : bond 0.00191 ( 18) link_BETA1-4 : angle 1.08240 ( 54) link_NAG-ASN : bond 0.00565 ( 42) link_NAG-ASN : angle 2.80700 ( 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 174 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7610 (m-40) cc_final: 0.6234 (m-40) REVERT: A 153 MET cc_start: 0.5274 (ptt) cc_final: 0.3753 (tmm) REVERT: B 97 LYS cc_start: 0.6819 (OUTLIER) cc_final: 0.6543 (mtpp) REVERT: B 153 MET cc_start: 0.6647 (tpp) cc_final: 0.6226 (ppp) REVERT: B 237 ARG cc_start: 0.8532 (mtp180) cc_final: 0.8092 (mtm-85) REVERT: B 281 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8723 (pp20) REVERT: B 400 PHE cc_start: 0.9247 (p90) cc_final: 0.8711 (p90) REVERT: B 408 ARG cc_start: 0.8255 (ptt90) cc_final: 0.7684 (ptm-80) REVERT: B 423 TYR cc_start: 0.7665 (t80) cc_final: 0.7039 (t80) REVERT: B 512 VAL cc_start: 0.9255 (t) cc_final: 0.9014 (p) REVERT: B 646 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7350 (tpt170) REVERT: C 97 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7405 (mmmm) REVERT: C 314 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8541 (tm-30) REVERT: C 392 PHE cc_start: 0.8036 (m-80) cc_final: 0.7750 (m-80) REVERT: C 400 PHE cc_start: 0.8539 (p90) cc_final: 0.8236 (p90) REVERT: C 453 TYR cc_start: 0.8280 (p90) cc_final: 0.7766 (p90) REVERT: C 512 VAL cc_start: 0.8774 (t) cc_final: 0.8473 (m) REVERT: C 985 ASP cc_start: 0.8106 (p0) cc_final: 0.7364 (p0) REVERT: C 988 GLU cc_start: 0.9031 (mp0) cc_final: 0.8782 (pm20) REVERT: C 990 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8516 (tm-30) outliers start: 32 outliers final: 12 residues processed: 164 average time/residue: 0.6502 time to fit residues: 125.3568 Evaluate side-chains 146 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 540 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 211 optimal weight: 3.9990 chunk 249 optimal weight: 10.0000 chunk 202 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 294 optimal weight: 3.9990 chunk 284 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 755 GLN B 907 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 = 0.4121 r_free = 0.4121 target = 0.126012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.075829 restraints weight = 55254.060| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.96 r_work: 0.2902 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 25920 Z= 0.208 Angle : 0.597 12.638 35409 Z= 0.295 Chirality : 0.046 0.235 4158 Planarity : 0.004 0.044 4476 Dihedral : 4.965 52.557 4607 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.06 % Allowed : 10.25 % 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: 0.38 (0.15), residues: 3072 helix: 2.19 (0.20), residues: 679 sheet: 0.09 (0.19), residues: 689 loop : -0.45 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 346 TYR 0.022 0.001 TYR A 200 PHE 0.022 0.001 PHE A 79 TRP 0.032 0.002 TRP C 104 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00471 (25818) covalent geometry : angle 0.57286 (35145) SS BOND : bond 0.00194 ( 42) SS BOND : angle 0.71010 ( 84) hydrogen bonds : bond 0.04442 ( 1022) hydrogen bonds : angle 5.58408 ( 2985) link_BETA1-4 : bond 0.00180 ( 18) link_BETA1-4 : angle 1.07512 ( 54) link_NAG-ASN : bond 0.00605 ( 42) link_NAG-ASN : angle 2.82006 ( 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 167 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7652 (m-40) cc_final: 0.7409 (m110) REVERT: A 153 MET cc_start: 0.5217 (ptt) cc_final: 0.3628 (tpp) REVERT: B 153 MET cc_start: 0.6555 (tpp) cc_final: 0.6108 (ppp) REVERT: B 237 ARG cc_start: 0.8522 (mtp180) cc_final: 0.8211 (ttp-110) REVERT: B 281 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8668 (pp20) REVERT: B 309 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8684 (mp0) REVERT: B 400 PHE cc_start: 0.9274 (p90) cc_final: 0.8702 (p90) REVERT: B 408 ARG cc_start: 0.8320 (ptt90) cc_final: 0.7763 (ptm-80) REVERT: B 423 TYR cc_start: 0.7680 (t80) cc_final: 0.7025 (t80) REVERT: B 512 VAL cc_start: 0.9261 (t) cc_final: 0.9007 (p) REVERT: B 646 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7285 (tpt170) REVERT: C 97 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7508 (mmmm) REVERT: C 194 PHE cc_start: 0.7382 (m-10) cc_final: 0.7135 (m-10) REVERT: C 314 GLN cc_start: 0.8846 (tm-30) cc_final: 0.8596 (tm-30) REVERT: C 378 LYS cc_start: 0.8179 (ttmm) cc_final: 0.7755 (tmmm) REVERT: C 392 PHE cc_start: 0.8108 (m-80) cc_final: 0.7814 (m-80) REVERT: C 400 PHE cc_start: 0.8594 (p90) cc_final: 0.8234 (p90) REVERT: C 453 TYR cc_start: 0.8300 (p90) cc_final: 0.7810 (p90) REVERT: C 512 VAL cc_start: 0.8725 (t) cc_final: 0.8398 (m) REVERT: C 988 GLU cc_start: 0.9024 (mp0) cc_final: 0.8816 (pm20) REVERT: C 990 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8571 (tm-30) outliers start: 29 outliers final: 18 residues processed: 159 average time/residue: 0.6075 time to fit residues: 113.9484 Evaluate side-chains 147 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 540 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 299 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 239 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 105 optimal weight: 0.1980 chunk 26 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 294 optimal weight: 0.0020 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A1011 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 907 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 = 0.4138 r_free = 0.4138 target = 0.127138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.076439 restraints weight = 55365.932| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.71 r_work: 0.2965 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25920 Z= 0.112 Angle : 0.555 12.693 35409 Z= 0.272 Chirality : 0.044 0.250 4158 Planarity : 0.003 0.041 4476 Dihedral : 4.796 53.019 4607 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.10 % Allowed : 10.72 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.15), residues: 3072 helix: 2.32 (0.20), residues: 680 sheet: 0.16 (0.20), residues: 652 loop : -0.35 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 403 TYR 0.020 0.001 TYR C1067 PHE 0.020 0.001 PHE A 79 TRP 0.035 0.001 TRP C 104 HIS 0.004 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00248 (25818) covalent geometry : angle 0.53078 (35145) SS BOND : bond 0.00129 ( 42) SS BOND : angle 0.67494 ( 84) hydrogen bonds : bond 0.03913 ( 1022) hydrogen bonds : angle 5.38427 ( 2985) link_BETA1-4 : bond 0.00298 ( 18) link_BETA1-4 : angle 0.92491 ( 54) link_NAG-ASN : bond 0.00528 ( 42) link_NAG-ASN : angle 2.68887 ( 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 165 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7545 (m-40) cc_final: 0.7285 (m110) REVERT: A 153 MET cc_start: 0.5285 (ptt) cc_final: 0.3661 (tpp) REVERT: B 97 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6687 (mtpp) REVERT: B 153 MET cc_start: 0.6492 (tpp) cc_final: 0.6164 (ppp) REVERT: B 237 ARG cc_start: 0.8561 (mtp180) cc_final: 0.8266 (ttp-110) REVERT: B 400 PHE cc_start: 0.9284 (p90) cc_final: 0.8659 (p90) REVERT: B 408 ARG cc_start: 0.8338 (ptt90) cc_final: 0.7761 (ptm-80) REVERT: B 423 TYR cc_start: 0.7639 (t80) cc_final: 0.6972 (t80) REVERT: B 512 VAL cc_start: 0.9269 (t) cc_final: 0.9011 (p) REVERT: B 646 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7306 (tpt170) REVERT: C 97 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7604 (mmmm) REVERT: C 194 PHE cc_start: 0.7310 (m-10) cc_final: 0.7081 (m-10) REVERT: C 314 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8532 (tm-30) REVERT: C 378 LYS cc_start: 0.8148 (ttmm) cc_final: 0.7713 (tmmm) REVERT: C 392 PHE cc_start: 0.8065 (m-80) cc_final: 0.7771 (m-80) REVERT: C 400 PHE cc_start: 0.8543 (p90) cc_final: 0.8212 (p90) REVERT: C 453 TYR cc_start: 0.8329 (p90) cc_final: 0.7849 (p90) REVERT: C 512 VAL cc_start: 0.8746 (t) cc_final: 0.8481 (m) REVERT: C 740 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8257 (tmm) REVERT: C 990 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8532 (tm-30) outliers start: 30 outliers final: 13 residues processed: 157 average time/residue: 0.6434 time to fit residues: 118.4525 Evaluate side-chains 146 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 740 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 45 optimal weight: 7.9990 chunk 285 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 253 optimal weight: 5.9990 chunk 231 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 286 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 957 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 907 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 = 0.4113 r_free = 0.4113 target = 0.125485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.074254 restraints weight = 55300.727| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.73 r_work: 0.2915 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25920 Z= 0.215 Angle : 0.619 12.920 35409 Z= 0.305 Chirality : 0.046 0.249 4158 Planarity : 0.004 0.043 4476 Dihedral : 4.982 52.588 4607 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.91 % Allowed : 11.16 % Favored : 87.93 % 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: 0.37 (0.15), residues: 3072 helix: 2.17 (0.20), residues: 679 sheet: 0.02 (0.19), residues: 692 loop : -0.42 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 319 TYR 0.024 0.002 TYR C 351 PHE 0.021 0.001 PHE A 898 TRP 0.036 0.002 TRP B 104 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00487 (25818) covalent geometry : angle 0.59323 (35145) SS BOND : bond 0.00274 ( 42) SS BOND : angle 1.00851 ( 84) hydrogen bonds : bond 0.04548 ( 1022) hydrogen bonds : angle 5.60771 ( 2985) link_BETA1-4 : bond 0.00154 ( 18) link_BETA1-4 : angle 1.16026 ( 54) link_NAG-ASN : bond 0.00621 ( 42) link_NAG-ASN : angle 2.84681 ( 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 149 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5300 (ptt) cc_final: 0.3631 (tpp) REVERT: B 97 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6760 (mtpp) REVERT: B 153 MET cc_start: 0.6484 (tpp) cc_final: 0.6108 (ppp) REVERT: B 189 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7343 (tt) REVERT: B 237 ARG cc_start: 0.8554 (mtp180) cc_final: 0.8214 (ttp-110) REVERT: B 400 PHE cc_start: 0.9310 (p90) cc_final: 0.8769 (p90) REVERT: B 408 ARG cc_start: 0.8355 (ptt90) cc_final: 0.7802 (ptm-80) REVERT: B 423 TYR cc_start: 0.7696 (t80) cc_final: 0.7286 (t80) REVERT: B 646 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7301 (tpt170) REVERT: C 97 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7494 (mmmm) REVERT: C 314 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8643 (tm-30) REVERT: C 378 LYS cc_start: 0.8154 (ttmm) cc_final: 0.7697 (tmmm) REVERT: C 392 PHE cc_start: 0.8042 (m-80) cc_final: 0.7770 (m-80) REVERT: C 400 PHE cc_start: 0.8590 (p90) cc_final: 0.8265 (p90) REVERT: C 453 TYR cc_start: 0.8299 (p90) cc_final: 0.7790 (p90) REVERT: C 512 VAL cc_start: 0.8693 (t) cc_final: 0.8398 (m) REVERT: C 740 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8220 (tmm) REVERT: C 990 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8598 (tm-30) outliers start: 25 outliers final: 14 residues processed: 143 average time/residue: 0.6552 time to fit residues: 109.6845 Evaluate side-chains 140 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 740 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 262 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 227 optimal weight: 0.6980 chunk 198 optimal weight: 0.8980 chunk 159 optimal weight: 5.9990 chunk 310 optimal weight: 0.3980 chunk 297 optimal weight: 0.7980 chunk 214 optimal weight: 0.9990 chunk 247 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 957 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 907 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 = 0.4131 r_free = 0.4131 target = 0.126623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.075834 restraints weight = 55086.436| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.71 r_work: 0.2954 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25920 Z= 0.123 Angle : 0.564 12.754 35409 Z= 0.277 Chirality : 0.045 0.238 4158 Planarity : 0.004 0.044 4476 Dihedral : 4.840 52.837 4607 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.80 % Allowed : 11.31 % Favored : 87.89 % 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: 0.49 (0.15), residues: 3072 helix: 2.33 (0.20), residues: 680 sheet: 0.06 (0.20), residues: 666 loop : -0.35 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 102 TYR 0.020 0.001 TYR C1067 PHE 0.030 0.001 PHE B 168 TRP 0.054 0.002 TRP B 104 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00274 (25818) covalent geometry : angle 0.53875 (35145) SS BOND : bond 0.00106 ( 42) SS BOND : angle 1.08226 ( 84) hydrogen bonds : bond 0.03956 ( 1022) hydrogen bonds : angle 5.40364 ( 2985) link_BETA1-4 : bond 0.00286 ( 18) link_BETA1-4 : angle 0.94032 ( 54) link_NAG-ASN : bond 0.00523 ( 42) link_NAG-ASN : angle 2.71046 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18191.54 seconds wall clock time: 307 minutes 57.49 seconds (18477.49 seconds total)