Starting phenix.real_space_refine on Thu Mar 5 21:43:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mjg_23872/03_2026/7mjg_23872.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mjg_23872/03_2026/7mjg_23872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mjg_23872/03_2026/7mjg_23872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mjg_23872/03_2026/7mjg_23872.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mjg_23872/03_2026/7mjg_23872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mjg_23872/03_2026/7mjg_23872.map" } resolution = 2.81 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= -0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 16080 2.51 5 N 4125 2.21 5 O 4944 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: 25260 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8140 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8140 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8140 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: 5.57, per 1000 atoms: 0.22 Number of scatterers: 25260 At special positions: 0 Unit cell: (140, 145, 197, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 4944 8.00 N 4125 7.00 C 16080 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=2.04 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: 1.92 Conformation dependent library (CDL) restraints added in 1.2 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: 5850 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 51 sheets defined 24.7% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 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: 4.095A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.670A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.480A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.511A 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: 4.134A 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: 3.654A 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: 3.888A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.521A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.042A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.602A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.997A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.675A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.927A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.612A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.031A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.609A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.606A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.888A 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: 3.536A 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: 3.994A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.610A 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: 3.802A 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: 3.658A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.891A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.583A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.955A 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: 3.679A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.502A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.961A 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: 3.605A 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: 3.503A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.288A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.617A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.046A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.732A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.985A 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: 3.536A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 163 removed outlier: 9.486A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.582A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.483A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.193A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.739A 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: 6.674A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.139A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.439A 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: 3.760A 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: 3.560A 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: 6.038A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.324A 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: 6.858A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.919A 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: 6.567A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.945A 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: 6.567A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.551A 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: 4.365A 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: 3.750A 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: 8.298A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.110A 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: 3.765A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.599A 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: 5.432A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 9.890A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 13.160A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.389A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.961A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.518A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.480A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.772A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.712A 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: 3.673A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.635A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.962A 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: 3.611A 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: 6.003A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.365A 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: 3.692A 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: 6.567A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.927A 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: 6.567A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.536A 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: 4.385A 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: 8.128A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.698A 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: 4.143A 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: 3.910A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.702A 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: 9.439A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.329A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.785A 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: 5.275A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.066A 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: 3.772A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.285A 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: 6.882A 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: 3.647A 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: 6.192A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.396A 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: 6.562A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.928A 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: 6.562A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.543A 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: 4.371A 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 1077 hydrogen bonds defined for protein. 2970 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: 6.77 Time building geometry restraints manager: 2.52 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: 7484 1.34 - 1.46: 6496 1.46 - 1.58: 11712 1.58 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 25830 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 C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.74e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.62e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.60e+00 ... (remaining 25825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 34028 2.03 - 4.06: 1029 4.06 - 6.09: 75 6.09 - 8.13: 24 8.13 - 10.16: 7 Bond angle restraints: 35163 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 110.70 116.32 -5.62 1.22e+00 6.72e-01 2.12e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.24 -5.54 1.22e+00 6.72e-01 2.07e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.87 -5.17 1.22e+00 6.72e-01 1.80e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 122.34 -8.24 2.00e+00 2.50e-01 1.70e+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 35158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 14929 18.00 - 35.99: 1013 35.99 - 53.99: 157 53.99 - 71.98: 57 71.98 - 89.98: 29 Dihedral angle restraints: 16185 sinusoidal: 7098 harmonic: 9087 Sorted by residual: dihedral pdb=" CA LEU B 517 " pdb=" C LEU B 517 " pdb=" N LEU B 518 " pdb=" CA LEU B 518 " ideal model delta harmonic sigma weight residual 180.00 154.13 25.87 0 5.00e+00 4.00e-02 2.68e+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 180.00 154.39 25.61 0 5.00e+00 4.00e-02 2.62e+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 180.00 157.44 22.56 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 16182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3199 0.059 - 0.118: 805 0.118 - 0.177: 137 0.177 - 0.236: 15 0.236 - 0.294: 5 Chirality restraints: 4161 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+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 2.15e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 4158 not shown) Planarity restraints: 4521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 902 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C MET C 902 " 0.056 2.00e-02 2.50e+03 pdb=" O MET C 902 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA C 903 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 135 " 0.014 2.00e-02 2.50e+03 2.20e-02 8.50e+00 pdb=" CG PHE B 135 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE B 135 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE B 135 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 135 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE B 135 " 0.015 2.00e-02 2.50e+03 pdb=" CZ PHE B 135 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 920 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.77e+00 pdb=" C GLN C 920 " 0.048 2.00e-02 2.50e+03 pdb=" O GLN C 920 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS C 921 " -0.016 2.00e-02 2.50e+03 ... (remaining 4518 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 6673 2.81 - 3.33: 21099 3.33 - 3.85: 42903 3.85 - 4.38: 49556 4.38 - 4.90: 84969 Nonbonded interactions: 205200 Sorted by model distance: nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.286 3.040 nonbonded pdb=" O ASP A 80 " pdb=" OH TYR A 265 " model vdw 2.316 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.319 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.324 3.040 ... (remaining 205195 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 25.440 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 25932 Z= 0.224 Angle : 0.803 15.365 35427 Z= 0.417 Chirality : 0.054 0.294 4161 Planarity : 0.007 0.066 4479 Dihedral : 12.886 89.977 10209 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.64 (0.14), residues: 3072 helix: 0.15 (0.18), residues: 644 sheet: 0.10 (0.18), residues: 700 loop : -0.84 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 357 TYR 0.030 0.002 TYR A 200 PHE 0.043 0.002 PHE B 135 TRP 0.015 0.002 TRP A 886 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00468 (25830) covalent geometry : angle 0.77503 (35163) SS BOND : bond 0.00222 ( 42) SS BOND : angle 1.30180 ( 84) hydrogen bonds : bond 0.11684 ( 1029) hydrogen bonds : angle 7.43795 ( 2970) link_BETA1-4 : bond 0.00669 ( 18) link_BETA1-4 : angle 1.36848 ( 54) link_NAG-ASN : bond 0.00707 ( 42) link_NAG-ASN : angle 3.41666 ( 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 242 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.8162 (t80) cc_final: 0.7956 (t80) REVERT: A 985 ASP cc_start: 0.7936 (m-30) cc_final: 0.7562 (m-30) REVERT: A 1002 GLN cc_start: 0.8474 (tt0) cc_final: 0.8156 (tt0) REVERT: B 169 GLU cc_start: 0.8558 (tt0) cc_final: 0.8065 (mp0) REVERT: B 189 LEU cc_start: 0.8912 (tp) cc_final: 0.8630 (tp) REVERT: B 240 THR cc_start: 0.7964 (m) cc_final: 0.7697 (t) REVERT: B 460 ASN cc_start: 0.9242 (m-40) cc_final: 0.8798 (m-40) REVERT: C 125 ASN cc_start: 0.7495 (t0) cc_final: 0.7126 (m110) REVERT: C 212 LEU cc_start: 0.3002 (tt) cc_final: 0.2504 (mm) REVERT: C 365 TYR cc_start: 0.8832 (m-80) cc_final: 0.8372 (m-80) REVERT: C 402 ILE cc_start: 0.8898 (pt) cc_final: 0.8693 (pt) REVERT: C 408 ARG cc_start: 0.9131 (ptt90) cc_final: 0.8732 (ppt170) REVERT: C 936 ASP cc_start: 0.8242 (m-30) cc_final: 0.7987 (m-30) REVERT: C 985 ASP cc_start: 0.7709 (p0) cc_final: 0.7195 (p0) outliers start: 0 outliers final: 1 residues processed: 242 average time/residue: 0.6824 time to fit residues: 189.0871 Evaluate side-chains 114 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.0170 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 207 HIS B 81 ASN B 196 ASN B 360 ASN B 498 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 926 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.099812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.061799 restraints weight = 73166.589| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.94 r_work: 0.2995 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 25932 Z= 0.204 Angle : 0.614 11.137 35427 Z= 0.312 Chirality : 0.045 0.281 4161 Planarity : 0.005 0.046 4479 Dihedral : 6.648 110.229 4607 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.95 % Allowed : 6.14 % Favored : 92.91 % 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: 0.03 (0.14), residues: 3072 helix: 1.48 (0.20), residues: 675 sheet: 0.19 (0.19), residues: 675 loop : -0.62 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 995 TYR 0.023 0.002 TYR A 170 PHE 0.020 0.001 PHE B 135 TRP 0.013 0.001 TRP A 104 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00455 (25830) covalent geometry : angle 0.59093 (35163) SS BOND : bond 0.00154 ( 42) SS BOND : angle 0.75940 ( 84) hydrogen bonds : bond 0.04468 ( 1029) hydrogen bonds : angle 5.98338 ( 2970) link_BETA1-4 : bond 0.00112 ( 18) link_BETA1-4 : angle 1.19158 ( 54) link_NAG-ASN : bond 0.00614 ( 42) link_NAG-ASN : angle 2.77742 ( 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 149 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.8170 (t80) cc_final: 0.7929 (t80) REVERT: A 985 ASP cc_start: 0.8356 (m-30) cc_final: 0.7910 (m-30) REVERT: B 169 GLU cc_start: 0.8734 (tt0) cc_final: 0.8441 (tp30) REVERT: B 189 LEU cc_start: 0.8725 (tp) cc_final: 0.8433 (tp) REVERT: B 460 ASN cc_start: 0.9242 (m-40) cc_final: 0.8931 (m-40) REVERT: B 498 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8177 (mp10) REVERT: B 501 TYR cc_start: 0.7569 (m-80) cc_final: 0.7122 (m-80) REVERT: B 505 TYR cc_start: 0.7083 (t80) cc_final: 0.6518 (t80) REVERT: B 762 GLN cc_start: 0.8753 (mm110) cc_final: 0.8524 (mm110) REVERT: C 125 ASN cc_start: 0.7768 (t0) cc_final: 0.7223 (m110) REVERT: C 212 LEU cc_start: 0.3835 (tt) cc_final: 0.3163 (mm) REVERT: C 408 ARG cc_start: 0.9085 (ptt90) cc_final: 0.8680 (ppt170) REVERT: C 780 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8463 (mp0) outliers start: 26 outliers final: 6 residues processed: 143 average time/residue: 0.5959 time to fit residues: 100.1661 Evaluate side-chains 99 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 143 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 195 optimal weight: 0.6980 chunk 208 optimal weight: 10.0000 chunk 183 optimal weight: 0.6980 chunk 186 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 131 optimal weight: 0.0010 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN B 901 GLN C 87 ASN C 314 GLN C 613 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.100093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.063009 restraints weight = 73240.510| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 4.05 r_work: 0.3014 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25932 Z= 0.117 Angle : 0.561 12.484 35427 Z= 0.280 Chirality : 0.044 0.281 4161 Planarity : 0.004 0.040 4479 Dihedral : 5.963 58.208 4605 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.21 % Allowed : 7.24 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.15), residues: 3072 helix: 1.89 (0.21), residues: 668 sheet: 0.26 (0.19), residues: 694 loop : -0.44 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 403 TYR 0.020 0.001 TYR C1067 PHE 0.016 0.001 PHE B 400 TRP 0.015 0.001 TRP C 104 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00249 (25830) covalent geometry : angle 0.53606 (35163) SS BOND : bond 0.00120 ( 42) SS BOND : angle 0.59645 ( 84) hydrogen bonds : bond 0.03939 ( 1029) hydrogen bonds : angle 5.66121 ( 2970) link_BETA1-4 : bond 0.00246 ( 18) link_BETA1-4 : angle 1.07464 ( 54) link_NAG-ASN : bond 0.00630 ( 42) link_NAG-ASN : angle 2.77753 ( 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 139 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.9358 (p) cc_final: 0.9043 (t) REVERT: A 201 PHE cc_start: 0.8136 (t80) cc_final: 0.7923 (t80) REVERT: A 923 ILE cc_start: 0.9628 (OUTLIER) cc_final: 0.9426 (mp) REVERT: A 979 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.8114 (t0) REVERT: A 985 ASP cc_start: 0.8338 (m-30) cc_final: 0.7871 (m-30) REVERT: B 169 GLU cc_start: 0.8767 (tt0) cc_final: 0.8080 (mp0) REVERT: B 189 LEU cc_start: 0.8728 (tp) cc_final: 0.8441 (tp) REVERT: B 460 ASN cc_start: 0.9258 (m-40) cc_final: 0.8973 (m-40) REVERT: B 505 TYR cc_start: 0.7360 (t80) cc_final: 0.7008 (t80) REVERT: B 762 GLN cc_start: 0.8717 (mm110) cc_final: 0.8480 (mm110) REVERT: C 125 ASN cc_start: 0.7765 (t0) cc_final: 0.7102 (m110) REVERT: C 408 ARG cc_start: 0.9080 (ptt90) cc_final: 0.8639 (ppt170) REVERT: C 780 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8424 (mp0) outliers start: 33 outliers final: 12 residues processed: 132 average time/residue: 0.5528 time to fit residues: 87.0439 Evaluate side-chains 106 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 160 optimal weight: 3.9990 chunk 30 optimal weight: 30.0000 chunk 234 optimal weight: 4.9990 chunk 214 optimal weight: 0.9990 chunk 33 optimal weight: 30.0000 chunk 146 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 chunk 297 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN B 196 ASN B 824 ASN B 907 ASN C 613 GLN C 824 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.097334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.059300 restraints weight = 73779.276| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 4.03 r_work: 0.2929 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 25932 Z= 0.308 Angle : 0.660 11.260 35427 Z= 0.330 Chirality : 0.047 0.260 4161 Planarity : 0.004 0.057 4479 Dihedral : 5.921 58.462 4605 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.24 % Allowed : 7.79 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.16 (0.15), residues: 3072 helix: 1.86 (0.20), residues: 681 sheet: -0.00 (0.20), residues: 628 loop : -0.53 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 403 TYR 0.021 0.002 TYR C 756 PHE 0.024 0.002 PHE C 275 TRP 0.016 0.002 TRP C 104 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00696 (25830) covalent geometry : angle 0.63647 (35163) SS BOND : bond 0.00162 ( 42) SS BOND : angle 0.71369 ( 84) hydrogen bonds : bond 0.04762 ( 1029) hydrogen bonds : angle 5.77814 ( 2970) link_BETA1-4 : bond 0.00234 ( 18) link_BETA1-4 : angle 1.37704 ( 54) link_NAG-ASN : bond 0.00729 ( 42) link_NAG-ASN : angle 2.85824 ( 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 127 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.8427 (t80) cc_final: 0.8047 (t80) REVERT: A 985 ASP cc_start: 0.8373 (m-30) cc_final: 0.7938 (m-30) REVERT: A 1010 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8835 (mp10) REVERT: B 189 LEU cc_start: 0.8697 (tp) cc_final: 0.8387 (tp) REVERT: B 196 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8429 (m-40) REVERT: B 200 TYR cc_start: 0.8812 (m-80) cc_final: 0.8322 (t80) REVERT: B 460 ASN cc_start: 0.9208 (m-40) cc_final: 0.8916 (m-40) REVERT: B 505 TYR cc_start: 0.7385 (t80) cc_final: 0.7043 (t80) REVERT: B 512 VAL cc_start: 0.8951 (t) cc_final: 0.8719 (m) REVERT: B 762 GLN cc_start: 0.8804 (mm110) cc_final: 0.8524 (mm110) REVERT: C 125 ASN cc_start: 0.7689 (t0) cc_final: 0.7003 (m110) REVERT: C 173 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.6443 (tm-30) REVERT: C 392 PHE cc_start: 0.8545 (m-80) cc_final: 0.8333 (m-80) REVERT: C 408 ARG cc_start: 0.9054 (ptt90) cc_final: 0.8649 (ppt170) REVERT: C 780 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8596 (mp0) outliers start: 34 outliers final: 10 residues processed: 118 average time/residue: 0.5293 time to fit residues: 75.0954 Evaluate side-chains 99 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 52 optimal weight: 4.9990 chunk 46 optimal weight: 20.0000 chunk 163 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 216 optimal weight: 5.9990 chunk 199 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 301 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 221 optimal weight: 9.9990 chunk 63 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN B 907 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 613 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.098369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.061171 restraints weight = 72923.441| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.92 r_work: 0.2971 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25932 Z= 0.137 Angle : 0.546 10.853 35427 Z= 0.275 Chirality : 0.044 0.281 4161 Planarity : 0.004 0.041 4479 Dihedral : 5.498 59.959 4605 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.32 % Allowed : 7.86 % Favored : 90.83 % 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: 0.30 (0.15), residues: 3072 helix: 1.98 (0.20), residues: 691 sheet: 0.08 (0.19), residues: 630 loop : -0.46 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 319 TYR 0.020 0.001 TYR C1067 PHE 0.015 0.001 PHE B 400 TRP 0.021 0.001 TRP C 104 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00301 (25830) covalent geometry : angle 0.52317 (35163) SS BOND : bond 0.00103 ( 42) SS BOND : angle 0.56001 ( 84) hydrogen bonds : bond 0.04044 ( 1029) hydrogen bonds : angle 5.51003 ( 2970) link_BETA1-4 : bond 0.00254 ( 18) link_BETA1-4 : angle 1.06100 ( 54) link_NAG-ASN : bond 0.00552 ( 42) link_NAG-ASN : angle 2.59007 ( 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 132 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.9413 (p) cc_final: 0.9114 (t) REVERT: A 201 PHE cc_start: 0.8344 (t80) cc_final: 0.8002 (t80) REVERT: A 985 ASP cc_start: 0.8339 (m-30) cc_final: 0.7862 (m-30) REVERT: A 1017 GLU cc_start: 0.9105 (tt0) cc_final: 0.8875 (tm-30) REVERT: B 189 LEU cc_start: 0.8716 (tp) cc_final: 0.8419 (tp) REVERT: B 196 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8277 (m-40) REVERT: B 200 TYR cc_start: 0.8775 (m-80) cc_final: 0.8354 (t80) REVERT: B 460 ASN cc_start: 0.9219 (m-40) cc_final: 0.8931 (m-40) REVERT: B 505 TYR cc_start: 0.7370 (t80) cc_final: 0.7046 (t80) REVERT: B 512 VAL cc_start: 0.8899 (t) cc_final: 0.8690 (m) REVERT: B 740 MET cc_start: 0.9352 (OUTLIER) cc_final: 0.8667 (tmm) REVERT: B 745 ASP cc_start: 0.8552 (p0) cc_final: 0.7785 (t0) REVERT: B 762 GLN cc_start: 0.8735 (mm110) cc_final: 0.8452 (mm110) REVERT: C 125 ASN cc_start: 0.7764 (t0) cc_final: 0.7027 (m110) REVERT: C 153 MET cc_start: 0.4603 (pp-130) cc_final: 0.4351 (pp-130) REVERT: C 173 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6406 (tm-30) REVERT: C 408 ARG cc_start: 0.9054 (ptt90) cc_final: 0.8654 (ppt170) REVERT: C 780 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8560 (mp0) outliers start: 36 outliers final: 12 residues processed: 122 average time/residue: 0.5487 time to fit residues: 79.6221 Evaluate side-chains 99 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 123 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 228 optimal weight: 7.9990 chunk 251 optimal weight: 10.0000 chunk 276 optimal weight: 0.8980 chunk 141 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 824 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 779 GLN C1011 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.095621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.058522 restraints weight = 74373.657| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.88 r_work: 0.2925 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 25932 Z= 0.362 Angle : 0.679 10.971 35427 Z= 0.341 Chirality : 0.048 0.252 4161 Planarity : 0.004 0.041 4479 Dihedral : 5.716 58.312 4605 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.35 % Allowed : 8.95 % Favored : 89.69 % 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: 0.03 (0.15), residues: 3072 helix: 1.86 (0.20), residues: 695 sheet: -0.28 (0.19), residues: 644 loop : -0.61 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 78 TYR 0.021 0.002 TYR A 756 PHE 0.026 0.002 PHE A 898 TRP 0.019 0.002 TRP C 104 HIS 0.005 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00814 (25830) covalent geometry : angle 0.65735 (35163) SS BOND : bond 0.00180 ( 42) SS BOND : angle 0.74443 ( 84) hydrogen bonds : bond 0.04817 ( 1029) hydrogen bonds : angle 5.79114 ( 2970) link_BETA1-4 : bond 0.00258 ( 18) link_BETA1-4 : angle 1.36955 ( 54) link_NAG-ASN : bond 0.00774 ( 42) link_NAG-ASN : angle 2.78598 ( 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 121 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 84 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 985 ASP cc_start: 0.8314 (m-30) cc_final: 0.7864 (m-30) REVERT: A 1002 GLN cc_start: 0.9043 (tt0) cc_final: 0.8379 (tp-100) REVERT: A 1017 GLU cc_start: 0.9138 (tt0) cc_final: 0.8874 (tm-30) REVERT: B 189 LEU cc_start: 0.8664 (tp) cc_final: 0.8348 (tp) REVERT: B 200 TYR cc_start: 0.8845 (m-80) cc_final: 0.8378 (t80) REVERT: B 460 ASN cc_start: 0.9171 (m-40) cc_final: 0.8905 (m-40) REVERT: B 505 TYR cc_start: 0.7355 (t80) cc_final: 0.7016 (t80) REVERT: B 762 GLN cc_start: 0.8813 (mm110) cc_final: 0.8548 (mm110) REVERT: C 125 ASN cc_start: 0.7890 (t0) cc_final: 0.7241 (m110) REVERT: C 173 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.6486 (tm-30) REVERT: C 324 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8107 (pm20) REVERT: C 408 ARG cc_start: 0.9029 (ptt90) cc_final: 0.8654 (ppt170) REVERT: C 780 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8651 (mp0) outliers start: 37 outliers final: 15 residues processed: 111 average time/residue: 0.5159 time to fit residues: 69.1421 Evaluate side-chains 95 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 88 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 281 optimal weight: 1.9990 chunk 294 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 283 optimal weight: 5.9990 chunk 272 optimal weight: 0.6980 chunk 278 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 613 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.099530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.063329 restraints weight = 75803.281| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.78 r_work: 0.2973 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25932 Z= 0.135 Angle : 0.557 11.101 35427 Z= 0.280 Chirality : 0.045 0.280 4161 Planarity : 0.004 0.044 4479 Dihedral : 5.390 59.082 4605 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.99 % Allowed : 9.43 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 3072 helix: 2.10 (0.20), residues: 692 sheet: -0.11 (0.19), residues: 647 loop : -0.48 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 78 TYR 0.020 0.001 TYR C1067 PHE 0.018 0.001 PHE C 392 TRP 0.028 0.001 TRP C 104 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00296 (25830) covalent geometry : angle 0.53618 (35163) SS BOND : bond 0.00108 ( 42) SS BOND : angle 0.54629 ( 84) hydrogen bonds : bond 0.04031 ( 1029) hydrogen bonds : angle 5.52588 ( 2970) link_BETA1-4 : bond 0.00274 ( 18) link_BETA1-4 : angle 1.03310 ( 54) link_NAG-ASN : bond 0.00535 ( 42) link_NAG-ASN : angle 2.53070 ( 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 111 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 985 ASP cc_start: 0.8306 (m-30) cc_final: 0.7844 (m-30) REVERT: A 1017 GLU cc_start: 0.9117 (tt0) cc_final: 0.8831 (tm-30) REVERT: B 189 LEU cc_start: 0.8753 (tp) cc_final: 0.8447 (tp) REVERT: B 200 TYR cc_start: 0.8870 (m-80) cc_final: 0.8452 (t80) REVERT: B 460 ASN cc_start: 0.9183 (m-40) cc_final: 0.8766 (m-40) REVERT: B 505 TYR cc_start: 0.7344 (t80) cc_final: 0.6984 (t80) REVERT: B 762 GLN cc_start: 0.8739 (mm110) cc_final: 0.8426 (mm110) REVERT: C 173 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.6801 (tm-30) REVERT: C 324 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8171 (pm20) REVERT: C 408 ARG cc_start: 0.9047 (ptt90) cc_final: 0.8684 (ppt170) REVERT: C 780 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8613 (mp0) outliers start: 27 outliers final: 11 residues processed: 105 average time/residue: 0.5649 time to fit residues: 70.8055 Evaluate side-chains 89 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 292 optimal weight: 2.9990 chunk 228 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 285 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.097147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.061203 restraints weight = 76265.007| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.73 r_work: 0.2920 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 25932 Z= 0.318 Angle : 0.654 11.265 35427 Z= 0.329 Chirality : 0.047 0.255 4161 Planarity : 0.004 0.042 4479 Dihedral : 5.543 56.626 4605 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.95 % Allowed : 9.72 % Favored : 89.33 % 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: 0.09 (0.15), residues: 3072 helix: 2.04 (0.20), residues: 692 sheet: -0.31 (0.19), residues: 644 loop : -0.60 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 78 TYR 0.020 0.002 TYR A 265 PHE 0.022 0.002 PHE A 898 TRP 0.025 0.002 TRP C 104 HIS 0.005 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00715 (25830) covalent geometry : angle 0.63297 (35163) SS BOND : bond 0.00166 ( 42) SS BOND : angle 0.72299 ( 84) hydrogen bonds : bond 0.04664 ( 1029) hydrogen bonds : angle 5.72323 ( 2970) link_BETA1-4 : bond 0.00161 ( 18) link_BETA1-4 : angle 1.37816 ( 54) link_NAG-ASN : bond 0.00734 ( 42) link_NAG-ASN : angle 2.71848 ( 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 112 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 985 ASP cc_start: 0.8330 (m-30) cc_final: 0.7896 (m-30) REVERT: A 1017 GLU cc_start: 0.9151 (tt0) cc_final: 0.8853 (tm-30) REVERT: B 189 LEU cc_start: 0.8691 (tp) cc_final: 0.8389 (tp) REVERT: B 200 TYR cc_start: 0.8830 (m-80) cc_final: 0.8379 (t80) REVERT: B 460 ASN cc_start: 0.9137 (m-40) cc_final: 0.8720 (m-40) REVERT: B 505 TYR cc_start: 0.7496 (t80) cc_final: 0.7075 (t80) REVERT: B 762 GLN cc_start: 0.8784 (mm110) cc_final: 0.8475 (mm110) REVERT: C 144 TYR cc_start: 0.6554 (t80) cc_final: 0.6292 (m-10) REVERT: C 173 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6874 (tm-30) REVERT: C 269 TYR cc_start: 0.7895 (m-10) cc_final: 0.7670 (m-10) REVERT: C 324 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8263 (pm20) REVERT: C 408 ARG cc_start: 0.8993 (ptt90) cc_final: 0.8660 (ppt170) REVERT: C 780 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8628 (mp0) REVERT: C 1017 GLU cc_start: 0.9129 (tt0) cc_final: 0.8883 (tm-30) outliers start: 26 outliers final: 12 residues processed: 105 average time/residue: 0.5319 time to fit residues: 66.4358 Evaluate side-chains 94 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 285 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 255 optimal weight: 0.0070 chunk 76 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 240 optimal weight: 0.7980 chunk 198 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 chunk 308 optimal weight: 0.8980 chunk 182 optimal weight: 0.8980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.097912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.061124 restraints weight = 73306.566| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.83 r_work: 0.2993 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25932 Z= 0.109 Angle : 0.545 11.301 35427 Z= 0.274 Chirality : 0.044 0.285 4161 Planarity : 0.004 0.043 4479 Dihedral : 5.188 57.638 4605 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.91 % Allowed : 9.90 % Favored : 89.18 % 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: 0.37 (0.15), residues: 3072 helix: 2.25 (0.20), residues: 691 sheet: -0.09 (0.20), residues: 641 loop : -0.42 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 995 TYR 0.019 0.001 TYR B1067 PHE 0.014 0.001 PHE C 92 TRP 0.036 0.001 TRP C 104 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00237 (25830) covalent geometry : angle 0.52433 (35163) SS BOND : bond 0.00120 ( 42) SS BOND : angle 0.54566 ( 84) hydrogen bonds : bond 0.03809 ( 1029) hydrogen bonds : angle 5.38852 ( 2970) link_BETA1-4 : bond 0.00340 ( 18) link_BETA1-4 : angle 0.94878 ( 54) link_NAG-ASN : bond 0.00505 ( 42) link_NAG-ASN : angle 2.47482 ( 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 108 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 985 ASP cc_start: 0.8285 (m-30) cc_final: 0.7787 (m-30) REVERT: A 1017 GLU cc_start: 0.9082 (tt0) cc_final: 0.8833 (tm-30) REVERT: B 189 LEU cc_start: 0.8764 (tp) cc_final: 0.8473 (tp) REVERT: B 200 TYR cc_start: 0.8808 (m-80) cc_final: 0.8422 (t80) REVERT: B 460 ASN cc_start: 0.9185 (m-40) cc_final: 0.8804 (m-40) REVERT: B 505 TYR cc_start: 0.7378 (t80) cc_final: 0.6907 (t80) REVERT: B 762 GLN cc_start: 0.8707 (mm110) cc_final: 0.8423 (mm110) REVERT: C 324 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8198 (pm20) REVERT: C 408 ARG cc_start: 0.9080 (ptt90) cc_final: 0.8655 (ppt170) REVERT: C 780 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8607 (mp0) REVERT: C 1017 GLU cc_start: 0.9130 (tt0) cc_final: 0.8905 (tm-30) outliers start: 25 outliers final: 14 residues processed: 100 average time/residue: 0.5914 time to fit residues: 70.5935 Evaluate side-chains 96 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 27 optimal weight: 0.9980 chunk 259 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 265 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 235 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.099201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.063395 restraints weight = 76145.172| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.73 r_work: 0.2974 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25932 Z= 0.142 Angle : 0.546 11.367 35427 Z= 0.274 Chirality : 0.045 0.270 4161 Planarity : 0.004 0.042 4479 Dihedral : 5.039 59.451 4605 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.73 % Allowed : 10.01 % Favored : 89.25 % 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: 0.45 (0.15), residues: 3072 helix: 2.32 (0.20), residues: 694 sheet: 0.04 (0.19), residues: 666 loop : -0.42 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.019 0.001 TYR B1067 PHE 0.019 0.001 PHE A 135 TRP 0.034 0.001 TRP C 104 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00316 (25830) covalent geometry : angle 0.52520 (35163) SS BOND : bond 0.00112 ( 42) SS BOND : angle 0.55792 ( 84) hydrogen bonds : bond 0.03876 ( 1029) hydrogen bonds : angle 5.32978 ( 2970) link_BETA1-4 : bond 0.00239 ( 18) link_BETA1-4 : angle 1.09606 ( 54) link_NAG-ASN : bond 0.00519 ( 42) link_NAG-ASN : angle 2.47884 ( 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 100 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 985 ASP cc_start: 0.8286 (m-30) cc_final: 0.7806 (m-30) REVERT: A 1017 GLU cc_start: 0.9099 (tt0) cc_final: 0.8827 (tm-30) REVERT: B 189 LEU cc_start: 0.8711 (tp) cc_final: 0.8408 (tp) REVERT: B 200 TYR cc_start: 0.8793 (m-80) cc_final: 0.8419 (t80) REVERT: B 460 ASN cc_start: 0.9169 (m-40) cc_final: 0.8578 (t0) REVERT: B 762 GLN cc_start: 0.8706 (mm110) cc_final: 0.8432 (mm110) REVERT: C 153 MET cc_start: 0.4811 (pp-130) cc_final: 0.4589 (pp-130) REVERT: C 189 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8088 (mt) REVERT: C 324 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8171 (pm20) REVERT: C 408 ARG cc_start: 0.9064 (ptt90) cc_final: 0.8638 (ppt170) REVERT: C 780 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8591 (mp0) REVERT: C 1017 GLU cc_start: 0.9122 (tt0) cc_final: 0.8887 (tm-30) REVERT: C 1092 GLU cc_start: 0.8344 (pm20) cc_final: 0.7797 (pp20) outliers start: 20 outliers final: 13 residues processed: 94 average time/residue: 0.5582 time to fit residues: 62.7537 Evaluate side-chains 92 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 239 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 257 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 174 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.099584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.063867 restraints weight = 75806.712| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.64 r_work: 0.2987 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25932 Z= 0.123 Angle : 0.535 11.424 35427 Z= 0.269 Chirality : 0.044 0.274 4161 Planarity : 0.004 0.042 4479 Dihedral : 4.886 57.328 4605 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.66 % Allowed : 10.31 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.15), residues: 3072 helix: 2.36 (0.20), residues: 693 sheet: 0.10 (0.20), residues: 664 loop : -0.39 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 403 TYR 0.019 0.001 TYR B1067 PHE 0.015 0.001 PHE B 79 TRP 0.036 0.001 TRP C 104 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00275 (25830) covalent geometry : angle 0.51480 (35163) SS BOND : bond 0.00108 ( 42) SS BOND : angle 0.53928 ( 84) hydrogen bonds : bond 0.03735 ( 1029) hydrogen bonds : angle 5.25124 ( 2970) link_BETA1-4 : bond 0.00270 ( 18) link_BETA1-4 : angle 1.01398 ( 54) link_NAG-ASN : bond 0.00486 ( 42) link_NAG-ASN : angle 2.43849 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8982.33 seconds wall clock time: 153 minutes 28.73 seconds (9208.73 seconds total)