Starting phenix.real_space_refine on Fri Mar 6 06:05:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xj8_33221/03_2026/7xj8_33221.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xj8_33221/03_2026/7xj8_33221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xj8_33221/03_2026/7xj8_33221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xj8_33221/03_2026/7xj8_33221.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xj8_33221/03_2026/7xj8_33221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xj8_33221/03_2026/7xj8_33221.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.046 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 126 5.16 5 C 18271 2.51 5 N 4736 2.21 5 O 5573 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.03s 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: 28706 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 6563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 840, 6563 Classifications: {'peptide': 840} Link IDs: {'PTRANS': 46, 'TRANS': 793} Chain breaks: 9 Chain: "B" Number of atoms: 8126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8126 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 8 Chain: "C" Number of atoms: 8126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8126 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 8 Chain: "F" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "G" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "H" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "I" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "J" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 808 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 941 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: "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: "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: "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: "V" 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: "W" 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: "X" 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.31, per 1000 atoms: 0.22 Number of scatterers: 28706 At special positions: 0 Unit cell: (143.5, 143.5, 230.42, 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 126 16.00 O 5573 8.00 N 4736 7.00 C 18271 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, 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 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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=2.04 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=2.04 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 101 " - pdb=" SG CYS K 106 " 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 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 V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 709 " " NAG D 1 " - " ASN C 801 " " NAG E 1 " - " ASN C1074 " " NAG L 1 " - " ASN C1098 " " NAG M 1 " - " ASN C1134 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1074 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN A 717 " " NAG U 1 " - " ASN A 801 " " NAG V 1 " - " ASN A1074 " " NAG W 1 " - " ASN A1098 " " NAG X 1 " - " ASN A1134 " Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 956.0 milliseconds 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6720 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 54 sheets defined 21.2% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.568A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.535A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.719A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.359A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.965A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.504A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.168A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.317A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.874A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.568A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.660A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.669A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.747A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.566A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.187A 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 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.326A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.364A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.901A pdb=" N LEU C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.537A pdb=" N LYS C 386 " --> pdb=" O SER C 383 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 383 through 387' Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.595A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.632A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.835A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 755 removed outlier: 4.059A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.650A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.584A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.166A 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: 3.559A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (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 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.638A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.167A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.709A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.626A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 30 No H-bonds generated for 'chain 'I' and resid 28 through 30' Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'J' and resid 30 through 32 No H-bonds generated for 'chain 'J' and resid 30 through 32' Processing helix chain 'K' and resid 28 through 31 removed outlier: 4.063A pdb=" N SER K 31 " --> pdb=" O THR K 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 28 through 31' Processing helix chain 'K' and resid 87 through 91 removed outlier: 4.091A pdb=" N THR K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.433A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.808A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.933A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.243A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 133 through 142 removed outlier: 8.462A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.507A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.345A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.140A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.392A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.026A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.974A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.846A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB2, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB3, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB4, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB5, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.088A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.775A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.482A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.021A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.652A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.449A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.259A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.851A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.274A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.059A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 356 through 358 removed outlier: 4.446A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.880A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.849A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC7, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AC8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AC9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD1, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.808A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.496A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.358A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.903A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.797A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.222A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.738A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.526A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.704A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.027A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.710A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE5, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE6, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AE7, first strand: chain 'F' and resid 10 through 12 removed outlier: 7.258A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AE9, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.608A pdb=" N GLU G 10 " --> pdb=" O THR G 118 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N TYR G 32 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE G 52 " --> pdb=" O TYR G 32 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N PHE G 34 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG G 50 " --> pdb=" O PHE G 34 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE G 57 " --> pdb=" O ILE G 52 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.914A pdb=" N VAL H 19 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.696A pdb=" N GLU H 105 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE H 48 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLN H 37 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU H 46 " --> pdb=" O GLN H 37 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR H 49 " --> pdb=" O SER H 53 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.602A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 10 through 12 removed outlier: 8.450A pdb=" N TYR I 32 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE I 52 " --> pdb=" O TYR I 32 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE I 34 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG I 50 " --> pdb=" O PHE I 34 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE I 57 " --> pdb=" O ILE I 52 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 4 through 6 removed outlier: 3.529A pdb=" N SER J 64 " --> pdb=" O THR J 75 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.531A pdb=" N VAL J 86 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER J 54 " --> pdb=" O TYR J 50 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.547A pdb=" N ALA K 79 " --> pdb=" O CYS K 22 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR K 78 " --> pdb=" O ASP K 73 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.543A pdb=" N THR K 120 " --> pdb=" O GLU K 10 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.543A pdb=" N THR K 120 " --> pdb=" O GLU K 10 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA K 98 " --> pdb=" O ILE K 112 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE K 112 " --> pdb=" O ALA K 98 " (cutoff:3.500A) 1105 hydrogen bonds defined for protein. 2994 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.14 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4623 1.31 - 1.44: 8242 1.44 - 1.57: 16322 1.57 - 1.70: 0 1.70 - 1.82: 162 Bond restraints: 29349 Sorted by residual: bond pdb=" N ILE B 402 " pdb=" CA ILE B 402 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.50e-02 4.44e+03 7.21e+00 bond pdb=" N ARG B 403 " pdb=" CA ARG B 403 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.77e+00 bond pdb=" N ASP B 405 " pdb=" CA ASP B 405 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.04e+00 bond pdb=" C ILE A 332 " pdb=" O ILE A 332 " ideal model delta sigma weight residual 1.231 1.186 0.045 2.00e-02 2.50e+03 5.16e+00 bond pdb=" N GLU B 406 " pdb=" CA GLU B 406 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.42e-02 4.96e+03 4.58e+00 ... (remaining 29344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 38554 1.45 - 2.90: 1123 2.90 - 4.35: 186 4.35 - 5.81: 22 5.81 - 7.26: 6 Bond angle restraints: 39891 Sorted by residual: angle pdb=" N VAL B 159 " pdb=" CA VAL B 159 " pdb=" C VAL B 159 " ideal model delta sigma weight residual 113.71 110.27 3.44 9.50e-01 1.11e+00 1.31e+01 angle pdb=" C GLY F 68 " pdb=" N THR F 69 " pdb=" CA THR F 69 " ideal model delta sigma weight residual 121.54 128.03 -6.49 1.91e+00 2.74e-01 1.16e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.79 -4.09 1.22e+00 6.72e-01 1.12e+01 angle pdb=" CA ARG B 403 " pdb=" C ARG B 403 " pdb=" O ARG B 403 " ideal model delta sigma weight residual 121.56 118.07 3.49 1.09e+00 8.42e-01 1.02e+01 angle pdb=" N GLN B1010 " pdb=" CA GLN B1010 " pdb=" CB GLN B1010 " ideal model delta sigma weight residual 110.22 114.79 -4.57 1.54e+00 4.22e-01 8.79e+00 ... (remaining 39886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 16487 18.03 - 36.06: 1272 36.06 - 54.09: 251 54.09 - 72.12: 65 72.12 - 90.15: 30 Dihedral angle restraints: 18105 sinusoidal: 7663 harmonic: 10442 Sorted by residual: dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 162.08 -69.08 1 1.00e+01 1.00e-02 6.17e+01 dihedral pdb=" CB CYS H 23 " pdb=" SG CYS H 23 " pdb=" SG CYS H 88 " pdb=" CB CYS H 88 " ideal model delta sinusoidal sigma weight residual 93.00 151.42 -58.42 1 1.00e+01 1.00e-02 4.57e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -28.03 -57.97 1 1.00e+01 1.00e-02 4.51e+01 ... (remaining 18102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3834 0.059 - 0.118: 751 0.118 - 0.177: 50 0.177 - 0.236: 3 0.236 - 0.295: 2 Chirality restraints: 4640 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " 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 B1302 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 4637 not shown) Planarity restraints: 5105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1074 " -0.029 2.00e-02 2.50e+03 4.44e-02 2.47e+01 pdb=" CG ASN A1074 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A1074 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A1074 " 0.079 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 81 " 0.064 5.00e-02 4.00e+02 9.96e-02 1.59e+01 pdb=" N PRO C 82 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO C 82 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 82 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO C 987 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.036 5.00e-02 4.00e+02 ... (remaining 5102 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 535 2.68 - 3.23: 26638 3.23 - 3.79: 42305 3.79 - 4.34: 55949 4.34 - 4.90: 95839 Nonbonded interactions: 221266 Sorted by model distance: nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.119 3.040 nonbonded pdb=" NE2 GLN A 804 " pdb=" OE1 GLN A 935 " model vdw 2.178 3.120 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.190 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.193 3.040 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.207 3.040 ... (remaining 221261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' 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' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'I' } 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: 8.950 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: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.880 Find NCS groups from input model: 0.500 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: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 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 : 0.004 0.045 29439 Z= 0.186 Angle : 0.630 37.018 40116 Z= 0.319 Chirality : 0.046 0.295 4640 Planarity : 0.004 0.100 5075 Dihedral : 13.543 90.155 11250 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 3529 helix: 2.27 (0.21), residues: 630 sheet: 0.14 (0.16), residues: 1036 loop : -0.84 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 50 TYR 0.014 0.001 TYR B 495 PHE 0.028 0.001 PHE B 906 TRP 0.018 0.001 TRP C 886 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00404 (29349) covalent geometry : angle 0.58515 (39891) SS BOND : bond 0.00257 ( 45) SS BOND : angle 1.18359 ( 90) hydrogen bonds : bond 0.20895 ( 1101) hydrogen bonds : angle 7.58813 ( 2994) link_BETA1-4 : bond 0.00395 ( 15) link_BETA1-4 : angle 0.87036 ( 45) link_NAG-ASN : bond 0.00338 ( 30) link_NAG-ASN : angle 4.81837 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7547 (t0) cc_final: 0.7346 (t0) REVERT: A 979 ASP cc_start: 0.8516 (t70) cc_final: 0.8269 (t0) REVERT: A 983 ARG cc_start: 0.8701 (ttp80) cc_final: 0.8302 (ttp80) REVERT: B 823 PHE cc_start: 0.8140 (t80) cc_final: 0.7906 (t80) REVERT: C 200 TYR cc_start: 0.6645 (m-80) cc_final: 0.6400 (m-80) REVERT: C 478 LYS cc_start: 0.8692 (tmmt) cc_final: 0.8486 (tmtt) REVERT: C 1145 LEU cc_start: 0.8566 (mt) cc_final: 0.8289 (tp) REVERT: G 48 MET cc_start: 0.6495 (mmm) cc_final: 0.5800 (mmt) REVERT: I 46 GLU cc_start: 0.7604 (tp30) cc_final: 0.6832 (tt0) REVERT: I 63 LYS cc_start: 0.8578 (pttt) cc_final: 0.8376 (pttt) REVERT: K 81 MET cc_start: 0.4647 (mtp) cc_final: 0.3654 (tpt) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.1632 time to fit residues: 68.9392 Evaluate side-chains 203 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 0.1980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 804 GLN B 935 GLN B 957 GLN C 853 GLN C 901 GLN C1106 GLN F 6 GLN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.138802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.082503 restraints weight = 50978.816| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.86 r_work: 0.2837 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 29439 Z= 0.212 Angle : 0.613 8.365 40116 Z= 0.319 Chirality : 0.047 0.303 4640 Planarity : 0.004 0.061 5075 Dihedral : 6.506 59.988 4797 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.73 % Allowed : 5.77 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 0.00 (0.14), residues: 3529 helix: 2.21 (0.21), residues: 644 sheet: 0.22 (0.16), residues: 1028 loop : -0.93 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 98 TYR 0.027 0.002 TYR A 170 PHE 0.031 0.002 PHE C 559 TRP 0.012 0.002 TRP C 886 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00521 (29349) covalent geometry : angle 0.59771 (39891) SS BOND : bond 0.00379 ( 45) SS BOND : angle 1.29372 ( 90) hydrogen bonds : bond 0.06085 ( 1101) hydrogen bonds : angle 5.69594 ( 2994) link_BETA1-4 : bond 0.00328 ( 15) link_BETA1-4 : angle 0.96709 ( 45) link_NAG-ASN : bond 0.00272 ( 30) link_NAG-ASN : angle 2.61682 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.3954 (tmm) cc_final: 0.3594 (tmm) REVERT: A 979 ASP cc_start: 0.8686 (t70) cc_final: 0.8326 (t0) REVERT: A 983 ARG cc_start: 0.8892 (ttp80) cc_final: 0.8547 (ttp80) REVERT: B 563 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8520 (mm-40) REVERT: B 592 PHE cc_start: 0.6547 (t80) cc_final: 0.5999 (t80) REVERT: B 1010 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.7354 (mp10) REVERT: C 753 LEU cc_start: 0.9353 (mt) cc_final: 0.9075 (mt) REVERT: C 1145 LEU cc_start: 0.8469 (mt) cc_final: 0.8260 (tp) REVERT: G 48 MET cc_start: 0.6827 (mmm) cc_final: 0.6143 (mmt) REVERT: H 4 MET cc_start: 0.8261 (mmp) cc_final: 0.8024 (mmm) REVERT: I 46 GLU cc_start: 0.7920 (tp30) cc_final: 0.6981 (tt0) REVERT: I 63 LYS cc_start: 0.8754 (pttt) cc_final: 0.8522 (pttt) REVERT: I 101 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8614 (tm-30) REVERT: K 81 MET cc_start: 0.5230 (mtp) cc_final: 0.3720 (tpt) outliers start: 23 outliers final: 17 residues processed: 233 average time/residue: 0.1702 time to fit residues: 65.2500 Evaluate side-chains 218 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain I residue 57 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 86 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 309 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 329 optimal weight: 5.9990 chunk 277 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 300 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 207 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 957 GLN C 121 ASN C 188 ASN C 853 GLN C 901 GLN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 HIS ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN K 35 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.139146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.079400 restraints weight = 51076.656| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.09 r_work: 0.2851 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29439 Z= 0.153 Angle : 0.554 8.479 40116 Z= 0.286 Chirality : 0.045 0.277 4640 Planarity : 0.004 0.059 5075 Dihedral : 5.954 57.566 4797 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.89 % Allowed : 8.77 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 0.10 (0.14), residues: 3529 helix: 2.31 (0.21), residues: 649 sheet: 0.26 (0.16), residues: 1042 loop : -0.88 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 98 TYR 0.019 0.001 TYR C1067 PHE 0.043 0.001 PHE A 157 TRP 0.018 0.001 TRP G 47 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00367 (29349) covalent geometry : angle 0.54013 (39891) SS BOND : bond 0.00336 ( 45) SS BOND : angle 1.08974 ( 90) hydrogen bonds : bond 0.05452 ( 1101) hydrogen bonds : angle 5.31788 ( 2994) link_BETA1-4 : bond 0.00444 ( 15) link_BETA1-4 : angle 0.89653 ( 45) link_NAG-ASN : bond 0.00270 ( 30) link_NAG-ASN : angle 2.46839 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4066 (tmm) cc_final: 0.3693 (tmm) REVERT: A 983 ARG cc_start: 0.8889 (ttp80) cc_final: 0.8662 (ttp80) REVERT: B 133 PHE cc_start: 0.8111 (m-80) cc_final: 0.7413 (m-80) REVERT: B 423 TYR cc_start: 0.7554 (t80) cc_final: 0.7102 (t80) REVERT: B 1010 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.7507 (mp10) REVERT: C 237 ARG cc_start: 0.7374 (mtm-85) cc_final: 0.7140 (mtm-85) REVERT: C 478 LYS cc_start: 0.8564 (tmtt) cc_final: 0.8358 (tmtt) REVERT: H 4 MET cc_start: 0.8260 (mmp) cc_final: 0.7995 (mmm) REVERT: K 81 MET cc_start: 0.5213 (mtp) cc_final: 0.3662 (tpt) outliers start: 28 outliers final: 21 residues processed: 232 average time/residue: 0.1594 time to fit residues: 61.1325 Evaluate side-chains 221 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain I residue 57 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 72 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 270 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 343 optimal weight: 0.0980 chunk 262 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 350 optimal weight: 6.9990 chunk 263 optimal weight: 1.9990 chunk 277 optimal weight: 0.8980 chunk 315 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN B 207 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 121 ASN C 853 GLN C 901 GLN G 109 HIS ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.139913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.080351 restraints weight = 50799.539| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.79 r_work: 0.2886 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29439 Z= 0.119 Angle : 0.520 8.025 40116 Z= 0.268 Chirality : 0.044 0.263 4640 Planarity : 0.004 0.058 5075 Dihedral : 5.472 56.954 4797 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.99 % Allowed : 10.08 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 0.19 (0.14), residues: 3529 helix: 2.48 (0.21), residues: 642 sheet: 0.30 (0.16), residues: 1034 loop : -0.84 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 98 TYR 0.020 0.001 TYR C 170 PHE 0.029 0.001 PHE B 592 TRP 0.010 0.001 TRP G 47 HIS 0.019 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00277 (29349) covalent geometry : angle 0.50695 (39891) SS BOND : bond 0.00272 ( 45) SS BOND : angle 0.90812 ( 90) hydrogen bonds : bond 0.04865 ( 1101) hydrogen bonds : angle 5.05708 ( 2994) link_BETA1-4 : bond 0.00414 ( 15) link_BETA1-4 : angle 0.86633 ( 45) link_NAG-ASN : bond 0.00284 ( 30) link_NAG-ASN : angle 2.32922 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7908 (m-40) cc_final: 0.7655 (p0) REVERT: A 153 MET cc_start: 0.4018 (tmm) cc_final: 0.3647 (tmm) REVERT: B 133 PHE cc_start: 0.8068 (m-80) cc_final: 0.7078 (m-80) REVERT: B 786 LYS cc_start: 0.8705 (ptpp) cc_final: 0.8447 (mtmm) REVERT: C 237 ARG cc_start: 0.7489 (mtm-85) cc_final: 0.7274 (mtm-85) REVERT: G 46 GLU cc_start: 0.7542 (pt0) cc_final: 0.7338 (pt0) REVERT: G 48 MET cc_start: 0.7059 (mmm) cc_final: 0.6525 (mmm) REVERT: H 4 MET cc_start: 0.8273 (mmp) cc_final: 0.7943 (mmm) REVERT: K 81 MET cc_start: 0.4989 (mtp) cc_final: 0.3390 (tpt) outliers start: 31 outliers final: 19 residues processed: 237 average time/residue: 0.1668 time to fit residues: 65.7939 Evaluate side-chains 219 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 37 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 257 optimal weight: 0.3980 chunk 153 optimal weight: 4.9990 chunk 319 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 321 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 312 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 313 optimal weight: 5.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS C 853 GLN C 901 GLN G 109 HIS ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.136455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.077852 restraints weight = 50856.513| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.09 r_work: 0.2778 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 29439 Z= 0.273 Angle : 0.631 8.457 40116 Z= 0.325 Chirality : 0.048 0.276 4640 Planarity : 0.004 0.061 5075 Dihedral : 5.603 58.651 4797 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.04 % Allowed : 10.69 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: -0.07 (0.14), residues: 3529 helix: 2.21 (0.21), residues: 629 sheet: 0.20 (0.16), residues: 1032 loop : -1.00 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 98 TYR 0.025 0.002 TYR F 87 PHE 0.040 0.002 PHE B 592 TRP 0.027 0.002 TRP G 47 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00676 (29349) covalent geometry : angle 0.61292 (39891) SS BOND : bond 0.00439 ( 45) SS BOND : angle 1.46284 ( 90) hydrogen bonds : bond 0.06393 ( 1101) hydrogen bonds : angle 5.23188 ( 2994) link_BETA1-4 : bond 0.00321 ( 15) link_BETA1-4 : angle 1.03115 ( 45) link_NAG-ASN : bond 0.00324 ( 30) link_NAG-ASN : angle 2.85929 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 219 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7910 (m-40) cc_final: 0.7665 (p0) REVERT: A 854 LYS cc_start: 0.5839 (mptt) cc_final: 0.4965 (mmtp) REVERT: A 988 GLU cc_start: 0.8708 (mp0) cc_final: 0.8436 (pm20) REVERT: A 1002 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8174 (tm-30) REVERT: B 767 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8998 (mt) REVERT: B 1106 GLN cc_start: 0.9297 (OUTLIER) cc_final: 0.8518 (pt0) REVERT: C 237 ARG cc_start: 0.7639 (mtm-85) cc_final: 0.7334 (mtm-85) REVERT: C 269 TYR cc_start: 0.7918 (m-80) cc_final: 0.7135 (m-80) REVERT: C 478 LYS cc_start: 0.8564 (tmtt) cc_final: 0.8297 (tmtt) REVERT: G 51 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7976 (tp) REVERT: I 46 GLU cc_start: 0.7908 (tp30) cc_final: 0.7708 (tp30) REVERT: K 81 MET cc_start: 0.4932 (mtp) cc_final: 0.3345 (tpt) outliers start: 64 outliers final: 36 residues processed: 264 average time/residue: 0.1653 time to fit residues: 73.1022 Evaluate side-chains 236 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 57 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 262 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 278 optimal weight: 0.5980 chunk 219 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN G 109 HIS ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.139468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.081731 restraints weight = 50711.963| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.18 r_work: 0.2837 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 29439 Z= 0.122 Angle : 0.539 8.690 40116 Z= 0.277 Chirality : 0.044 0.248 4640 Planarity : 0.004 0.059 5075 Dihedral : 5.118 57.164 4797 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.31 % Allowed : 12.15 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 0.10 (0.14), residues: 3529 helix: 2.42 (0.21), residues: 638 sheet: 0.25 (0.16), residues: 1032 loop : -0.90 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 98 TYR 0.019 0.001 TYR A1067 PHE 0.027 0.001 PHE B 140 TRP 0.033 0.001 TRP G 47 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00283 (29349) covalent geometry : angle 0.52307 (39891) SS BOND : bond 0.00253 ( 45) SS BOND : angle 1.44400 ( 90) hydrogen bonds : bond 0.04895 ( 1101) hydrogen bonds : angle 4.93497 ( 2994) link_BETA1-4 : bond 0.00423 ( 15) link_BETA1-4 : angle 0.84004 ( 45) link_NAG-ASN : bond 0.00280 ( 30) link_NAG-ASN : angle 2.37531 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 213 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4007 (tmm) cc_final: 0.3709 (tmm) REVERT: B 786 LYS cc_start: 0.8554 (ptpp) cc_final: 0.8297 (mtmm) REVERT: C 237 ARG cc_start: 0.7578 (mtm-85) cc_final: 0.7310 (mtm-85) REVERT: G 51 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8072 (tp) REVERT: H 4 MET cc_start: 0.8287 (mmp) cc_final: 0.8024 (mmm) REVERT: I 87 ARG cc_start: 0.7201 (mtm-85) cc_final: 0.6780 (mtt90) REVERT: I 104 ASP cc_start: 0.8429 (m-30) cc_final: 0.8191 (m-30) REVERT: K 81 MET cc_start: 0.4923 (mtp) cc_final: 0.3352 (tpt) outliers start: 41 outliers final: 34 residues processed: 243 average time/residue: 0.1609 time to fit residues: 65.2320 Evaluate side-chains 235 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain K residue 34 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 46 optimal weight: 0.8980 chunk 295 optimal weight: 10.0000 chunk 318 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 102 optimal weight: 0.1980 chunk 258 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 285 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 209 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 HIS ** J 38 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 = 0.3963 r_free = 0.3963 target = 0.139667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.082841 restraints weight = 50559.385| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.96 r_work: 0.2860 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29439 Z= 0.125 Angle : 0.534 8.576 40116 Z= 0.275 Chirality : 0.044 0.244 4640 Planarity : 0.004 0.059 5075 Dihedral : 4.858 57.085 4797 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.50 % Allowed : 12.54 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.14), residues: 3529 helix: 2.39 (0.21), residues: 649 sheet: 0.28 (0.16), residues: 1030 loop : -0.81 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 98 TYR 0.019 0.001 TYR I 32 PHE 0.039 0.001 PHE A 157 TRP 0.040 0.001 TRP G 47 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00297 (29349) covalent geometry : angle 0.51931 (39891) SS BOND : bond 0.00255 ( 45) SS BOND : angle 1.31915 ( 90) hydrogen bonds : bond 0.04726 ( 1101) hydrogen bonds : angle 4.82588 ( 2994) link_BETA1-4 : bond 0.00372 ( 15) link_BETA1-4 : angle 0.85511 ( 45) link_NAG-ASN : bond 0.00259 ( 30) link_NAG-ASN : angle 2.32067 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 212 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8492 (p90) cc_final: 0.8270 (p90) REVERT: A 153 MET cc_start: 0.3987 (tmm) cc_final: 0.3700 (tmm) REVERT: B 786 LYS cc_start: 0.8451 (ptpp) cc_final: 0.8191 (mtmm) REVERT: G 48 MET cc_start: 0.6862 (mmm) cc_final: 0.6310 (mmm) REVERT: H 4 MET cc_start: 0.8275 (mmp) cc_final: 0.8071 (mmm) REVERT: I 87 ARG cc_start: 0.7188 (mtm-85) cc_final: 0.6819 (mtt90) REVERT: I 104 ASP cc_start: 0.8395 (m-30) cc_final: 0.8174 (m-30) REVERT: K 81 MET cc_start: 0.4876 (mtp) cc_final: 0.3295 (tpt) outliers start: 47 outliers final: 39 residues processed: 245 average time/residue: 0.1669 time to fit residues: 68.3773 Evaluate side-chains 242 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain K residue 34 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 86 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 335 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 302 optimal weight: 20.0000 chunk 41 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 221 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 247 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 901 GLN G 109 HIS ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.138565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.079144 restraints weight = 50785.706| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.79 r_work: 0.2871 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29439 Z= 0.150 Angle : 0.545 10.498 40116 Z= 0.280 Chirality : 0.044 0.242 4640 Planarity : 0.004 0.059 5075 Dihedral : 4.834 57.338 4797 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.59 % Allowed : 12.89 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 0.13 (0.14), residues: 3529 helix: 2.33 (0.21), residues: 647 sheet: 0.26 (0.16), residues: 1046 loop : -0.84 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 98 TYR 0.019 0.001 TYR C1067 PHE 0.026 0.001 PHE C 559 TRP 0.040 0.001 TRP G 47 HIS 0.003 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00363 (29349) covalent geometry : angle 0.53153 (39891) SS BOND : bond 0.00282 ( 45) SS BOND : angle 1.20046 ( 90) hydrogen bonds : bond 0.04930 ( 1101) hydrogen bonds : angle 4.83833 ( 2994) link_BETA1-4 : bond 0.00351 ( 15) link_BETA1-4 : angle 0.84385 ( 45) link_NAG-ASN : bond 0.00238 ( 30) link_NAG-ASN : angle 2.34833 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 213 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8658 (mp) cc_final: 0.8432 (pt) REVERT: A 140 PHE cc_start: 0.8387 (p90) cc_final: 0.8169 (p90) REVERT: A 153 MET cc_start: 0.4088 (tmm) cc_final: 0.3786 (tmm) REVERT: A 854 LYS cc_start: 0.6351 (mmtp) cc_final: 0.6002 (mmtp) REVERT: B 786 LYS cc_start: 0.8726 (ptpp) cc_final: 0.8477 (mtmm) REVERT: G 48 MET cc_start: 0.6794 (mmm) cc_final: 0.6287 (mmm) REVERT: I 87 ARG cc_start: 0.7264 (mtm-85) cc_final: 0.6944 (mtt90) REVERT: K 2 MET cc_start: 0.2511 (ppp) cc_final: 0.0567 (tpt) REVERT: K 81 MET cc_start: 0.4856 (mtp) cc_final: 0.3280 (tpt) outliers start: 50 outliers final: 44 residues processed: 250 average time/residue: 0.1640 time to fit residues: 68.7409 Evaluate side-chains 249 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain K residue 34 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 315 optimal weight: 8.9990 chunk 349 optimal weight: 0.0370 chunk 109 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 351 optimal weight: 9.9990 chunk 33 optimal weight: 0.0470 chunk 41 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN G 109 HIS ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 57 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.139131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.079828 restraints weight = 50894.377| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.81 r_work: 0.2877 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29439 Z= 0.126 Angle : 0.537 11.264 40116 Z= 0.276 Chirality : 0.044 0.243 4640 Planarity : 0.004 0.059 5075 Dihedral : 4.733 57.004 4797 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.56 % Allowed : 13.14 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 0.19 (0.14), residues: 3529 helix: 2.38 (0.21), residues: 647 sheet: 0.33 (0.16), residues: 1032 loop : -0.83 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 98 TYR 0.018 0.001 TYR A1067 PHE 0.045 0.001 PHE A 157 TRP 0.044 0.001 TRP G 47 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00297 (29349) covalent geometry : angle 0.52415 (39891) SS BOND : bond 0.00257 ( 45) SS BOND : angle 1.22566 ( 90) hydrogen bonds : bond 0.04661 ( 1101) hydrogen bonds : angle 4.78121 ( 2994) link_BETA1-4 : bond 0.00381 ( 15) link_BETA1-4 : angle 0.82934 ( 45) link_NAG-ASN : bond 0.00262 ( 30) link_NAG-ASN : angle 2.26205 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 216 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8627 (mp) cc_final: 0.8415 (pt) REVERT: A 140 PHE cc_start: 0.8384 (p90) cc_final: 0.8165 (p90) REVERT: A 153 MET cc_start: 0.4147 (tmm) cc_final: 0.3847 (tmm) REVERT: A 854 LYS cc_start: 0.6326 (mmtp) cc_final: 0.5976 (mmtp) REVERT: A 988 GLU cc_start: 0.8724 (mp0) cc_final: 0.8373 (pm20) REVERT: B 200 TYR cc_start: 0.8322 (m-80) cc_final: 0.8107 (m-80) REVERT: B 786 LYS cc_start: 0.8699 (ptpp) cc_final: 0.8446 (mtmm) REVERT: F 87 TYR cc_start: 0.7740 (m-10) cc_final: 0.7529 (m-10) REVERT: G 48 MET cc_start: 0.6801 (mmm) cc_final: 0.6283 (mmm) REVERT: I 46 GLU cc_start: 0.7922 (tp30) cc_final: 0.6750 (tt0) REVERT: I 87 ARG cc_start: 0.7160 (mtm-85) cc_final: 0.6803 (mtt90) REVERT: K 2 MET cc_start: 0.2307 (ppp) cc_final: 0.1846 (ppp) REVERT: K 81 MET cc_start: 0.4812 (mtp) cc_final: 0.3263 (tpt) outliers start: 49 outliers final: 44 residues processed: 249 average time/residue: 0.1553 time to fit residues: 64.6000 Evaluate side-chains 249 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain K residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 97 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 137 optimal weight: 0.1980 chunk 206 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 84 optimal weight: 30.0000 chunk 134 optimal weight: 2.9990 chunk 313 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 chunk 221 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 HIS ** J 38 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 = 0.3952 r_free = 0.3952 target = 0.138871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.080441 restraints weight = 50624.323| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.25 r_work: 0.2826 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29439 Z= 0.136 Angle : 0.543 11.364 40116 Z= 0.278 Chirality : 0.044 0.241 4640 Planarity : 0.004 0.059 5075 Dihedral : 4.684 57.176 4797 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.44 % Allowed : 13.27 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 0.19 (0.14), residues: 3529 helix: 2.39 (0.21), residues: 641 sheet: 0.33 (0.16), residues: 1033 loop : -0.82 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 237 TYR 0.019 0.001 TYR A 170 PHE 0.024 0.001 PHE C 559 TRP 0.048 0.001 TRP G 47 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00327 (29349) covalent geometry : angle 0.52995 (39891) SS BOND : bond 0.00262 ( 45) SS BOND : angle 1.14440 ( 90) hydrogen bonds : bond 0.04727 ( 1101) hydrogen bonds : angle 4.77445 ( 2994) link_BETA1-4 : bond 0.00362 ( 15) link_BETA1-4 : angle 0.83337 ( 45) link_NAG-ASN : bond 0.00245 ( 30) link_NAG-ASN : angle 2.26328 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 213 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8532 (mp) cc_final: 0.8283 (pt) REVERT: A 140 PHE cc_start: 0.8363 (p90) cc_final: 0.8153 (p90) REVERT: A 153 MET cc_start: 0.4187 (tmm) cc_final: 0.3904 (tmm) REVERT: A 854 LYS cc_start: 0.6220 (mmtp) cc_final: 0.5903 (mmtp) REVERT: A 988 GLU cc_start: 0.8687 (mp0) cc_final: 0.8335 (pm20) REVERT: B 786 LYS cc_start: 0.8572 (ptpp) cc_final: 0.8325 (mtmm) REVERT: C 237 ARG cc_start: 0.7723 (mtm110) cc_final: 0.7476 (ptp90) REVERT: H 4 MET cc_start: 0.8327 (mmp) cc_final: 0.8082 (mmm) REVERT: I 46 GLU cc_start: 0.7938 (tp30) cc_final: 0.6791 (tt0) REVERT: I 87 ARG cc_start: 0.7035 (mtm-85) cc_final: 0.6730 (mtt90) REVERT: I 104 ASP cc_start: 0.8319 (m-30) cc_final: 0.8036 (t0) REVERT: K 2 MET cc_start: 0.1991 (ppp) cc_final: 0.1580 (ppp) REVERT: K 81 MET cc_start: 0.4811 (mtp) cc_final: 0.3284 (tpt) outliers start: 45 outliers final: 42 residues processed: 244 average time/residue: 0.1658 time to fit residues: 67.3993 Evaluate side-chains 246 residues out of total 3138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain K residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 237 optimal weight: 1.9990 chunk 279 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 180 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 190 optimal weight: 0.7980 chunk 303 optimal weight: 20.0000 chunk 251 optimal weight: 0.5980 chunk 259 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 HIS ** J 38 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 = 0.3961 r_free = 0.3961 target = 0.139579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.081811 restraints weight = 51035.570| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.15 r_work: 0.2856 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29439 Z= 0.117 Angle : 0.531 11.720 40116 Z= 0.272 Chirality : 0.044 0.242 4640 Planarity : 0.004 0.059 5075 Dihedral : 4.586 56.732 4797 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.29 % Rotamer: Outliers : 1.37 % Allowed : 13.59 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.14), residues: 3529 helix: 2.49 (0.21), residues: 636 sheet: 0.36 (0.16), residues: 1032 loop : -0.77 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 319 TYR 0.022 0.001 TYR C 170 PHE 0.047 0.001 PHE A 157 TRP 0.050 0.001 TRP G 47 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00273 (29349) covalent geometry : angle 0.51864 (39891) SS BOND : bond 0.00243 ( 45) SS BOND : angle 1.11605 ( 90) hydrogen bonds : bond 0.04436 ( 1101) hydrogen bonds : angle 4.70413 ( 2994) link_BETA1-4 : bond 0.00412 ( 15) link_BETA1-4 : angle 0.82589 ( 45) link_NAG-ASN : bond 0.00271 ( 30) link_NAG-ASN : angle 2.16402 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8409.48 seconds wall clock time: 144 minutes 0.84 seconds (8640.84 seconds total)