Starting phenix.real_space_refine on Tue Aug 26 21:06:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7p_39822/08_2025/8z7p_39822.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7p_39822/08_2025/8z7p_39822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z7p_39822/08_2025/8z7p_39822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7p_39822/08_2025/8z7p_39822.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7p_39822/08_2025/8z7p_39822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7p_39822/08_2025/8z7p_39822.cif" } resolution = 3.45 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= 0.050 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 207 5.16 5 C 26406 2.51 5 N 6786 2.21 5 O 8100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 282 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41499 Number of models: 1 Model: "" Number of chains: 36 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "A" Number of atoms: 8545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8545 Classifications: {'peptide': 1099} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 52, 'TRANS': 1046} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "B" Number of atoms: 8545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8545 Classifications: {'peptide': 1099} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 52, 'TRANS': 1046} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "C" Number of atoms: 8545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8545 Classifications: {'peptide': 1099} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 52, 'TRANS': 1046} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "Y" 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: "Z" 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: 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: "b" 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: "c" 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 9.94, per 1000 atoms: 0.24 Number of scatterers: 41499 At special positions: 0 Unit cell: (191.06, 181.74, 272.144, 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 207 16.00 O 8100 8.00 N 6786 7.00 C 26406 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 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 C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG A1301 " - " ASN A1134 " " NAG A1302 " - " ASN A1098 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 234 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 282 " " NAG B1301 " - " ASN B1134 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 234 " " NAG B1309 " - " ASN B 165 " " NAG B1310 " - " ASN B 282 " " NAG C1301 " - " ASN C1134 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 717 " " NAG C1305 " - " ASN C 801 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 234 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C 282 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 103 " " NAG D 703 " - " ASN D 322 " " NAG D 704 " - " ASN D 432 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 103 " " NAG E 703 " - " ASN E 322 " " NAG E 704 " - " ASN E 432 " " NAG F 701 " - " ASN F 53 " " NAG F 702 " - " ASN F 103 " " NAG F 703 " - " ASN F 322 " " NAG F 704 " - " ASN F 432 " " NAG G 1 " - " ASN D 90 " " NAG H 1 " - " ASN D 546 " " NAG I 1 " - " ASN A 17 " " NAG J 1 " - " ASN A 122 " " NAG K 1 " - " ASN A 149 " " NAG L 1 " - " ASN A 61 " " NAG M 1 " - " ASN A 343 " " NAG N 1 " - " ASN A 331 " " NAG O 1 " - " ASN E 90 " " NAG P 1 " - " ASN E 546 " " NAG Q 1 " - " ASN B 17 " " NAG R 1 " - " ASN B 122 " " NAG S 1 " - " ASN B 149 " " NAG T 1 " - " ASN B 61 " " NAG U 1 " - " ASN B 343 " " NAG V 1 " - " ASN B 331 " " NAG W 1 " - " ASN F 90 " " NAG X 1 " - " ASN F 546 " " NAG Y 1 " - " ASN C 17 " " NAG Z 1 " - " ASN C 122 " " NAG a 1 " - " ASN C 149 " " NAG b 1 " - " ASN C 61 " " NAG c 1 " - " ASN C 343 " " NAG d 1 " - " ASN C 331 " Time building additional restraints: 3.56 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 476.8 nanoseconds 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9534 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 51 sheets defined 38.6% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.953A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 4.047A pdb=" N VAL D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 144 through 155 removed outlier: 4.084A pdb=" N ASN D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 155 " --> pdb=" O ILE D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.791A pdb=" N VAL D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 176 through 194 removed outlier: 3.642A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 219 through 252 removed outlier: 3.844A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 4.137A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 280 removed outlier: 4.229A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 299 Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.627A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 386 Processing helix chain 'D' and resid 387 through 388 No H-bonds generated for 'chain 'D' and resid 387 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.569A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 447 Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 503 removed outlier: 3.736A pdb=" N LEU D 503 " --> pdb=" O PRO D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 532 removed outlier: 4.190A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.769A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.902A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.676A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.706A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 701 through 706 removed outlier: 3.613A pdb=" N SER A 704 " --> pdb=" O ALA A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.858A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 769 removed outlier: 3.516A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 842 removed outlier: 3.753A pdb=" N GLY A 842 " --> pdb=" O GLY A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 848 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.759A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 894 No H-bonds generated for 'chain 'A' and resid 892 through 894' Processing helix chain 'A' and resid 895 through 1033 removed outlier: 3.900A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.954A pdb=" N GLU E 37 " --> pdb=" O ASN E 33 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 4.047A pdb=" N VAL E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 144 through 155 removed outlier: 4.084A pdb=" N ASN E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU E 150 " --> pdb=" O PRO E 146 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER E 155 " --> pdb=" O ILE E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 172 removed outlier: 3.790A pdb=" N VAL E 172 " --> pdb=" O TRP E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 176 through 194 removed outlier: 3.644A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 219 through 252 removed outlier: 3.846A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 4.137A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 280 removed outlier: 4.228A pdb=" N SER E 280 " --> pdb=" O ASN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 299 Processing helix chain 'E' and resid 303 through 319 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.626A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER E 331 " --> pdb=" O PHE E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 386 Processing helix chain 'E' and resid 387 through 388 No H-bonds generated for 'chain 'E' and resid 387 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 399 through 413 removed outlier: 3.568A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 Processing helix chain 'E' and resid 431 through 447 Processing helix chain 'E' and resid 449 through 466 Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 503 removed outlier: 3.735A pdb=" N LEU E 503 " --> pdb=" O PRO E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 512 through 532 removed outlier: 4.195A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.768A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.909A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 390 removed outlier: 3.677A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.705A 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 616 through 620 Processing helix chain 'B' and resid 701 through 706 removed outlier: 3.613A pdb=" N SER B 704 " --> pdb=" O ALA B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.886A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 769 removed outlier: 3.516A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 842 removed outlier: 3.753A pdb=" N GLY B 842 " --> pdb=" O GLY B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.758A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 894 No H-bonds generated for 'chain 'B' and resid 892 through 894' Processing helix chain 'B' and resid 895 through 1033 removed outlier: 3.899A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.952A pdb=" N GLU F 37 " --> pdb=" O ASN F 33 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 81 removed outlier: 4.048A pdb=" N VAL F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 144 through 155 removed outlier: 4.085A pdb=" N ASN F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU F 150 " --> pdb=" O PRO F 146 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER F 155 " --> pdb=" O ILE F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 172 removed outlier: 3.790A pdb=" N VAL F 172 " --> pdb=" O TRP F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 175 No H-bonds generated for 'chain 'F' and resid 173 through 175' Processing helix chain 'F' and resid 176 through 194 removed outlier: 3.640A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 219 through 252 removed outlier: 3.846A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 4.137A pdb=" N ASN F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 280 removed outlier: 4.229A pdb=" N SER F 280 " --> pdb=" O ASN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 299 Processing helix chain 'F' and resid 303 through 319 Processing helix chain 'F' and resid 324 through 331 removed outlier: 3.626A pdb=" N TRP F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER F 331 " --> pdb=" O PHE F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 386 Processing helix chain 'F' and resid 387 through 388 No H-bonds generated for 'chain 'F' and resid 387 through 388' Processing helix chain 'F' and resid 389 through 393 Processing helix chain 'F' and resid 399 through 413 removed outlier: 3.570A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 422 Processing helix chain 'F' and resid 431 through 447 Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 469 through 471 No H-bonds generated for 'chain 'F' and resid 469 through 471' Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 499 through 503 removed outlier: 3.737A pdb=" N LEU F 503 " --> pdb=" O PRO F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 512 through 532 removed outlier: 4.190A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.768A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 574 Processing helix chain 'F' and resid 581 through 588 Processing helix chain 'F' and resid 588 through 599 Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.905A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.676A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.706A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 701 through 706 removed outlier: 3.614A pdb=" N SER C 704 " --> pdb=" O ALA C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.858A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 769 removed outlier: 3.516A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 842 removed outlier: 3.753A pdb=" N GLY C 842 " --> pdb=" O GLY C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 848 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.759A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 894 No H-bonds generated for 'chain 'C' and resid 892 through 894' Processing helix chain 'C' and resid 895 through 1033 removed outlier: 3.899A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.136A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.005A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 78 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.005A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.164A pdb=" N PHE A 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B 541 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.673A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 83 through 85 removed outlier: 13.237A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 11.640A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 11.060A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY A 142 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.659A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 310 through 319 removed outlier: 3.501A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.850A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB5, first strand: chain 'A' and resid 538 through 542 removed outlier: 3.572A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 541 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 664 through 665 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 727 removed outlier: 7.508A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'E' and resid 131 through 133 Processing sheet with id=AC2, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.138A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 347 through 350 Processing sheet with id=AC4, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.998A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG B 78 " --> pdb=" O ILE B 68 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.998A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.159A pdb=" N PHE B 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.667A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 83 through 85 removed outlier: 13.255A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 11.642A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 11.063A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY B 142 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.671A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 310 through 319 removed outlier: 3.522A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.844A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'B' and resid 664 through 665 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.506A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'F' and resid 131 through 133 Processing sheet with id=AE1, first strand: chain 'F' and resid 262 through 263 removed outlier: 6.137A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'F' and resid 347 through 350 Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.992A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG C 78 " --> pdb=" O ILE C 68 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.992A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.660A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 83 through 85 removed outlier: 13.252A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 11.651A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.669A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 310 through 319 removed outlier: 6.984A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.855A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF3, first strand: chain 'C' and resid 664 through 665 Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 727 removed outlier: 6.511A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AF6, first strand: chain 'C' and resid 1094 through 1097 1829 hydrogen bonds defined for protein. 5196 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: 10.38 Time building geometry restraints manager: 4.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 13226 1.34 - 1.46: 10271 1.46 - 1.58: 18695 1.58 - 1.70: 0 1.70 - 1.81: 300 Bond restraints: 42492 Sorted by residual: bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.64e+00 bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" C1 BMA d 3 " pdb=" C2 BMA d 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.54e+00 bond pdb=" C1 BMA V 3 " pdb=" C2 BMA V 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.51e+00 ... (remaining 42487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 56656 1.45 - 2.91: 999 2.91 - 4.36: 107 4.36 - 5.82: 27 5.82 - 7.27: 6 Bond angle restraints: 57795 Sorted by residual: angle pdb=" N ALA C 292 " pdb=" CA ALA C 292 " pdb=" C ALA C 292 " ideal model delta sigma weight residual 114.09 110.30 3.79 1.55e+00 4.16e-01 5.98e+00 angle pdb=" N ALA B 292 " pdb=" CA ALA B 292 " pdb=" C ALA B 292 " ideal model delta sigma weight residual 114.09 110.31 3.78 1.55e+00 4.16e-01 5.93e+00 angle pdb=" N ALA A 292 " pdb=" CA ALA A 292 " pdb=" C ALA A 292 " ideal model delta sigma weight residual 114.09 110.35 3.74 1.55e+00 4.16e-01 5.83e+00 angle pdb=" N GLY A 72 " pdb=" CA GLY A 72 " pdb=" C GLY A 72 " ideal model delta sigma weight residual 110.29 113.26 -2.97 1.28e+00 6.10e-01 5.38e+00 angle pdb=" N GLY B 72 " pdb=" CA GLY B 72 " pdb=" C GLY B 72 " ideal model delta sigma weight residual 110.29 113.24 -2.95 1.28e+00 6.10e-01 5.31e+00 ... (remaining 57790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.96: 25585 21.96 - 43.91: 596 43.91 - 65.87: 129 65.87 - 87.83: 42 87.83 - 109.79: 72 Dihedral angle restraints: 26424 sinusoidal: 11595 harmonic: 14829 Sorted by residual: dihedral pdb=" C2 NAG T 1 " pdb=" C3 NAG T 1 " pdb=" C4 NAG T 1 " pdb=" O4 NAG T 1 " ideal model delta sinusoidal sigma weight residual 175.11 65.32 109.79 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" C2 NAG T 1 " pdb=" C3 NAG T 1 " pdb=" C4 NAG T 1 " pdb=" C5 NAG T 1 " ideal model delta sinusoidal sigma weight residual 53.78 -56.00 109.78 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" C2 NAG b 1 " pdb=" C3 NAG b 1 " pdb=" C4 NAG b 1 " pdb=" O4 NAG b 1 " ideal model delta sinusoidal sigma weight residual 175.11 65.33 109.78 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 26421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 5712 0.054 - 0.108: 833 0.108 - 0.163: 94 0.163 - 0.217: 0 0.217 - 0.271: 6 Chirality restraints: 6645 Sorted by residual: chirality pdb=" C5 BMA d 3 " pdb=" C4 BMA d 3 " pdb=" C6 BMA d 3 " pdb=" O5 BMA d 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C5 BMA V 3 " pdb=" C4 BMA V 3 " pdb=" C6 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 6642 not shown) Planarity restraints: 7428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 294 " -0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO C 295 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 295 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 295 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO A 295 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 294 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO B 295 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 295 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 295 " 0.018 5.00e-02 4.00e+02 ... (remaining 7425 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 11163 2.80 - 3.33: 38111 3.33 - 3.85: 68063 3.85 - 4.38: 76302 4.38 - 4.90: 134515 Nonbonded interactions: 328154 Sorted by model distance: nonbonded pdb=" OH TYR C 837 " pdb=" OD1 ASP C 848 " model vdw 2.281 3.040 nonbonded pdb=" OH TYR B 837 " pdb=" OD1 ASP B 848 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR A 837 " pdb=" OD1 ASP A 848 " model vdw 2.282 3.040 nonbonded pdb=" OG SER B 151 " pdb=" O7 NAG S 1 " model vdw 2.302 3.040 nonbonded pdb=" O ASN C 99 " pdb=" NH1 ARG C 102 " model vdw 2.302 3.120 ... (remaining 328149 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'N' selection = chain 'V' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.730 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 37.620 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.170 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5005 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 : 0.003 0.041 42639 Z= 0.143 Angle : 0.469 7.271 58182 Z= 0.234 Chirality : 0.040 0.271 6645 Planarity : 0.003 0.032 7362 Dihedral : 11.941 109.786 16728 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.86 % Allowed : 5.37 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.11), residues: 5052 helix: 0.81 (0.12), residues: 1767 sheet: -0.84 (0.19), residues: 672 loop : -2.74 (0.10), residues: 2613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 582 TYR 0.020 0.001 TYR F 385 PHE 0.006 0.001 PHE A 833 TRP 0.004 0.000 TRP F 168 HIS 0.002 0.000 HIS F 34 Details of bonding type rmsd covalent geometry : bond 0.00277 (42492) covalent geometry : angle 0.46379 (57795) SS BOND : bond 0.00086 ( 54) SS BOND : angle 0.32982 ( 108) hydrogen bonds : bond 0.18035 ( 1814) hydrogen bonds : angle 6.51798 ( 5196) link_BETA1-4 : bond 0.00443 ( 27) link_BETA1-4 : angle 1.26109 ( 81) link_NAG-ASN : bond 0.00241 ( 66) link_NAG-ASN : angle 1.03450 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 4443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 858 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 578 ASN cc_start: 0.6949 (t0) cc_final: 0.6631 (t0) REVERT: E 578 ASN cc_start: 0.7092 (t0) cc_final: 0.6777 (t0) REVERT: C 131 CYS cc_start: 0.4545 (OUTLIER) cc_final: 0.4341 (m) REVERT: C 376 THR cc_start: 0.7078 (p) cc_final: 0.6798 (p) outliers start: 126 outliers final: 25 residues processed: 956 average time/residue: 0.2036 time to fit residues: 321.0102 Evaluate side-chains 412 residues out of total 4443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 386 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 494 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN D 101 GLN D 117 ASN D 137 ASN D 194 ASN ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN D 524 GLN D 531 GLN ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN A 134 GLN A 173 GLN A 183 GLN A 207 HIS A 321 GLN A 334 ASN A 394 ASN A 414 GLN A 580 GLN A 853 GLN A 872 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN A1071 GLN E 101 GLN E 117 ASN E 137 ASN E 194 ASN E 345 HIS ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 524 GLN E 531 GLN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 99 ASN B 134 GLN B 173 GLN B 183 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 321 GLN B 394 ASN B 414 GLN B 580 GLN B 853 GLN B 872 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN B1071 GLN F 101 GLN F 117 ASN F 137 ASN F 194 ASN ** F 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 HIS ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 524 GLN F 531 GLN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 134 GLN C 173 GLN C 183 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 394 ASN C 414 GLN C 580 GLN C 853 GLN C 872 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5240 r_free = 0.5240 target = 0.246370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.5079 r_free = 0.5079 target = 0.229181 restraints weight = 77025.612| |-----------------------------------------------------------------------------| r_work (start): 0.5062 rms_B_bonded: 2.11 r_work: 0.4918 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.4897 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.4897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5716 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.108 42639 Z= 0.391 Angle : 0.854 14.171 58182 Z= 0.418 Chirality : 0.053 0.330 6645 Planarity : 0.006 0.062 7362 Dihedral : 11.954 105.168 7454 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.90 % Allowed : 11.01 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.11), residues: 5052 helix: 1.16 (0.12), residues: 1821 sheet: -0.98 (0.19), residues: 714 loop : -2.25 (0.11), residues: 2517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 577 TYR 0.035 0.003 TYR C 266 PHE 0.048 0.004 PHE B 565 TRP 0.024 0.002 TRP B 104 HIS 0.013 0.002 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00931 (42492) covalent geometry : angle 0.83523 (57795) SS BOND : bond 0.00763 ( 54) SS BOND : angle 1.53662 ( 108) hydrogen bonds : bond 0.04481 ( 1814) hydrogen bonds : angle 5.38826 ( 5196) link_BETA1-4 : bond 0.00709 ( 27) link_BETA1-4 : angle 2.16740 ( 81) link_NAG-ASN : bond 0.00664 ( 66) link_NAG-ASN : angle 2.72680 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 4443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 359 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 350 ASP cc_start: 0.3589 (t0) cc_final: 0.3376 (t0) REVERT: A 216 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6526 (pt) REVERT: A 269 TYR cc_start: 0.8007 (m-80) cc_final: 0.7717 (m-80) REVERT: A 346 ARG cc_start: 0.7131 (ttp80) cc_final: 0.6914 (tmm-80) REVERT: A 599 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8712 (t) REVERT: B 18 LEU cc_start: 0.6895 (mt) cc_final: 0.6678 (mt) REVERT: B 24 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6364 (mp) REVERT: B 90 VAL cc_start: 0.8587 (OUTLIER) cc_final: 0.8302 (m) REVERT: B 216 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6553 (pt) REVERT: B 269 TYR cc_start: 0.8216 (m-80) cc_final: 0.7884 (m-80) REVERT: B 296 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8172 (tp) REVERT: B 346 ARG cc_start: 0.7100 (ttp80) cc_final: 0.6870 (tmm-80) REVERT: F 350 ASP cc_start: 0.3432 (t0) cc_final: 0.3226 (t0) REVERT: C 58 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8296 (m-10) REVERT: C 131 CYS cc_start: 0.5149 (OUTLIER) cc_final: 0.4761 (m) REVERT: C 216 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6498 (pt) REVERT: C 269 TYR cc_start: 0.8173 (m-80) cc_final: 0.7784 (m-80) REVERT: C 296 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8191 (tp) REVERT: C 346 ARG cc_start: 0.7114 (ttp80) cc_final: 0.6817 (tmm-80) outliers start: 172 outliers final: 101 residues processed: 508 average time/residue: 0.1908 time to fit residues: 163.5615 Evaluate side-chains 403 residues out of total 4443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 292 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 192 ARG Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 510 TYR Chi-restraints excluded: chain F residue 540 HIS Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 108 optimal weight: 0.8980 chunk 379 optimal weight: 5.9990 chunk 303 optimal weight: 5.9990 chunk 172 optimal weight: 40.0000 chunk 292 optimal weight: 20.0000 chunk 72 optimal weight: 0.9990 chunk 179 optimal weight: 9.9990 chunk 409 optimal weight: 6.9990 chunk 220 optimal weight: 40.0000 chunk 301 optimal weight: 6.9990 chunk 300 optimal weight: 0.1980 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 HIS A 87 ASN ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 HIS B 69 HIS B 183 GLN B 919 ASN ** B 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 HIS ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS C 87 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5231 r_free = 0.5231 target = 0.246127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.5064 r_free = 0.5064 target = 0.228261 restraints weight = 76501.719| |-----------------------------------------------------------------------------| r_work (start): 0.5060 rms_B_bonded: 2.13 r_work: 0.4919 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4897 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.4897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5727 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 42639 Z= 0.251 Angle : 0.716 12.941 58182 Z= 0.345 Chirality : 0.048 0.316 6645 Planarity : 0.004 0.050 7362 Dihedral : 10.818 101.936 7446 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.54 % Allowed : 12.17 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.11), residues: 5052 helix: 1.34 (0.12), residues: 1821 sheet: -1.12 (0.18), residues: 702 loop : -2.07 (0.11), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 577 TYR 0.035 0.002 TYR C 917 PHE 0.043 0.002 PHE A 898 TRP 0.019 0.001 TRP C 353 HIS 0.010 0.001 HIS E 540 Details of bonding type rmsd covalent geometry : bond 0.00587 (42492) covalent geometry : angle 0.69877 (57795) SS BOND : bond 0.00618 ( 54) SS BOND : angle 1.21581 ( 108) hydrogen bonds : bond 0.03795 ( 1814) hydrogen bonds : angle 5.10426 ( 5196) link_BETA1-4 : bond 0.00328 ( 27) link_BETA1-4 : angle 2.10364 ( 81) link_NAG-ASN : bond 0.00476 ( 66) link_NAG-ASN : angle 2.38436 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 328 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 592 PHE cc_start: 0.1401 (OUTLIER) cc_final: 0.0792 (t80) REVERT: A 269 TYR cc_start: 0.8146 (m-80) cc_final: 0.7881 (m-80) REVERT: E 592 PHE cc_start: 0.1028 (OUTLIER) cc_final: 0.0418 (t80) REVERT: B 90 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8227 (m) REVERT: B 452 LEU cc_start: 0.5707 (mp) cc_final: 0.5191 (mp) REVERT: C 58 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8059 (m-10) REVERT: C 131 CYS cc_start: 0.5240 (OUTLIER) cc_final: 0.4745 (m) REVERT: C 141 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7854 (mt) REVERT: C 269 TYR cc_start: 0.8270 (m-80) cc_final: 0.7985 (m-80) REVERT: C 281 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8089 (pt0) outliers start: 156 outliers final: 100 residues processed: 464 average time/residue: 0.2307 time to fit residues: 179.1988 Evaluate side-chains 397 residues out of total 4443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 290 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 472 GLN Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 472 GLN Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain F residue 192 ARG Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 540 HIS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 462 optimal weight: 30.0000 chunk 165 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 chunk 268 optimal weight: 7.9990 chunk 450 optimal weight: 1.9990 chunk 474 optimal weight: 30.0000 chunk 198 optimal weight: 10.0000 chunk 410 optimal weight: 0.9980 chunk 181 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS A 207 HIS A 354 ASN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 774 GLN ** B 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 HIS ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 146 HIS C 207 HIS C 354 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5196 r_free = 0.5196 target = 0.242713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.5029 r_free = 0.5029 target = 0.225190 restraints weight = 75795.077| |-----------------------------------------------------------------------------| r_work (start): 0.5023 rms_B_bonded: 2.13 r_work: 0.4863 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.4842 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.4842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5862 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.109 42639 Z= 0.408 Angle : 0.839 12.380 58182 Z= 0.415 Chirality : 0.053 0.389 6645 Planarity : 0.006 0.067 7362 Dihedral : 10.788 106.375 7432 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.37 % Favored : 93.59 % Rotamer: Outliers : 4.62 % Allowed : 13.21 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -1.07 (0.12), residues: 5052 helix: 1.35 (0.12), residues: 1788 sheet: -1.42 (0.18), residues: 708 loop : -2.09 (0.11), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 577 TYR 0.029 0.003 TYR A 265 PHE 0.050 0.003 PHE B 565 TRP 0.028 0.002 TRP C 104 HIS 0.017 0.002 HIS F 345 Details of bonding type rmsd covalent geometry : bond 0.00972 (42492) covalent geometry : angle 0.82035 (57795) SS BOND : bond 0.00844 ( 54) SS BOND : angle 1.31983 ( 108) hydrogen bonds : bond 0.04192 ( 1814) hydrogen bonds : angle 5.39838 ( 5196) link_BETA1-4 : bond 0.00626 ( 27) link_BETA1-4 : angle 2.43106 ( 81) link_NAG-ASN : bond 0.00538 ( 66) link_NAG-ASN : angle 2.62683 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 4443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 288 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 592 PHE cc_start: 0.1257 (OUTLIER) cc_final: 0.0561 (t80) REVERT: A 117 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7778 (tp) REVERT: A 131 CYS cc_start: 0.5648 (OUTLIER) cc_final: 0.5151 (m) REVERT: A 160 TYR cc_start: 0.7328 (OUTLIER) cc_final: 0.7051 (p90) REVERT: A 346 ARG cc_start: 0.7282 (tmm-80) cc_final: 0.7000 (ttt90) REVERT: E 592 PHE cc_start: 0.0604 (OUTLIER) cc_final: 0.0315 (t80) REVERT: B 24 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6044 (mp) REVERT: B 63 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8157 (p) REVERT: B 90 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8454 (m) REVERT: B 117 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7687 (tp) REVERT: B 244 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7768 (mt) REVERT: B 281 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7928 (pt0) REVERT: B 452 LEU cc_start: 0.5644 (mp) cc_final: 0.5299 (mp) REVERT: C 58 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.8099 (m-10) REVERT: C 90 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8383 (m) REVERT: C 131 CYS cc_start: 0.5627 (OUTLIER) cc_final: 0.4984 (m) REVERT: C 599 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8628 (t) outliers start: 204 outliers final: 134 residues processed: 467 average time/residue: 0.1955 time to fit residues: 154.0794 Evaluate side-chains 410 residues out of total 4443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 261 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 472 GLN Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 471 ASP Chi-restraints excluded: chain E residue 472 GLN Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 510 TYR Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 510 TYR Chi-restraints excluded: chain F residue 540 HIS Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 591 LEU Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 315 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 425 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 282 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 456 optimal weight: 3.9990 chunk 439 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 chunk 360 optimal weight: 50.0000 chunk 359 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS A 137 ASN ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 HIS ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5200 r_free = 0.5200 target = 0.243143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.5032 r_free = 0.5032 target = 0.225303 restraints weight = 75869.321| |-----------------------------------------------------------------------------| r_work (start): 0.5034 rms_B_bonded: 2.11 r_work: 0.4878 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4851 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.4851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5857 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 42639 Z= 0.332 Angle : 0.792 14.758 58182 Z= 0.385 Chirality : 0.050 0.366 6645 Planarity : 0.005 0.067 7362 Dihedral : 10.574 105.382 7432 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.19 % Allowed : 14.64 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -0.98 (0.12), residues: 5052 helix: 1.45 (0.12), residues: 1788 sheet: -1.33 (0.19), residues: 675 loop : -2.08 (0.11), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 577 TYR 0.027 0.002 TYR B 265 PHE 0.041 0.003 PHE B 565 TRP 0.025 0.002 TRP A 353 HIS 0.008 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00789 (42492) covalent geometry : angle 0.77206 (57795) SS BOND : bond 0.00723 ( 54) SS BOND : angle 1.27481 ( 108) hydrogen bonds : bond 0.03910 ( 1814) hydrogen bonds : angle 5.30903 ( 5196) link_BETA1-4 : bond 0.00435 ( 27) link_BETA1-4 : angle 2.41275 ( 81) link_NAG-ASN : bond 0.00386 ( 66) link_NAG-ASN : angle 2.68254 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 4443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 281 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 59 VAL cc_start: 0.6353 (OUTLIER) cc_final: 0.6129 (t) REVERT: D 347 THR cc_start: 0.2162 (OUTLIER) cc_final: 0.1957 (m) REVERT: D 592 PHE cc_start: 0.1241 (OUTLIER) cc_final: 0.0534 (t80) REVERT: A 117 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7926 (tp) REVERT: A 131 CYS cc_start: 0.5640 (OUTLIER) cc_final: 0.5142 (m) REVERT: A 346 ARG cc_start: 0.7294 (tmm-80) cc_final: 0.7048 (ttt90) REVERT: E 347 THR cc_start: 0.3392 (OUTLIER) cc_final: 0.2991 (m) REVERT: E 592 PHE cc_start: 0.1366 (OUTLIER) cc_final: 0.0811 (t80) REVERT: B 24 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.5994 (mp) REVERT: B 90 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8335 (m) REVERT: B 117 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7676 (tp) REVERT: B 131 CYS cc_start: 0.5431 (OUTLIER) cc_final: 0.4991 (m) REVERT: B 244 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7864 (mt) REVERT: B 646 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6707 (mmp80) REVERT: C 24 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6112 (mp) REVERT: C 58 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.8091 (m-10) REVERT: C 90 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8372 (m) REVERT: C 131 CYS cc_start: 0.5442 (OUTLIER) cc_final: 0.4809 (m) REVERT: C 141 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8090 (mt) REVERT: C 346 ARG cc_start: 0.7197 (tmm-80) cc_final: 0.6809 (ttt90) REVERT: C 599 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8584 (t) outliers start: 185 outliers final: 133 residues processed: 446 average time/residue: 0.2037 time to fit residues: 154.8775 Evaluate side-chains 414 residues out of total 4443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 262 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 472 GLN Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 471 ASP Chi-restraints excluded: chain E residue 472 GLN Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 510 TYR Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 345 HIS Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 510 TYR Chi-restraints excluded: chain F residue 540 HIS Chi-restraints excluded: chain F residue 591 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 462 optimal weight: 30.0000 chunk 249 optimal weight: 0.9990 chunk 219 optimal weight: 20.0000 chunk 298 optimal weight: 0.9980 chunk 252 optimal weight: 0.9980 chunk 405 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 355 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 GLN ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 148 ASN ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5227 r_free = 0.5227 target = 0.245960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5061 r_free = 0.5061 target = 0.227956 restraints weight = 77077.973| |-----------------------------------------------------------------------------| r_work (start): 0.5057 rms_B_bonded: 2.15 r_work: 0.4914 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4892 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.4892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5747 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 42639 Z= 0.136 Angle : 0.684 19.152 58182 Z= 0.323 Chirality : 0.046 0.312 6645 Planarity : 0.004 0.051 7362 Dihedral : 9.908 101.651 7428 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.29 % Allowed : 15.48 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.12), residues: 5052 helix: 1.52 (0.12), residues: 1779 sheet: -0.92 (0.19), residues: 660 loop : -1.82 (0.11), residues: 2613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 983 TYR 0.022 0.001 TYR B 423 PHE 0.043 0.002 PHE B 970 TRP 0.021 0.001 TRP A 353 HIS 0.019 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00313 (42492) covalent geometry : angle 0.66825 (57795) SS BOND : bond 0.00430 ( 54) SS BOND : angle 0.84689 ( 108) hydrogen bonds : bond 0.03406 ( 1814) hydrogen bonds : angle 5.02226 ( 5196) link_BETA1-4 : bond 0.00417 ( 27) link_BETA1-4 : angle 2.19903 ( 81) link_NAG-ASN : bond 0.00314 ( 66) link_NAG-ASN : angle 2.21638 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 4443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 289 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 592 PHE cc_start: 0.1152 (OUTLIER) cc_final: 0.0490 (t80) REVERT: A 131 CYS cc_start: 0.5423 (OUTLIER) cc_final: 0.4987 (m) REVERT: A 314 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7206 (tt0) REVERT: E 347 THR cc_start: 0.3635 (OUTLIER) cc_final: 0.3295 (m) REVERT: B 90 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8125 (m) REVERT: B 131 CYS cc_start: 0.5037 (OUTLIER) cc_final: 0.4677 (m) REVERT: B 693 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6858 (pt) REVERT: C 58 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7953 (m-10) REVERT: C 90 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8176 (m) REVERT: C 131 CYS cc_start: 0.5110 (OUTLIER) cc_final: 0.4530 (m) REVERT: C 141 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7911 (mt) REVERT: C 452 LEU cc_start: 0.5797 (mp) cc_final: 0.5404 (mp) REVERT: C 693 ILE cc_start: 0.6986 (OUTLIER) cc_final: 0.6785 (pt) outliers start: 145 outliers final: 89 residues processed: 417 average time/residue: 0.2143 time to fit residues: 152.4243 Evaluate side-chains 366 residues out of total 4443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 265 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 472 GLN Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 472 GLN Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 510 TYR Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 287 GLN Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 540 HIS Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 591 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 920 GLN Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 288 optimal weight: 3.9990 chunk 484 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 336 optimal weight: 20.0000 chunk 460 optimal weight: 30.0000 chunk 423 optimal weight: 0.5980 chunk 402 optimal weight: 0.8980 chunk 212 optimal weight: 7.9990 chunk 370 optimal weight: 5.9990 chunk 205 optimal weight: 20.0000 chunk 254 optimal weight: 2.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS A 137 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN A 920 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 HIS ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5214 r_free = 0.5214 target = 0.244536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.5047 r_free = 0.5047 target = 0.226628 restraints weight = 76379.248| |-----------------------------------------------------------------------------| r_work (start): 0.5046 rms_B_bonded: 2.13 r_work: 0.4894 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.4872 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.4872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 42639 Z= 0.227 Angle : 0.738 15.540 58182 Z= 0.352 Chirality : 0.048 0.458 6645 Planarity : 0.004 0.052 7362 Dihedral : 9.945 103.379 7425 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.38 % Allowed : 15.59 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.12), residues: 5052 helix: 1.47 (0.12), residues: 1788 sheet: -0.93 (0.19), residues: 669 loop : -1.84 (0.11), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 577 TYR 0.026 0.002 TYR B 265 PHE 0.031 0.002 PHE A 86 TRP 0.019 0.001 TRP A 353 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00542 (42492) covalent geometry : angle 0.71989 (57795) SS BOND : bond 0.00582 ( 54) SS BOND : angle 1.04499 ( 108) hydrogen bonds : bond 0.03548 ( 1814) hydrogen bonds : angle 5.10958 ( 5196) link_BETA1-4 : bond 0.00409 ( 27) link_BETA1-4 : angle 2.27112 ( 81) link_NAG-ASN : bond 0.00392 ( 66) link_NAG-ASN : angle 2.46119 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 4443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 273 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 592 PHE cc_start: 0.0835 (OUTLIER) cc_final: 0.0165 (t80) REVERT: A 90 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8315 (m) REVERT: A 131 CYS cc_start: 0.5497 (OUTLIER) cc_final: 0.5032 (m) REVERT: A 314 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7298 (tt0) REVERT: E 270 MET cc_start: 0.6442 (tmm) cc_final: 0.6018 (ptm) REVERT: E 347 THR cc_start: 0.3645 (OUTLIER) cc_final: 0.3310 (m) REVERT: B 90 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8226 (m) REVERT: B 131 CYS cc_start: 0.5246 (OUTLIER) cc_final: 0.4841 (m) REVERT: B 244 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7719 (mt) REVERT: B 281 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7805 (pt0) REVERT: B 314 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7275 (tt0) REVERT: C 58 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8007 (m-10) REVERT: C 90 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8118 (m) REVERT: C 131 CYS cc_start: 0.5322 (OUTLIER) cc_final: 0.4686 (m) REVERT: C 141 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7943 (mt) REVERT: C 314 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7259 (tt0) REVERT: C 452 LEU cc_start: 0.5939 (mp) cc_final: 0.5649 (mp) outliers start: 149 outliers final: 109 residues processed: 403 average time/residue: 0.1999 time to fit residues: 137.6588 Evaluate side-chains 392 residues out of total 4443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 268 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 472 GLN Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 510 TYR Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 287 GLN Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 540 HIS Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 591 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 920 GLN Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 280 optimal weight: 0.3980 chunk 22 optimal weight: 5.9990 chunk 495 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 361 optimal weight: 20.0000 chunk 469 optimal weight: 7.9990 chunk 152 optimal weight: 0.0010 chunk 325 optimal weight: 1.9990 chunk 313 optimal weight: 50.0000 chunk 306 optimal weight: 40.0000 overall best weight: 2.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 146 HIS ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 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 = 0.5218 r_free = 0.5218 target = 0.244917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.5053 r_free = 0.5053 target = 0.227293 restraints weight = 76534.705| |-----------------------------------------------------------------------------| r_work (start): 0.5050 rms_B_bonded: 2.09 r_work: 0.4903 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.4881 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.4881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5782 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 42639 Z= 0.198 Angle : 0.732 15.650 58182 Z= 0.349 Chirality : 0.047 0.369 6645 Planarity : 0.004 0.051 7362 Dihedral : 9.793 102.680 7425 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.29 % Allowed : 16.04 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.12), residues: 5052 helix: 1.34 (0.12), residues: 1803 sheet: -0.88 (0.19), residues: 669 loop : -1.81 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 577 TYR 0.024 0.002 TYR C 423 PHE 0.028 0.002 PHE B 86 TRP 0.018 0.001 TRP A 353 HIS 0.015 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00469 (42492) covalent geometry : angle 0.71440 (57795) SS BOND : bond 0.00501 ( 54) SS BOND : angle 0.94162 ( 108) hydrogen bonds : bond 0.03494 ( 1814) hydrogen bonds : angle 5.09071 ( 5196) link_BETA1-4 : bond 0.00396 ( 27) link_BETA1-4 : angle 2.22090 ( 81) link_NAG-ASN : bond 0.00339 ( 66) link_NAG-ASN : angle 2.46501 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 4443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 266 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 553 LYS cc_start: 0.5564 (tptt) cc_final: 0.4907 (tttt) REVERT: D 592 PHE cc_start: 0.0959 (OUTLIER) cc_final: 0.0282 (t80) REVERT: A 90 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8292 (m) REVERT: A 131 CYS cc_start: 0.5409 (OUTLIER) cc_final: 0.4954 (m) REVERT: A 138 ASP cc_start: 0.6680 (OUTLIER) cc_final: 0.6151 (t0) REVERT: A 177 MET cc_start: 0.5923 (ptp) cc_final: 0.5546 (ptp) REVERT: A 314 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7303 (tt0) REVERT: A 646 ARG cc_start: 0.6819 (OUTLIER) cc_final: 0.6585 (mmp80) REVERT: E 190 MET cc_start: 0.5554 (pmm) cc_final: 0.5225 (pmm) REVERT: E 270 MET cc_start: 0.6117 (tmm) cc_final: 0.5447 (ptm) REVERT: E 347 THR cc_start: 0.3905 (OUTLIER) cc_final: 0.3559 (m) REVERT: B 90 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8184 (m) REVERT: B 131 CYS cc_start: 0.5112 (OUTLIER) cc_final: 0.4721 (m) REVERT: B 143 VAL cc_start: 0.7343 (OUTLIER) cc_final: 0.6986 (t) REVERT: B 244 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7657 (mt) REVERT: B 281 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7841 (pt0) REVERT: B 314 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7290 (tt0) REVERT: B 646 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6541 (mmp80) REVERT: C 58 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8006 (m-10) REVERT: C 90 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8210 (m) REVERT: C 131 CYS cc_start: 0.5249 (OUTLIER) cc_final: 0.4603 (m) REVERT: C 141 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8004 (mt) REVERT: C 314 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7218 (tt0) REVERT: C 452 LEU cc_start: 0.5934 (OUTLIER) cc_final: 0.5646 (mp) outliers start: 145 outliers final: 108 residues processed: 391 average time/residue: 0.2320 time to fit residues: 154.5634 Evaluate side-chains 386 residues out of total 4443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 258 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 383 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 471 ASP Chi-restraints excluded: chain E residue 472 GLN Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 510 TYR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 287 GLN Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 540 HIS Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 920 GLN Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 363 optimal weight: 20.0000 chunk 185 optimal weight: 9.9990 chunk 253 optimal weight: 0.9990 chunk 385 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 231 optimal weight: 0.0070 chunk 247 optimal weight: 0.9980 chunk 59 optimal weight: 0.0770 chunk 112 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 287 optimal weight: 4.9990 overall best weight: 1.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5229 r_free = 0.5229 target = 0.245993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.228098 restraints weight = 77046.362| |-----------------------------------------------------------------------------| r_work (start): 0.5059 rms_B_bonded: 2.12 r_work: 0.4914 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.4892 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.4892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5755 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 42639 Z= 0.147 Angle : 0.719 20.792 58182 Z= 0.341 Chirality : 0.046 0.288 6645 Planarity : 0.004 0.050 7362 Dihedral : 9.462 100.528 7425 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.88 % Allowed : 16.63 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.12), residues: 5052 helix: 1.34 (0.12), residues: 1794 sheet: -0.71 (0.19), residues: 669 loop : -1.69 (0.12), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.029 0.001 TYR B 423 PHE 0.023 0.002 PHE A 238 TRP 0.018 0.001 TRP A 353 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00341 (42492) covalent geometry : angle 0.70396 (57795) SS BOND : bond 0.00461 ( 54) SS BOND : angle 0.88784 ( 108) hydrogen bonds : bond 0.03433 ( 1814) hydrogen bonds : angle 5.02421 ( 5196) link_BETA1-4 : bond 0.00390 ( 27) link_BETA1-4 : angle 2.17751 ( 81) link_NAG-ASN : bond 0.00280 ( 66) link_NAG-ASN : angle 2.20161 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 4443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 269 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 592 PHE cc_start: 0.0935 (OUTLIER) cc_final: 0.0302 (t80) REVERT: A 90 VAL cc_start: 0.8570 (OUTLIER) cc_final: 0.8330 (m) REVERT: A 131 CYS cc_start: 0.5518 (OUTLIER) cc_final: 0.5094 (m) REVERT: A 143 VAL cc_start: 0.7187 (OUTLIER) cc_final: 0.6869 (t) REVERT: A 177 MET cc_start: 0.5736 (ptp) cc_final: 0.5365 (ptp) REVERT: A 314 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7222 (tt0) REVERT: E 190 MET cc_start: 0.5659 (pmm) cc_final: 0.5448 (pmm) REVERT: E 270 MET cc_start: 0.5910 (tmm) cc_final: 0.5594 (ptm) REVERT: E 347 THR cc_start: 0.3849 (OUTLIER) cc_final: 0.3548 (m) REVERT: B 90 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8189 (m) REVERT: B 131 CYS cc_start: 0.5059 (OUTLIER) cc_final: 0.4715 (m) REVERT: B 149 ASN cc_start: 0.5961 (OUTLIER) cc_final: 0.5590 (p0) REVERT: B 244 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7618 (mt) REVERT: B 281 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7792 (pt0) REVERT: B 314 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7277 (tt0) REVERT: F 553 LYS cc_start: 0.5426 (tptt) cc_final: 0.4846 (tttt) REVERT: C 58 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7940 (m-10) REVERT: C 90 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8156 (m) REVERT: C 131 CYS cc_start: 0.5179 (OUTLIER) cc_final: 0.4521 (m) REVERT: C 141 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7898 (mt) REVERT: C 177 MET cc_start: 0.6128 (ptp) cc_final: 0.5875 (ptp) REVERT: C 314 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7130 (tt0) outliers start: 127 outliers final: 96 residues processed: 383 average time/residue: 0.2417 time to fit residues: 157.3004 Evaluate side-chains 371 residues out of total 4443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 258 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 540 HIS Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 471 ASP Chi-restraints excluded: chain E residue 472 GLN Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 287 GLN Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 540 HIS Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 920 GLN Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 170 optimal weight: 5.9990 chunk 217 optimal weight: 0.0070 chunk 76 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 464 optimal weight: 3.9990 chunk 447 optimal weight: 2.9990 chunk 137 optimal weight: 30.0000 chunk 259 optimal weight: 0.8980 chunk 144 optimal weight: 7.9990 chunk 314 optimal weight: 4.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 ASN D 330 ASN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN A 920 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 ASN ** F 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5234 r_free = 0.5234 target = 0.246463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5067 r_free = 0.5067 target = 0.228445 restraints weight = 76565.124| |-----------------------------------------------------------------------------| r_work (start): 0.5062 rms_B_bonded: 2.12 r_work: 0.4923 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.4897 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.4897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5737 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 42639 Z= 0.139 Angle : 0.713 17.122 58182 Z= 0.338 Chirality : 0.046 0.294 6645 Planarity : 0.004 0.050 7362 Dihedral : 9.281 99.421 7424 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.65 % Allowed : 16.81 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.12), residues: 5052 helix: 1.29 (0.12), residues: 1797 sheet: -0.67 (0.20), residues: 675 loop : -1.60 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.029 0.001 TYR C 423 PHE 0.023 0.002 PHE A 238 TRP 0.022 0.001 TRP F 271 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00324 (42492) covalent geometry : angle 0.69960 (57795) SS BOND : bond 0.00411 ( 54) SS BOND : angle 0.85357 ( 108) hydrogen bonds : bond 0.03426 ( 1814) hydrogen bonds : angle 4.98737 ( 5196) link_BETA1-4 : bond 0.00394 ( 27) link_BETA1-4 : angle 2.16623 ( 81) link_NAG-ASN : bond 0.00271 ( 66) link_NAG-ASN : angle 2.09909 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 4443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 267 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 553 LYS cc_start: 0.5658 (tptt) cc_final: 0.4921 (tttt) REVERT: D 592 PHE cc_start: 0.0982 (OUTLIER) cc_final: 0.0355 (t80) REVERT: A 90 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8322 (m) REVERT: A 131 CYS cc_start: 0.5448 (OUTLIER) cc_final: 0.5005 (m) REVERT: A 143 VAL cc_start: 0.7152 (OUTLIER) cc_final: 0.6834 (t) REVERT: A 314 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: A 869 MET cc_start: 0.0594 (ttm) cc_final: -0.0452 (mtp) REVERT: E 270 MET cc_start: 0.5864 (tmm) cc_final: 0.5573 (ptm) REVERT: B 90 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8268 (m) REVERT: B 131 CYS cc_start: 0.5052 (OUTLIER) cc_final: 0.4710 (m) REVERT: B 244 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7613 (mt) REVERT: B 281 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7816 (pt0) REVERT: B 314 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7255 (tt0) REVERT: F 553 LYS cc_start: 0.5357 (tptt) cc_final: 0.4760 (tttt) REVERT: C 58 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.7934 (m-10) REVERT: C 131 CYS cc_start: 0.5154 (OUTLIER) cc_final: 0.4494 (m) REVERT: C 141 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7839 (mt) REVERT: C 143 VAL cc_start: 0.7091 (OUTLIER) cc_final: 0.6828 (t) REVERT: C 177 MET cc_start: 0.6105 (ptp) cc_final: 0.5774 (ptp) REVERT: C 314 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7049 (tt0) REVERT: C 947 LYS cc_start: 0.6084 (pttp) cc_final: 0.5741 (pttt) outliers start: 117 outliers final: 92 residues processed: 371 average time/residue: 0.2156 time to fit residues: 136.4516 Evaluate side-chains 364 residues out of total 4443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 257 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 920 GLN Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 471 ASP Chi-restraints excluded: chain E residue 472 GLN Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 287 GLN Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 540 HIS Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 920 GLN Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 72 optimal weight: 2.9990 chunk 473 optimal weight: 4.9990 chunk 360 optimal weight: 0.0040 chunk 277 optimal weight: 9.9990 chunk 293 optimal weight: 0.5980 chunk 406 optimal weight: 0.9990 chunk 420 optimal weight: 0.7980 chunk 125 optimal weight: 30.0000 chunk 451 optimal weight: 0.8980 chunk 306 optimal weight: 50.0000 chunk 393 optimal weight: 0.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 ASN A 920 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5245 r_free = 0.5245 target = 0.247435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5080 r_free = 0.5080 target = 0.229606 restraints weight = 77399.299| |-----------------------------------------------------------------------------| r_work (start): 0.5059 rms_B_bonded: 2.16 r_work: 0.4918 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4896 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.4896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5704 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 42639 Z= 0.121 Angle : 0.708 15.017 58182 Z= 0.334 Chirality : 0.046 0.287 6645 Planarity : 0.004 0.050 7362 Dihedral : 9.117 97.940 7424 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.22 % Allowed : 17.15 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.12), residues: 5052 helix: 1.28 (0.12), residues: 1797 sheet: -0.60 (0.19), residues: 681 loop : -1.55 (0.12), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.031 0.001 TYR B 423 PHE 0.021 0.001 PHE C 238 TRP 0.024 0.001 TRP E 566 HIS 0.007 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00275 (42492) covalent geometry : angle 0.69506 (57795) SS BOND : bond 0.00372 ( 54) SS BOND : angle 0.83727 ( 108) hydrogen bonds : bond 0.03389 ( 1814) hydrogen bonds : angle 4.92012 ( 5196) link_BETA1-4 : bond 0.00408 ( 27) link_BETA1-4 : angle 2.15130 ( 81) link_NAG-ASN : bond 0.00272 ( 66) link_NAG-ASN : angle 1.96341 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10213.78 seconds wall clock time: 175 minutes 40.81 seconds (10540.81 seconds total)