Starting phenix.real_space_refine on Sat Feb 7 17:30:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kzz_62680/02_2026/9kzz_62680.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kzz_62680/02_2026/9kzz_62680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kzz_62680/02_2026/9kzz_62680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kzz_62680/02_2026/9kzz_62680.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kzz_62680/02_2026/9kzz_62680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kzz_62680/02_2026/9kzz_62680.map" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 142 5.16 5 C 21764 2.51 5 N 5630 2.21 5 O 6744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 225 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34280 Number of models: 1 Model: "" Number of chains: 38 Chain: "H" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1517 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 2 Chain: "L" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1608 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain breaks: 1 Chain: "C" Number of atoms: 7980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7980 Classifications: {'peptide': 1020} Link IDs: {'PTRANS': 57, 'TRANS': 962} Chain breaks: 7 Chain: "B" Number of atoms: 7950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 7950 Classifications: {'peptide': 1016} Link IDs: {'PTRANS': 58, 'TRANS': 957} Chain breaks: 7 Chain: "A" Number of atoms: 7955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 7955 Classifications: {'peptide': 1016} Link IDs: {'PTRANS': 58, 'TRANS': 957} Chain breaks: 8 Chain: "I" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1517 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 2 Chain: "M" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1608 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain breaks: 1 Chain: "J" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1517 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 2 Chain: "N" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1608 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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: "K" 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: 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: "Y" 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: "Z" 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: "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: 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: "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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 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: "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: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 7.86, per 1000 atoms: 0.23 Number of scatterers: 34280 At special positions: 0 Unit cell: (146.324, 148.188, 209.7, 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 142 16.00 O 6744 8.00 N 5630 7.00 C 21764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " 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 C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS I 146 " - pdb=" SG CYS I 202 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 135 " - pdb=" SG CYS M 195 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " distance=2.03 Simple disulfide: pdb=" SG CYS J 146 " - pdb=" SG CYS J 202 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 135 " - pdb=" SG CYS N 195 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 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 T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B1074 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C 657 " " NAG D 1 " - " ASN C 61 " " NAG E 1 " - " ASN C 122 " " NAG F 1 " - " ASN C 165 " " NAG G 1 " - " ASN C 331 " " NAG K 1 " - " ASN C 616 " " NAG O 1 " - " ASN C 709 " " NAG P 1 " - " ASN C 717 " " NAG Q 1 " - " ASN C 801 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C1134 " " NAG T 1 " - " ASN B 122 " " NAG U 1 " - " ASN B 165 " " NAG V 1 " - " ASN B 331 " " NAG W 1 " - " ASN B 709 " " NAG X 1 " - " ASN B 717 " " NAG Y 1 " - " ASN B 801 " " NAG Z 1 " - " ASN B1098 " " NAG a 1 " - " ASN B1134 " " NAG b 1 " - " ASN A 122 " " NAG c 1 " - " ASN A 165 " " NAG d 1 " - " ASN A 331 " " NAG e 1 " - " ASN A 709 " " NAG f 1 " - " ASN A 717 " " NAG g 1 " - " ASN A 801 " " NAG h 1 " - " ASN A1098 " " NAG i 1 " - " ASN A1134 " Time building additional restraints: 3.45 Conformation dependent library (CDL) restraints added in 1.4 seconds 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7974 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 70 sheets defined 19.3% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.597A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 162 through 164 No H-bonds generated for 'chain 'H' and resid 162 through 164' Processing helix chain 'L' and resid 122 through 127 removed outlier: 3.879A pdb=" N LEU L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 190 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.554A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.168A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.910A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.509A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 removed outlier: 4.045A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 483 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.631A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.696A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.699A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 815 removed outlier: 3.549A pdb=" N LYS C 814 " --> pdb=" O LYS C 811 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG C 815 " --> pdb=" O PRO C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 811 through 815' Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.836A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.506A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 4.116A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 968 removed outlier: 3.596A pdb=" N ALA C 956 " --> pdb=" O VAL C 952 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.554A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.575A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.978A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 4.182A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 408 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 479 through 483 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.576A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.652A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.624A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.578A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.510A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.038A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.529A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.754A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.526A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.757A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.822A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 757 Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.512A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.891A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.700A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.216A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.157A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 989 through 1033 removed outlier: 3.668A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.638A pdb=" N THR I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 86 through 90 Processing helix chain 'I' and resid 160 through 164 Processing helix chain 'M' and resid 122 through 128 removed outlier: 3.501A pdb=" N LEU M 126 " --> pdb=" O SER M 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.780A pdb=" N THR J 31 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'J' and resid 86 through 90 Processing helix chain 'J' and resid 162 through 164 No H-bonds generated for 'chain 'J' and resid 162 through 164' Processing helix chain 'N' and resid 122 through 127 removed outlier: 3.737A pdb=" N LEU N 126 " --> pdb=" O SER N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 190 removed outlier: 4.038A pdb=" N HIS N 190 " --> pdb=" O TYR N 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.882A pdb=" N ASP H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.021A pdb=" N LEU H 108 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 126 through 128 Processing sheet with id=AA5, first strand: chain 'H' and resid 159 through 160 removed outlier: 3.695A pdb=" N HIS H 206 " --> pdb=" O THR H 211 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR H 211 " --> pdb=" O HIS H 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 175 through 176 Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.702A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.052A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.686A pdb=" N ASN L 138 " --> pdb=" O SER L 115 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE L 119 " --> pdb=" O VAL L 134 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 146 through 151 Processing sheet with id=AB2, first strand: chain 'C' and resid 22 through 30 removed outlier: 3.682A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 9.572A pdb=" N ASN C 61 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY C 268 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR C 63 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TYR C 266 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N PHE C 65 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA C 264 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA C 262 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 43 through 44 removed outlier: 4.774A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.133A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.041A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AB7, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AB8, first strand: chain 'C' and resid 132 through 133 Processing sheet with id=AB9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.530A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 325 through 328 removed outlier: 4.955A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE C 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.546A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AC4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.046A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AC6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.952A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.442A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 787 through 789 removed outlier: 5.992A pdb=" N ILE C 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.990A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AD2, first strand: chain 'B' and resid 22 through 31 removed outlier: 7.720A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.959A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.161A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.966A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.084A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHE B 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.638A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.108A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AE2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.959A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.959A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B1094 " --> pdb=" O THR B1105 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.756A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.600A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.514A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.584A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.802A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AF2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.190A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.941A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.317A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.750A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AF7, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.902A pdb=" N ASP I 33 " --> pdb=" O GLY I 98 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.854A pdb=" N LEU I 108 " --> pdb=" O ARG I 97 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 126 through 127 removed outlier: 3.519A pdb=" N LYS I 149 " --> pdb=" O SER I 126 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LYS I 149 " --> pdb=" O LEU I 184 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU I 184 " --> pdb=" O LYS I 149 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 142 through 145 Processing sheet with id=AG3, first strand: chain 'I' and resid 158 through 159 Processing sheet with id=AG4, first strand: chain 'M' and resid 4 through 5 removed outlier: 3.712A pdb=" N ASP M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'M' and resid 10 through 13 removed outlier: 7.055A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU M 47 " --> pdb=" O TRP M 35 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 115 through 119 removed outlier: 3.740A pdb=" N ASN M 138 " --> pdb=" O SER M 115 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE M 119 " --> pdb=" O VAL M 134 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL M 134 " --> pdb=" O PHE M 119 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA M 131 " --> pdb=" O LEU M 182 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N TYR M 174 " --> pdb=" O ASN M 139 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 148 through 151 Processing sheet with id=AG8, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AG9, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.850A pdb=" N ASP J 33 " --> pdb=" O GLY J 98 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.912A pdb=" N LEU J 108 " --> pdb=" O ARG J 97 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 142 through 147 removed outlier: 3.717A pdb=" N SER J 186 " --> pdb=" O CYS J 146 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N SER J 183 " --> pdb=" O ALA J 174 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA J 174 " --> pdb=" O SER J 183 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER J 185 " --> pdb=" O PHE J 172 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AH4, first strand: chain 'N' and resid 4 through 6 removed outlier: 3.709A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'N' and resid 10 through 13 removed outlier: 7.086A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'N' and resid 115 through 117 removed outlier: 5.427A pdb=" N VAL N 134 " --> pdb=" O LEU N 180 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU N 180 " --> pdb=" O VAL N 134 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU N 136 " --> pdb=" O SER N 178 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N SER N 178 " --> pdb=" O LEU N 136 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASN N 138 " --> pdb=" O LEU N 176 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU N 176 " --> pdb=" O ASN N 138 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'N' and resid 146 through 151 removed outlier: 3.661A pdb=" N TYR N 193 " --> pdb=" O PHE N 210 " (cutoff:3.500A) 1237 hydrogen bonds defined for protein. 3249 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: 9.78 Time building geometry restraints manager: 4.33 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: 10826 1.34 - 1.46: 8786 1.46 - 1.58: 15268 1.58 - 1.70: 0 1.70 - 1.82: 176 Bond restraints: 35056 Sorted by residual: bond pdb=" C1 NAG W 2 " pdb=" O5 NAG W 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.46e+00 bond pdb=" C PRO B 986 " pdb=" N PRO B 987 " ideal model delta sigma weight residual 1.336 1.362 -0.026 1.25e-02 6.40e+03 4.44e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.31e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.15e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.86e+00 ... (remaining 35051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 46710 1.98 - 3.95: 870 3.95 - 5.93: 84 5.93 - 7.90: 20 7.90 - 9.88: 3 Bond angle restraints: 47687 Sorted by residual: angle pdb=" N ILE M 29 " pdb=" CA ILE M 29 " pdb=" C ILE M 29 " ideal model delta sigma weight residual 113.10 109.32 3.78 9.70e-01 1.06e+00 1.52e+01 angle pdb=" N THR A 581 " pdb=" CA THR A 581 " pdb=" C THR A 581 " ideal model delta sigma weight residual 114.75 109.90 4.85 1.26e+00 6.30e-01 1.48e+01 angle pdb=" CA LEU B 18 " pdb=" C LEU B 18 " pdb=" N ILE B 19 " ideal model delta sigma weight residual 117.71 122.55 -4.84 1.28e+00 6.10e-01 1.43e+01 angle pdb=" C ASP A 228 " pdb=" N LEU A 229 " pdb=" CA LEU A 229 " ideal model delta sigma weight residual 120.94 127.70 -6.76 1.90e+00 2.77e-01 1.27e+01 angle pdb=" N ILE N 29 " pdb=" CA ILE N 29 " pdb=" C ILE N 29 " ideal model delta sigma weight residual 112.43 109.16 3.27 9.20e-01 1.18e+00 1.27e+01 ... (remaining 47682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 21095 21.85 - 43.70: 568 43.70 - 65.55: 88 65.55 - 87.41: 68 87.41 - 109.26: 40 Dihedral angle restraints: 21859 sinusoidal: 9445 harmonic: 12414 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -127.72 41.72 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CA LEU C 560 " pdb=" C LEU C 560 " pdb=" N PRO C 561 " pdb=" CA PRO C 561 " ideal model delta harmonic sigma weight residual -180.00 -155.59 -24.41 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ARG C 498 " pdb=" C ARG C 498 " pdb=" N PRO C 499 " pdb=" CA PRO C 499 " ideal model delta harmonic sigma weight residual 180.00 157.14 22.86 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 21856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 5581 0.130 - 0.260: 19 0.260 - 0.390: 14 0.390 - 0.520: 1 0.520 - 0.650: 1 Chirality restraints: 5616 Sorted by residual: chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.20e+00 chirality pdb=" C1 NAG h 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG h 1 " pdb=" O5 NAG h 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 5613 not shown) Planarity restraints: 6080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 498 " -0.047 5.00e-02 4.00e+02 7.15e-02 8.19e+00 pdb=" N PRO C 499 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 499 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 499 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 738 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.84e+00 pdb=" C CYS C 738 " -0.038 2.00e-02 2.50e+03 pdb=" O CYS C 738 " 0.014 2.00e-02 2.50e+03 pdb=" N THR C 739 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 336 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO B 337 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " 0.025 5.00e-02 4.00e+02 ... (remaining 6077 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2490 2.74 - 3.28: 33828 3.28 - 3.82: 55708 3.82 - 4.36: 65708 4.36 - 4.90: 114974 Nonbonded interactions: 272708 Sorted by model distance: nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.196 3.040 nonbonded pdb=" OG1 THR C 581 " pdb=" OE1 GLU C 583 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.223 3.040 nonbonded pdb=" O ASP M 186 " pdb=" OH TYR M 193 " model vdw 2.224 3.040 nonbonded pdb=" OG SER C 884 " pdb=" OG1 THR C 887 " model vdw 2.241 3.040 ... (remaining 272703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 66 or resid 82 through 144 or resid 154 through \ 620 or resid 641 through 826 or resid 855 through 1303)) selection = (chain 'B' and (resid 15 through 210 or resid 216 through 620 or resid 641 throu \ gh 1303)) selection = (chain 'C' and (resid 15 through 66 or resid 82 through 210 or resid 216 through \ 245 or resid 262 through 826 or resid 855 through 1303)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'i' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'K' selection = chain 'T' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'f' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 20.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 34.930 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.120 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 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 0.042 35185 Z= 0.168 Angle : 0.653 9.894 48020 Z= 0.360 Chirality : 0.046 0.650 5616 Planarity : 0.004 0.072 6041 Dihedral : 12.009 109.258 13723 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.17 % Allowed : 5.58 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.12), residues: 4205 helix: -1.44 (0.17), residues: 619 sheet: -1.23 (0.14), residues: 1164 loop : -2.15 (0.12), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 815 TYR 0.010 0.001 TYR A 380 PHE 0.008 0.001 PHE L 140 TRP 0.007 0.001 TRP A 886 HIS 0.002 0.000 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00308 (35056) covalent geometry : angle 0.63473 (47687) SS BOND : bond 0.00146 ( 54) SS BOND : angle 0.58350 ( 108) hydrogen bonds : bond 0.24315 ( 1215) hydrogen bonds : angle 9.66253 ( 3249) link_BETA1-4 : bond 0.00803 ( 36) link_BETA1-4 : angle 2.48664 ( 108) link_NAG-ASN : bond 0.00249 ( 39) link_NAG-ASN : angle 2.20043 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1255 residues out of total 3725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 1137 time to evaluate : 1.238 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: H 7 SER cc_start: 0.6375 (t) cc_final: 0.6094 (p) REVERT: H 34 MET cc_start: 0.6817 (mmm) cc_final: 0.6599 (mmm) REVERT: H 40 VAL cc_start: 0.8645 (t) cc_final: 0.8374 (t) REVERT: H 45 LEU cc_start: 0.7494 (mt) cc_final: 0.7278 (mt) REVERT: H 70 SER cc_start: 0.8220 (t) cc_final: 0.7770 (p) REVERT: H 78 LEU cc_start: 0.7691 (tp) cc_final: 0.7437 (tp) REVERT: H 85 LEU cc_start: 0.8895 (mt) cc_final: 0.8450 (mt) REVERT: H 92 VAL cc_start: 0.8699 (t) cc_final: 0.8298 (p) REVERT: H 108 LEU cc_start: 0.7581 (tp) cc_final: 0.7274 (tp) REVERT: H 113 THR cc_start: 0.6650 (t) cc_final: 0.6194 (m) REVERT: L 46 LEU cc_start: 0.7795 (pt) cc_final: 0.7432 (pt) REVERT: L 78 LEU cc_start: 0.8213 (mt) cc_final: 0.7824 (mt) REVERT: L 86 TYR cc_start: 0.7957 (m-80) cc_final: 0.7665 (m-80) REVERT: L 141 TYR cc_start: 0.7192 (t80) cc_final: 0.5990 (t80) REVERT: C 28 TYR cc_start: 0.6708 (m-80) cc_final: 0.5973 (m-80) REVERT: C 41 LYS cc_start: 0.7982 (ptpt) cc_final: 0.7727 (mtmm) REVERT: C 125 ASN cc_start: 0.7479 (m-40) cc_final: 0.7180 (m-40) REVERT: C 130 VAL cc_start: 0.6988 (m) cc_final: 0.6769 (p) REVERT: C 139 PRO cc_start: 0.7881 (Cg_endo) cc_final: 0.7504 (Cg_exo) REVERT: C 196 ASN cc_start: 0.6694 (t0) cc_final: 0.6471 (t0) REVERT: C 210 ILE cc_start: 0.7244 (OUTLIER) cc_final: 0.6931 (pt) REVERT: C 266 TYR cc_start: 0.7254 (m-80) cc_final: 0.7027 (m-80) REVERT: C 310 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8017 (ttpt) REVERT: C 339 HIS cc_start: 0.7144 (t-90) cc_final: 0.6942 (t-90) REVERT: C 355 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7672 (tpt-90) REVERT: C 386 LYS cc_start: 0.7959 (tppp) cc_final: 0.7756 (tppp) REVERT: C 396 TYR cc_start: 0.7543 (m-80) cc_final: 0.7311 (m-80) REVERT: C 434 ILE cc_start: 0.7981 (mt) cc_final: 0.7479 (mm) REVERT: C 436 TRP cc_start: 0.7829 (p90) cc_final: 0.7563 (p90) REVERT: C 511 VAL cc_start: 0.8239 (t) cc_final: 0.8033 (p) REVERT: C 559 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.8037 (t80) REVERT: C 572 THR cc_start: 0.8183 (m) cc_final: 0.7849 (p) REVERT: C 586 ASP cc_start: 0.7547 (m-30) cc_final: 0.7237 (m-30) REVERT: C 610 VAL cc_start: 0.8499 (m) cc_final: 0.8236 (t) REVERT: C 658 ASN cc_start: 0.7084 (OUTLIER) cc_final: 0.6662 (p0) REVERT: C 663 ASP cc_start: 0.7112 (t0) cc_final: 0.6745 (t70) REVERT: C 703 ASN cc_start: 0.8595 (t0) cc_final: 0.8239 (t0) REVERT: C 739 THR cc_start: 0.8192 (m) cc_final: 0.7928 (t) REVERT: C 776 LYS cc_start: 0.7878 (ttpp) cc_final: 0.7582 (ttpp) REVERT: C 868 GLU cc_start: 0.7249 (mp0) cc_final: 0.7044 (mp0) REVERT: C 882 ILE cc_start: 0.8414 (pt) cc_final: 0.8126 (mt) REVERT: C 937 SER cc_start: 0.8313 (m) cc_final: 0.8013 (t) REVERT: C 947 LYS cc_start: 0.8362 (mtpt) cc_final: 0.8095 (mtpp) REVERT: C 955 ASN cc_start: 0.7446 (m-40) cc_final: 0.7240 (m-40) REVERT: C 964 LYS cc_start: 0.7656 (tppp) cc_final: 0.7179 (tppp) REVERT: C 1086 LYS cc_start: 0.7961 (ptpt) cc_final: 0.7588 (mtmm) REVERT: C 1118 ASP cc_start: 0.6925 (t0) cc_final: 0.6656 (t0) REVERT: C 1123 SER cc_start: 0.7938 (t) cc_final: 0.7400 (p) REVERT: C 1128 VAL cc_start: 0.8365 (m) cc_final: 0.8055 (p) REVERT: C 1130 ILE cc_start: 0.8581 (pt) cc_final: 0.8356 (mt) REVERT: B 90 VAL cc_start: 0.8275 (m) cc_final: 0.8026 (p) REVERT: B 191 GLU cc_start: 0.7138 (pt0) cc_final: 0.6768 (pt0) REVERT: B 195 LYS cc_start: 0.8506 (ttpt) cc_final: 0.8072 (ttpp) REVERT: B 221 SER cc_start: 0.7944 (t) cc_final: 0.7699 (m) REVERT: B 266 TYR cc_start: 0.7370 (m-80) cc_final: 0.6950 (m-10) REVERT: B 278 LYS cc_start: 0.8027 (tppp) cc_final: 0.7662 (tttp) REVERT: B 312 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7792 (pp) REVERT: B 338 PHE cc_start: 0.8297 (m-10) cc_final: 0.8037 (m-80) REVERT: B 346 THR cc_start: 0.8217 (m) cc_final: 0.7682 (p) REVERT: B 354 ASN cc_start: 0.7997 (t0) cc_final: 0.7678 (p0) REVERT: B 386 LYS cc_start: 0.8299 (mmmm) cc_final: 0.6614 (mmmm) REVERT: B 390 LEU cc_start: 0.8530 (mm) cc_final: 0.8033 (mm) REVERT: B 559 PHE cc_start: 0.8106 (m-10) cc_final: 0.7708 (m-10) REVERT: B 644 GLN cc_start: 0.8342 (tp40) cc_final: 0.8142 (tp40) REVERT: B 712 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8131 (tt) REVERT: B 719 THR cc_start: 0.8338 (m) cc_final: 0.8044 (p) REVERT: B 750 SER cc_start: 0.7896 (t) cc_final: 0.7595 (m) REVERT: B 759 PHE cc_start: 0.7188 (t80) cc_final: 0.6823 (t80) REVERT: B 764 LYS cc_start: 0.7437 (tppp) cc_final: 0.7161 (tppp) REVERT: B 780 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6907 (mt-10) REVERT: B 868 GLU cc_start: 0.7357 (mp0) cc_final: 0.7061 (mp0) REVERT: B 916 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7655 (tt) REVERT: B 1017 GLU cc_start: 0.6509 (mm-30) cc_final: 0.5552 (mm-30) REVERT: B 1028 LYS cc_start: 0.8316 (mttm) cc_final: 0.8011 (mttm) REVERT: B 1094 VAL cc_start: 0.7998 (m) cc_final: 0.6893 (t) REVERT: B 1116 THR cc_start: 0.8349 (p) cc_final: 0.7657 (p) REVERT: A 28 TYR cc_start: 0.6620 (m-80) cc_final: 0.6383 (m-80) REVERT: A 65 PHE cc_start: 0.7846 (m-10) cc_final: 0.7308 (m-80) REVERT: A 138 ASP cc_start: 0.7146 (t0) cc_final: 0.6924 (t0) REVERT: A 139 PRO cc_start: 0.8143 (Cg_endo) cc_final: 0.7940 (Cg_exo) REVERT: A 170 TYR cc_start: 0.7117 (t80) cc_final: 0.6549 (t80) REVERT: A 195 LYS cc_start: 0.8268 (ttmt) cc_final: 0.7946 (ttpt) REVERT: A 221 SER cc_start: 0.7986 (t) cc_final: 0.7688 (m) REVERT: A 244 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6780 (tm) REVERT: A 280 ASN cc_start: 0.6771 (m-40) cc_final: 0.6550 (m-40) REVERT: A 300 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7861 (mttm) REVERT: A 340 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7191 (mm-30) REVERT: A 356 LYS cc_start: 0.7700 (tttp) cc_final: 0.7420 (mtpp) REVERT: A 390 LEU cc_start: 0.8686 (mt) cc_final: 0.8477 (mt) REVERT: A 396 TYR cc_start: 0.7529 (m-80) cc_final: 0.7047 (m-80) REVERT: A 424 LYS cc_start: 0.7542 (tttt) cc_final: 0.7317 (ttpt) REVERT: A 439 ASN cc_start: 0.7458 (t0) cc_final: 0.7160 (t0) REVERT: A 440 LYS cc_start: 0.8652 (mtmt) cc_final: 0.8332 (mtmt) REVERT: A 493 GLN cc_start: 0.6477 (mm-40) cc_final: 0.5881 (mm-40) REVERT: A 511 VAL cc_start: 0.8198 (t) cc_final: 0.7908 (p) REVERT: A 546 LEU cc_start: 0.8164 (tp) cc_final: 0.7963 (tt) REVERT: A 586 ASP cc_start: 0.7655 (t0) cc_final: 0.7343 (m-30) REVERT: A 693 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8690 (pt) REVERT: A 775 ASP cc_start: 0.7184 (m-30) cc_final: 0.6901 (m-30) REVERT: A 776 LYS cc_start: 0.7957 (ttpp) cc_final: 0.7667 (ttpp) REVERT: A 780 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6715 (mt-10) REVERT: A 933 LYS cc_start: 0.8245 (mtmt) cc_final: 0.8040 (mtmt) REVERT: A 966 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8036 (tt) REVERT: A 976 VAL cc_start: 0.8551 (t) cc_final: 0.8274 (p) REVERT: A 1001 LEU cc_start: 0.8677 (tp) cc_final: 0.8458 (tt) REVERT: A 1005 GLN cc_start: 0.7697 (tp40) cc_final: 0.7491 (tp-100) REVERT: A 1116 THR cc_start: 0.8603 (p) cc_final: 0.7877 (p) REVERT: I 47 TRP cc_start: 0.7473 (t60) cc_final: 0.7099 (t60) REVERT: I 70 SER cc_start: 0.8164 (t) cc_final: 0.7791 (p) REVERT: I 92 VAL cc_start: 0.8797 (t) cc_final: 0.8464 (p) REVERT: I 113 THR cc_start: 0.6637 (t) cc_final: 0.6331 (m) REVERT: I 144 LEU cc_start: 0.5938 (OUTLIER) cc_final: 0.5582 (mt) REVERT: I 200 TYR cc_start: 0.5888 (m-80) cc_final: 0.5626 (m-10) REVERT: M 10 SER cc_start: 0.6326 (t) cc_final: 0.6057 (m) REVERT: M 33 LEU cc_start: 0.8090 (tt) cc_final: 0.7719 (tt) REVERT: M 37 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7079 (tp40) REVERT: M 49 TYR cc_start: 0.7848 (p90) cc_final: 0.7246 (p90) REVERT: M 73 LEU cc_start: 0.8653 (tp) cc_final: 0.8371 (tp) REVERT: M 86 TYR cc_start: 0.7962 (m-80) cc_final: 0.7512 (m-80) REVERT: M 94 MET cc_start: 0.7014 (mmt) cc_final: 0.6601 (mmt) REVERT: M 125 GLN cc_start: 0.7855 (tt0) cc_final: 0.7623 (tm-30) REVERT: M 167 GLN cc_start: 0.7722 (tt0) cc_final: 0.7493 (tt0) REVERT: J 57 THR cc_start: 0.8282 (p) cc_final: 0.8056 (p) REVERT: J 70 SER cc_start: 0.7921 (t) cc_final: 0.7463 (p) REVERT: J 78 LEU cc_start: 0.7651 (tp) cc_final: 0.7391 (tp) REVERT: J 92 VAL cc_start: 0.8735 (t) cc_final: 0.8336 (p) REVERT: J 100 SER cc_start: 0.8003 (p) cc_final: 0.7737 (t) REVERT: N 33 LEU cc_start: 0.8066 (tt) cc_final: 0.7680 (tt) REVERT: N 46 LEU cc_start: 0.7714 (pt) cc_final: 0.7412 (pt) REVERT: N 73 LEU cc_start: 0.8417 (tp) cc_final: 0.8206 (tp) REVERT: N 78 LEU cc_start: 0.8320 (mt) cc_final: 0.8010 (mt) REVERT: N 174 TYR cc_start: 0.6758 (m-80) cc_final: 0.6359 (m-80) outliers start: 118 outliers final: 39 residues processed: 1207 average time/residue: 0.2207 time to fit residues: 428.3545 Evaluate side-chains 969 residues out of total 3725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 917 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 148 GLN Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 148 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.0020 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 81 GLN H 177 GLN L 148 GLN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 173 GLN C 196 ASN C 339 HIS C 414 GLN C 563 GLN C 907 ASN C 919 ASN C 925 ASN C1011 GLN C1135 ASN B 14 GLN B 30 ASN B 196 ASN B 239 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 394 ASN B 405 ASN B 658 ASN B 755 GLN B 955 ASN B 957 GLN B 965 GLN B1005 GLN A 81 ASN A 188 ASN A 245 HIS A 317 ASN A 339 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 895 GLN A 914 ASN A 919 ASN A 935 GLN A 955 ASN A 957 GLN A1011 GLN I 177 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN J 81 GLN ** N 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.165431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.129220 restraints weight = 59302.636| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.86 r_work: 0.3520 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 35185 Z= 0.247 Angle : 0.727 14.922 48020 Z= 0.364 Chirality : 0.049 0.474 5616 Planarity : 0.005 0.067 6041 Dihedral : 10.789 73.773 6262 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 4.21 % Allowed : 12.08 % Favored : 83.70 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.12), residues: 4205 helix: 0.29 (0.20), residues: 631 sheet: -0.70 (0.15), residues: 1151 loop : -1.84 (0.12), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 86 TYR 0.027 0.002 TYR J 105 PHE 0.028 0.002 PHE A 133 TRP 0.016 0.002 TRP N 149 HIS 0.008 0.002 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00566 (35056) covalent geometry : angle 0.69043 (47687) SS BOND : bond 0.00645 ( 54) SS BOND : angle 2.21602 ( 108) hydrogen bonds : bond 0.05320 ( 1215) hydrogen bonds : angle 6.97673 ( 3249) link_BETA1-4 : bond 0.00807 ( 36) link_BETA1-4 : angle 2.69515 ( 108) link_NAG-ASN : bond 0.00446 ( 39) link_NAG-ASN : angle 3.41559 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1124 residues out of total 3725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 967 time to evaluate : 1.396 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: H 7 SER cc_start: 0.6820 (t) cc_final: 0.6615 (m) REVERT: H 34 MET cc_start: 0.7402 (mmm) cc_final: 0.7018 (mmm) REVERT: H 45 LEU cc_start: 0.7706 (mt) cc_final: 0.7149 (mt) REVERT: H 70 SER cc_start: 0.8221 (t) cc_final: 0.7708 (p) REVERT: H 78 LEU cc_start: 0.8132 (tp) cc_final: 0.7905 (tp) REVERT: H 92 VAL cc_start: 0.8805 (t) cc_final: 0.8499 (p) REVERT: H 108 LEU cc_start: 0.7855 (tp) cc_final: 0.7534 (tp) REVERT: H 113 THR cc_start: 0.6579 (t) cc_final: 0.6195 (m) REVERT: L 4 MET cc_start: 0.7162 (mmm) cc_final: 0.6550 (mmm) REVERT: L 10 SER cc_start: 0.6614 (t) cc_final: 0.6285 (m) REVERT: L 33 LEU cc_start: 0.8194 (tt) cc_final: 0.7858 (tt) REVERT: L 37 GLN cc_start: 0.6796 (tp40) cc_final: 0.6493 (tp40) REVERT: L 71 PHE cc_start: 0.6606 (m-80) cc_final: 0.6006 (m-10) REVERT: L 78 LEU cc_start: 0.8212 (mt) cc_final: 0.7819 (mt) REVERT: L 85 THR cc_start: 0.7472 (m) cc_final: 0.6980 (p) REVERT: L 86 TYR cc_start: 0.8325 (m-80) cc_final: 0.7393 (m-80) REVERT: L 124 GLU cc_start: 0.6983 (tt0) cc_final: 0.6667 (tt0) REVERT: L 141 TYR cc_start: 0.7499 (t80) cc_final: 0.7197 (t80) REVERT: C 41 LYS cc_start: 0.8429 (ptpt) cc_final: 0.8072 (mtmm) REVERT: C 105 ILE cc_start: 0.7948 (mm) cc_final: 0.7735 (mm) REVERT: C 196 ASN cc_start: 0.7386 (t0) cc_final: 0.7065 (t0) REVERT: C 210 ILE cc_start: 0.7357 (OUTLIER) cc_final: 0.7016 (pt) REVERT: C 246 ARG cc_start: 0.6541 (OUTLIER) cc_final: 0.6023 (ppt90) REVERT: C 310 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8333 (ttpt) REVERT: C 424 LYS cc_start: 0.7932 (tttt) cc_final: 0.7713 (tttt) REVERT: C 436 TRP cc_start: 0.8122 (p90) cc_final: 0.7893 (p90) REVERT: C 511 VAL cc_start: 0.8388 (t) cc_final: 0.8154 (p) REVERT: C 559 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.8172 (t80) REVERT: C 586 ASP cc_start: 0.7872 (m-30) cc_final: 0.7574 (m-30) REVERT: C 603 ASN cc_start: 0.8214 (t0) cc_final: 0.7947 (t0) REVERT: C 663 ASP cc_start: 0.7431 (t0) cc_final: 0.7127 (t70) REVERT: C 703 ASN cc_start: 0.8732 (t0) cc_final: 0.8402 (t0) REVERT: C 776 LYS cc_start: 0.8254 (ttpp) cc_final: 0.7982 (ttpp) REVERT: C 882 ILE cc_start: 0.8646 (pt) cc_final: 0.8441 (mt) REVERT: C 937 SER cc_start: 0.8015 (m) cc_final: 0.7792 (t) REVERT: C 955 ASN cc_start: 0.7699 (m-40) cc_final: 0.7377 (m-40) REVERT: C 964 LYS cc_start: 0.8043 (tppp) cc_final: 0.7505 (tppp) REVERT: C 1086 LYS cc_start: 0.8224 (ptpt) cc_final: 0.7951 (ptpp) REVERT: C 1118 ASP cc_start: 0.7752 (t0) cc_final: 0.7424 (t0) REVERT: C 1123 SER cc_start: 0.8330 (t) cc_final: 0.7970 (t) REVERT: C 1128 VAL cc_start: 0.8473 (m) cc_final: 0.8090 (p) REVERT: C 1130 ILE cc_start: 0.8729 (pt) cc_final: 0.8487 (mt) REVERT: C 1139 ASP cc_start: 0.7858 (t0) cc_final: 0.7657 (t0) REVERT: B 221 SER cc_start: 0.8149 (t) cc_final: 0.7944 (m) REVERT: B 266 TYR cc_start: 0.8061 (m-80) cc_final: 0.7742 (m-80) REVERT: B 281 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7190 (pp20) REVERT: B 312 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8188 (tt) REVERT: B 346 THR cc_start: 0.8232 (m) cc_final: 0.7766 (p) REVERT: B 386 LYS cc_start: 0.8289 (mmmm) cc_final: 0.7570 (mtpp) REVERT: B 390 LEU cc_start: 0.8694 (mm) cc_final: 0.8336 (mm) REVERT: B 514 SER cc_start: 0.8534 (t) cc_final: 0.8269 (p) REVERT: B 558 LYS cc_start: 0.7965 (tptm) cc_final: 0.7630 (tptm) REVERT: B 644 GLN cc_start: 0.8464 (tp40) cc_final: 0.8201 (tp40) REVERT: B 658 ASN cc_start: 0.7169 (OUTLIER) cc_final: 0.6949 (p0) REVERT: B 712 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8464 (tt) REVERT: B 759 PHE cc_start: 0.7618 (t80) cc_final: 0.7104 (t80) REVERT: B 776 LYS cc_start: 0.8360 (ttpt) cc_final: 0.7942 (tttp) REVERT: B 780 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7723 (mt-10) REVERT: B 868 GLU cc_start: 0.7819 (mp0) cc_final: 0.7506 (mp0) REVERT: B 933 LYS cc_start: 0.8391 (mtmt) cc_final: 0.8174 (mtmm) REVERT: B 961 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8302 (p) REVERT: B 1017 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6863 (mm-30) REVERT: B 1073 LYS cc_start: 0.8402 (mtmt) cc_final: 0.8137 (mtpp) REVERT: B 1116 THR cc_start: 0.8734 (p) cc_final: 0.8100 (p) REVERT: A 28 TYR cc_start: 0.7022 (m-80) cc_final: 0.6668 (m-80) REVERT: A 138 ASP cc_start: 0.7511 (t0) cc_final: 0.7272 (t0) REVERT: A 190 ARG cc_start: 0.7288 (mtp85) cc_final: 0.6854 (mtp85) REVERT: A 221 SER cc_start: 0.8359 (t) cc_final: 0.8098 (m) REVERT: A 244 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7008 (tm) REVERT: A 280 ASN cc_start: 0.7258 (m-40) cc_final: 0.6928 (m-40) REVERT: A 284 THR cc_start: 0.7974 (p) cc_final: 0.7716 (t) REVERT: A 340 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7699 (mm-30) REVERT: A 356 LYS cc_start: 0.8238 (tttp) cc_final: 0.7969 (ttpp) REVERT: A 386 LYS cc_start: 0.8592 (mttt) cc_final: 0.8213 (mtmm) REVERT: A 387 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7952 (tm) REVERT: A 394 ASN cc_start: 0.8207 (m110) cc_final: 0.7993 (m-40) REVERT: A 396 TYR cc_start: 0.7982 (m-80) cc_final: 0.7711 (m-80) REVERT: A 439 ASN cc_start: 0.7911 (t0) cc_final: 0.7594 (t0) REVERT: A 440 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8442 (mtmt) REVERT: A 511 VAL cc_start: 0.8220 (t) cc_final: 0.7906 (p) REVERT: A 514 SER cc_start: 0.8827 (OUTLIER) cc_final: 0.8402 (p) REVERT: A 546 LEU cc_start: 0.8328 (tp) cc_final: 0.8122 (tt) REVERT: A 586 ASP cc_start: 0.8040 (t0) cc_final: 0.7651 (m-30) REVERT: A 603 ASN cc_start: 0.8081 (t0) cc_final: 0.7730 (t0) REVERT: A 776 LYS cc_start: 0.8411 (ttpp) cc_final: 0.8110 (ttmm) REVERT: A 780 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7310 (mt-10) REVERT: A 921 LYS cc_start: 0.8462 (mmmt) cc_final: 0.8128 (mmmt) REVERT: A 933 LYS cc_start: 0.8373 (mtmt) cc_final: 0.8169 (mtmt) REVERT: A 945 LEU cc_start: 0.8155 (mt) cc_final: 0.7939 (mp) REVERT: A 964 LYS cc_start: 0.8442 (tppt) cc_final: 0.7972 (mptt) REVERT: A 966 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8273 (tt) REVERT: A 1001 LEU cc_start: 0.8859 (tp) cc_final: 0.8657 (tt) REVERT: I 47 TRP cc_start: 0.7598 (t60) cc_final: 0.7316 (t60) REVERT: I 92 VAL cc_start: 0.8937 (t) cc_final: 0.8650 (p) REVERT: I 113 THR cc_start: 0.6340 (t) cc_final: 0.5896 (m) REVERT: M 24 ARG cc_start: 0.7689 (mtt180) cc_final: 0.7429 (mtt90) REVERT: M 27 GLN cc_start: 0.7888 (pm20) cc_final: 0.7633 (pm20) REVERT: M 33 LEU cc_start: 0.8261 (tt) cc_final: 0.7906 (tt) REVERT: M 37 GLN cc_start: 0.7236 (tm-30) cc_final: 0.6742 (tp-100) REVERT: M 71 PHE cc_start: 0.6586 (m-80) cc_final: 0.6205 (m-10) REVERT: M 78 LEU cc_start: 0.8200 (mt) cc_final: 0.7923 (mt) REVERT: M 94 MET cc_start: 0.7085 (mmt) cc_final: 0.6704 (mmm) REVERT: M 141 TYR cc_start: 0.6226 (t80) cc_final: 0.5810 (t80) REVERT: J 7 SER cc_start: 0.6768 (t) cc_final: 0.6395 (p) REVERT: J 34 MET cc_start: 0.6814 (mmm) cc_final: 0.6589 (mmm) REVERT: J 70 SER cc_start: 0.8025 (t) cc_final: 0.7665 (p) REVERT: J 78 LEU cc_start: 0.8029 (tp) cc_final: 0.7731 (tp) REVERT: J 92 VAL cc_start: 0.8897 (t) cc_final: 0.8533 (p) REVERT: J 100 SER cc_start: 0.8130 (p) cc_final: 0.7913 (p) REVERT: J 105 TYR cc_start: 0.8194 (p90) cc_final: 0.7896 (p90) REVERT: J 152 PHE cc_start: 0.5150 (t80) cc_final: 0.4711 (m-80) REVERT: N 14 SER cc_start: 0.8220 (m) cc_final: 0.7956 (p) REVERT: N 33 LEU cc_start: 0.8168 (tt) cc_final: 0.7956 (tt) REVERT: N 37 GLN cc_start: 0.6785 (tp40) cc_final: 0.6557 (tp40) REVERT: N 46 LEU cc_start: 0.7915 (pt) cc_final: 0.7548 (pt) outliers start: 157 outliers final: 94 residues processed: 1057 average time/residue: 0.2088 time to fit residues: 355.3269 Evaluate side-chains 985 residues out of total 3725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 878 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 148 GLN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 104 ARG Chi-restraints excluded: chain M residue 195 CYS Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain N residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 409 optimal weight: 3.9990 chunk 211 optimal weight: 0.4980 chunk 132 optimal weight: 0.5980 chunk 309 optimal weight: 0.6980 chunk 413 optimal weight: 0.7980 chunk 187 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 87 optimal weight: 0.3980 chunk 372 optimal weight: 0.6980 chunk 249 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 HIS ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 675 GLN B 196 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 339 HIS ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN A 343 ASN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 949 GLN A 955 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.164245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.128311 restraints weight = 59062.949| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.81 r_work: 0.3507 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 35185 Z= 0.219 Angle : 0.716 12.315 48020 Z= 0.355 Chirality : 0.050 0.493 5616 Planarity : 0.005 0.068 6041 Dihedral : 9.063 67.870 6243 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 5.21 % Allowed : 13.42 % Favored : 81.37 % 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 are not related in a simple way. whole: -1.50 (0.12), residues: 4205 helix: 0.66 (0.20), residues: 637 sheet: -0.56 (0.15), residues: 1186 loop : -1.75 (0.12), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.029 0.002 TYR I 105 PHE 0.030 0.002 PHE C 643 TRP 0.022 0.002 TRP L 149 HIS 0.018 0.002 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00502 (35056) covalent geometry : angle 0.68526 (47687) SS BOND : bond 0.00708 ( 54) SS BOND : angle 2.45478 ( 108) hydrogen bonds : bond 0.04687 ( 1215) hydrogen bonds : angle 6.53353 ( 3249) link_BETA1-4 : bond 0.00783 ( 36) link_BETA1-4 : angle 2.53984 ( 108) link_NAG-ASN : bond 0.00485 ( 39) link_NAG-ASN : angle 2.74404 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 3725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 903 time to evaluate : 1.156 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: H 34 MET cc_start: 0.7466 (mmm) cc_final: 0.7068 (mmm) REVERT: H 70 SER cc_start: 0.8301 (t) cc_final: 0.7825 (p) REVERT: H 92 VAL cc_start: 0.8844 (t) cc_final: 0.8540 (p) REVERT: H 108 LEU cc_start: 0.7831 (tp) cc_final: 0.7538 (tp) REVERT: H 113 THR cc_start: 0.6564 (t) cc_final: 0.6149 (m) REVERT: L 4 MET cc_start: 0.7215 (mmm) cc_final: 0.6725 (mmm) REVERT: L 10 SER cc_start: 0.6626 (t) cc_final: 0.6287 (m) REVERT: L 33 LEU cc_start: 0.8172 (tt) cc_final: 0.7850 (tt) REVERT: L 71 PHE cc_start: 0.6566 (m-80) cc_final: 0.5898 (m-10) REVERT: L 89 GLN cc_start: 0.5692 (tt0) cc_final: 0.5369 (tt0) REVERT: L 141 TYR cc_start: 0.7482 (t80) cc_final: 0.6893 (t80) REVERT: C 96 GLU cc_start: 0.6763 (mm-30) cc_final: 0.6495 (mm-30) REVERT: C 105 ILE cc_start: 0.7907 (mm) cc_final: 0.7528 (tt) REVERT: C 129 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7661 (mtmm) REVERT: C 196 ASN cc_start: 0.7524 (t0) cc_final: 0.7268 (t0) REVERT: C 210 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.7123 (pt) REVERT: C 239 GLN cc_start: 0.8072 (tt0) cc_final: 0.7786 (pt0) REVERT: C 246 ARG cc_start: 0.6555 (OUTLIER) cc_final: 0.6040 (ppt90) REVERT: C 310 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8356 (ttpt) REVERT: C 424 LYS cc_start: 0.8072 (tttt) cc_final: 0.7783 (tttt) REVERT: C 428 ASP cc_start: 0.7983 (p0) cc_final: 0.7755 (p0) REVERT: C 436 TRP cc_start: 0.8140 (p90) cc_final: 0.7938 (p90) REVERT: C 559 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.8148 (t80) REVERT: C 586 ASP cc_start: 0.7835 (m-30) cc_final: 0.7568 (m-30) REVERT: C 603 ASN cc_start: 0.8268 (t0) cc_final: 0.7994 (t0) REVERT: C 663 ASP cc_start: 0.7356 (t0) cc_final: 0.7056 (t0) REVERT: C 703 ASN cc_start: 0.8731 (t0) cc_final: 0.8390 (t0) REVERT: C 776 LYS cc_start: 0.8186 (ttpp) cc_final: 0.7948 (tttm) REVERT: C 856 ASN cc_start: 0.8489 (p0) cc_final: 0.8213 (p0) REVERT: C 937 SER cc_start: 0.8007 (m) cc_final: 0.7760 (t) REVERT: C 955 ASN cc_start: 0.7696 (m-40) cc_final: 0.7311 (m-40) REVERT: C 1014 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7833 (mtp180) REVERT: C 1086 LYS cc_start: 0.8443 (ptpt) cc_final: 0.8115 (ptpp) REVERT: C 1118 ASP cc_start: 0.7753 (t0) cc_final: 0.7424 (t0) REVERT: C 1123 SER cc_start: 0.8486 (t) cc_final: 0.8219 (t) REVERT: C 1128 VAL cc_start: 0.8557 (m) cc_final: 0.8191 (p) REVERT: C 1130 ILE cc_start: 0.8736 (pt) cc_final: 0.8504 (mt) REVERT: C 1139 ASP cc_start: 0.7841 (t0) cc_final: 0.7546 (t0) REVERT: C 1141 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7681 (pp) REVERT: B 34 ARG cc_start: 0.7290 (mtp85) cc_final: 0.6874 (mtp85) REVERT: B 133 PHE cc_start: 0.4148 (OUTLIER) cc_final: 0.3338 (p90) REVERT: B 191 GLU cc_start: 0.7260 (pt0) cc_final: 0.7032 (mt-10) REVERT: B 266 TYR cc_start: 0.8022 (m-80) cc_final: 0.7704 (m-80) REVERT: B 281 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7347 (pp20) REVERT: B 312 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8224 (tt) REVERT: B 335 LEU cc_start: 0.8407 (tp) cc_final: 0.8158 (tp) REVERT: B 346 THR cc_start: 0.8273 (m) cc_final: 0.7828 (p) REVERT: B 386 LYS cc_start: 0.8470 (mmmm) cc_final: 0.7676 (mtpp) REVERT: B 390 LEU cc_start: 0.8762 (mm) cc_final: 0.8434 (mm) REVERT: B 424 LYS cc_start: 0.7310 (ttpp) cc_final: 0.7109 (tmmt) REVERT: B 453 TYR cc_start: 0.6476 (p90) cc_final: 0.5854 (p90) REVERT: B 558 LYS cc_start: 0.8006 (tptm) cc_final: 0.7655 (tptm) REVERT: B 658 ASN cc_start: 0.7142 (OUTLIER) cc_final: 0.6928 (p0) REVERT: B 759 PHE cc_start: 0.7475 (t80) cc_final: 0.7000 (t80) REVERT: B 764 LYS cc_start: 0.7996 (tppp) cc_final: 0.7602 (tppp) REVERT: B 776 LYS cc_start: 0.8336 (ttpt) cc_final: 0.7909 (tttp) REVERT: B 780 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7735 (mt-10) REVERT: B 856 ASN cc_start: 0.7874 (p0) cc_final: 0.7628 (p0) REVERT: B 918 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7655 (mt-10) REVERT: B 961 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8323 (p) REVERT: B 1017 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6922 (mm-30) REVERT: B 1073 LYS cc_start: 0.8381 (mtmt) cc_final: 0.8143 (mtpp) REVERT: A 28 TYR cc_start: 0.7072 (m-80) cc_final: 0.6675 (m-80) REVERT: A 138 ASP cc_start: 0.7551 (t0) cc_final: 0.7334 (t0) REVERT: A 170 TYR cc_start: 0.7639 (t80) cc_final: 0.7248 (t80) REVERT: A 221 SER cc_start: 0.8331 (t) cc_final: 0.8003 (m) REVERT: A 237 ARG cc_start: 0.7873 (mtm110) cc_final: 0.7527 (mtp85) REVERT: A 244 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7163 (tm) REVERT: A 280 ASN cc_start: 0.7341 (m-40) cc_final: 0.7055 (m-40) REVERT: A 340 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7783 (mm-30) REVERT: A 356 LYS cc_start: 0.8305 (tttp) cc_final: 0.8044 (mtpp) REVERT: A 409 GLN cc_start: 0.6866 (tt0) cc_final: 0.6605 (tt0) REVERT: A 424 LYS cc_start: 0.7625 (tttp) cc_final: 0.7401 (ttpt) REVERT: A 439 ASN cc_start: 0.7940 (t0) cc_final: 0.7638 (t0) REVERT: A 440 LYS cc_start: 0.8792 (mtmt) cc_final: 0.8473 (mtmt) REVERT: A 511 VAL cc_start: 0.8289 (t) cc_final: 0.7974 (p) REVERT: A 514 SER cc_start: 0.8756 (OUTLIER) cc_final: 0.8341 (p) REVERT: A 546 LEU cc_start: 0.8417 (tp) cc_final: 0.8171 (tt) REVERT: A 586 ASP cc_start: 0.7974 (t0) cc_final: 0.7586 (m-30) REVERT: A 603 ASN cc_start: 0.8089 (t0) cc_final: 0.7746 (t0) REVERT: A 646 ARG cc_start: 0.7579 (ttp-110) cc_final: 0.7354 (ttp-110) REVERT: A 775 ASP cc_start: 0.7811 (m-30) cc_final: 0.7606 (m-30) REVERT: A 776 LYS cc_start: 0.8388 (ttpp) cc_final: 0.8020 (tttm) REVERT: A 780 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7282 (mt-10) REVERT: A 921 LYS cc_start: 0.8429 (mmmt) cc_final: 0.8096 (mmmt) REVERT: A 933 LYS cc_start: 0.8376 (mtmt) cc_final: 0.8167 (mtmt) REVERT: A 964 LYS cc_start: 0.8398 (tppt) cc_final: 0.7959 (mptt) REVERT: A 979 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.7204 (m-30) REVERT: A 983 ARG cc_start: 0.8270 (ttm-80) cc_final: 0.7971 (ttm-80) REVERT: A 1005 GLN cc_start: 0.8206 (tp40) cc_final: 0.7840 (tp40) REVERT: A 1041 ASP cc_start: 0.8072 (t0) cc_final: 0.7816 (t0) REVERT: A 1084 ASP cc_start: 0.7568 (t0) cc_final: 0.7035 (t0) REVERT: I 47 TRP cc_start: 0.7597 (t60) cc_final: 0.7334 (t60) REVERT: I 92 VAL cc_start: 0.8977 (t) cc_final: 0.8758 (p) REVERT: I 113 THR cc_start: 0.6438 (t) cc_final: 0.6171 (m) REVERT: M 3 GLN cc_start: 0.7971 (mp10) cc_final: 0.7709 (mp10) REVERT: M 22 THR cc_start: 0.8393 (m) cc_final: 0.8177 (t) REVERT: M 33 LEU cc_start: 0.8260 (tt) cc_final: 0.7890 (tt) REVERT: M 37 GLN cc_start: 0.7381 (tm-30) cc_final: 0.6986 (tp-100) REVERT: M 38 GLN cc_start: 0.7446 (tp40) cc_final: 0.7233 (tp40) REVERT: M 71 PHE cc_start: 0.6594 (m-80) cc_final: 0.6002 (m-10) REVERT: M 78 LEU cc_start: 0.8225 (mt) cc_final: 0.7928 (mt) REVERT: M 94 MET cc_start: 0.7008 (mmt) cc_final: 0.6640 (mmm) REVERT: M 141 TYR cc_start: 0.6227 (t80) cc_final: 0.5971 (t80) REVERT: J 34 MET cc_start: 0.6875 (mmm) cc_final: 0.6628 (mmm) REVERT: J 70 SER cc_start: 0.8030 (t) cc_final: 0.7681 (p) REVERT: J 78 LEU cc_start: 0.8100 (tp) cc_final: 0.7845 (tp) REVERT: J 92 VAL cc_start: 0.8934 (t) cc_final: 0.8594 (p) REVERT: J 100 SER cc_start: 0.8175 (p) cc_final: 0.7924 (p) REVERT: J 105 TYR cc_start: 0.8240 (p90) cc_final: 0.7954 (p90) REVERT: N 14 SER cc_start: 0.8120 (m) cc_final: 0.7788 (p) REVERT: N 27 GLN cc_start: 0.8211 (pm20) cc_final: 0.8002 (pm20) REVERT: N 33 LEU cc_start: 0.8146 (tt) cc_final: 0.7931 (tt) REVERT: N 37 GLN cc_start: 0.6715 (tp40) cc_final: 0.6423 (tp40) REVERT: N 46 LEU cc_start: 0.8024 (pt) cc_final: 0.7578 (pt) REVERT: N 79 GLN cc_start: 0.7611 (mp10) cc_final: 0.6949 (mp10) REVERT: N 126 LEU cc_start: 0.6323 (mt) cc_final: 0.6115 (mp) outliers start: 194 outliers final: 130 residues processed: 1010 average time/residue: 0.2179 time to fit residues: 353.6806 Evaluate side-chains 995 residues out of total 3725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 850 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain M residue 174 TYR Chi-restraints excluded: chain M residue 195 CYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 88 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 45 optimal weight: 1.9990 chunk 157 optimal weight: 0.3980 chunk 173 optimal weight: 0.9980 chunk 285 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 411 optimal weight: 0.7980 chunk 289 optimal weight: 1.9990 chunk 196 optimal weight: 0.2980 chunk 293 optimal weight: 0.6980 chunk 291 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 125 GLN ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 HIS ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 957 GLN M 89 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.163679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.127641 restraints weight = 58677.292| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.84 r_work: 0.3495 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 35185 Z= 0.220 Angle : 0.726 12.521 48020 Z= 0.361 Chirality : 0.049 0.494 5616 Planarity : 0.005 0.084 6041 Dihedral : 7.916 68.370 6236 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 5.40 % Allowed : 15.01 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.13), residues: 4205 helix: 0.88 (0.20), residues: 630 sheet: -0.47 (0.15), residues: 1197 loop : -1.74 (0.12), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 355 TYR 0.030 0.002 TYR I 105 PHE 0.037 0.002 PHE A 133 TRP 0.015 0.002 TRP L 149 HIS 0.010 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00505 (35056) covalent geometry : angle 0.69457 (47687) SS BOND : bond 0.00763 ( 54) SS BOND : angle 2.66584 ( 108) hydrogen bonds : bond 0.04403 ( 1215) hydrogen bonds : angle 6.29677 ( 3249) link_BETA1-4 : bond 0.00869 ( 36) link_BETA1-4 : angle 2.51147 ( 108) link_NAG-ASN : bond 0.00464 ( 39) link_NAG-ASN : angle 2.73803 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 3725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 892 time to evaluate : 1.308 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: H 34 MET cc_start: 0.7530 (mmm) cc_final: 0.7071 (mmm) REVERT: H 70 SER cc_start: 0.8328 (t) cc_final: 0.7868 (p) REVERT: H 92 VAL cc_start: 0.8846 (t) cc_final: 0.8584 (p) REVERT: H 108 LEU cc_start: 0.7818 (tp) cc_final: 0.7512 (tp) REVERT: H 113 THR cc_start: 0.6552 (t) cc_final: 0.6127 (m) REVERT: L 4 MET cc_start: 0.7323 (mmm) cc_final: 0.7002 (mmm) REVERT: L 10 SER cc_start: 0.6781 (t) cc_final: 0.6423 (m) REVERT: L 33 LEU cc_start: 0.8191 (tt) cc_final: 0.7900 (tt) REVERT: L 71 PHE cc_start: 0.6549 (m-80) cc_final: 0.6009 (m-80) REVERT: L 79 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7033 (mp10) REVERT: L 89 GLN cc_start: 0.5870 (tt0) cc_final: 0.5498 (tt0) REVERT: L 141 TYR cc_start: 0.7560 (t80) cc_final: 0.6975 (t80) REVERT: C 96 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6564 (mm-30) REVERT: C 105 ILE cc_start: 0.7944 (mm) cc_final: 0.7559 (tt) REVERT: C 129 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7618 (mtmm) REVERT: C 196 ASN cc_start: 0.7554 (t0) cc_final: 0.7294 (t0) REVERT: C 210 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.7142 (pt) REVERT: C 239 GLN cc_start: 0.8037 (tt0) cc_final: 0.7710 (pt0) REVERT: C 246 ARG cc_start: 0.6567 (OUTLIER) cc_final: 0.6088 (ppt90) REVERT: C 310 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8359 (ttpt) REVERT: C 424 LYS cc_start: 0.8091 (tttt) cc_final: 0.7778 (tttt) REVERT: C 559 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.8104 (t80) REVERT: C 586 ASP cc_start: 0.7865 (m-30) cc_final: 0.7624 (m-30) REVERT: C 603 ASN cc_start: 0.8325 (t0) cc_final: 0.8054 (t0) REVERT: C 663 ASP cc_start: 0.7430 (t0) cc_final: 0.7153 (t0) REVERT: C 703 ASN cc_start: 0.8729 (t0) cc_final: 0.8406 (t0) REVERT: C 740 MET cc_start: 0.7617 (ttp) cc_final: 0.7416 (ttp) REVERT: C 776 LYS cc_start: 0.8154 (ttpp) cc_final: 0.7862 (tttp) REVERT: C 856 ASN cc_start: 0.8406 (p0) cc_final: 0.8155 (p0) REVERT: C 937 SER cc_start: 0.8004 (m) cc_final: 0.7758 (t) REVERT: C 955 ASN cc_start: 0.7721 (m-40) cc_final: 0.7297 (m-40) REVERT: C 1014 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7863 (mtp180) REVERT: C 1086 LYS cc_start: 0.8411 (ptpt) cc_final: 0.8077 (ptpp) REVERT: C 1118 ASP cc_start: 0.7823 (t0) cc_final: 0.7479 (t0) REVERT: C 1123 SER cc_start: 0.8396 (t) cc_final: 0.8101 (t) REVERT: C 1128 VAL cc_start: 0.8573 (m) cc_final: 0.8237 (p) REVERT: C 1130 ILE cc_start: 0.8734 (pt) cc_final: 0.8519 (mt) REVERT: C 1139 ASP cc_start: 0.7855 (t0) cc_final: 0.7645 (t0) REVERT: B 34 ARG cc_start: 0.7284 (mtp85) cc_final: 0.6926 (mtp85) REVERT: B 133 PHE cc_start: 0.4452 (OUTLIER) cc_final: 0.3867 (p90) REVERT: B 134 GLN cc_start: 0.6810 (tp40) cc_final: 0.6489 (tp40) REVERT: B 266 TYR cc_start: 0.8041 (m-80) cc_final: 0.7716 (m-80) REVERT: B 281 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7292 (pp20) REVERT: B 312 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8227 (tt) REVERT: B 346 THR cc_start: 0.8301 (m) cc_final: 0.7903 (p) REVERT: B 386 LYS cc_start: 0.8519 (mmmm) cc_final: 0.7691 (mtpp) REVERT: B 390 LEU cc_start: 0.8781 (mm) cc_final: 0.8428 (mm) REVERT: B 428 ASP cc_start: 0.7908 (p0) cc_final: 0.7611 (p0) REVERT: B 453 TYR cc_start: 0.6549 (p90) cc_final: 0.5885 (p90) REVERT: B 558 LYS cc_start: 0.8036 (tptm) cc_final: 0.7734 (tptm) REVERT: B 751 ASN cc_start: 0.7949 (p0) cc_final: 0.7706 (p0) REVERT: B 759 PHE cc_start: 0.7606 (t80) cc_final: 0.7152 (t80) REVERT: B 764 LYS cc_start: 0.7998 (tppp) cc_final: 0.7596 (tppp) REVERT: B 776 LYS cc_start: 0.8306 (ttpt) cc_final: 0.7865 (tttp) REVERT: B 780 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7759 (mt-10) REVERT: B 856 ASN cc_start: 0.7937 (p0) cc_final: 0.7596 (p0) REVERT: B 965 GLN cc_start: 0.7954 (mt0) cc_final: 0.7443 (mt0) REVERT: B 1017 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6866 (mm-30) REVERT: B 1073 LYS cc_start: 0.8395 (mtmt) cc_final: 0.8087 (mtpp) REVERT: A 28 TYR cc_start: 0.7108 (m-80) cc_final: 0.6690 (m-80) REVERT: A 138 ASP cc_start: 0.7581 (t0) cc_final: 0.7351 (t0) REVERT: A 153 MET cc_start: 0.7558 (mtm) cc_final: 0.7279 (mtm) REVERT: A 170 TYR cc_start: 0.7670 (t80) cc_final: 0.7274 (t80) REVERT: A 221 SER cc_start: 0.8335 (t) cc_final: 0.7902 (p) REVERT: A 237 ARG cc_start: 0.7826 (mtm110) cc_final: 0.7489 (mtp85) REVERT: A 244 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7199 (tm) REVERT: A 280 ASN cc_start: 0.7699 (m-40) cc_final: 0.7149 (m-40) REVERT: A 340 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7809 (mm-30) REVERT: A 356 LYS cc_start: 0.8280 (tttp) cc_final: 0.8035 (mtpp) REVERT: A 365 TYR cc_start: 0.7484 (m-80) cc_final: 0.7185 (m-80) REVERT: A 386 LYS cc_start: 0.8472 (mttt) cc_final: 0.8185 (ptpp) REVERT: A 409 GLN cc_start: 0.6967 (tt0) cc_final: 0.6601 (tt0) REVERT: A 424 LYS cc_start: 0.7670 (tttp) cc_final: 0.7433 (ttpt) REVERT: A 439 ASN cc_start: 0.8031 (t0) cc_final: 0.7734 (t0) REVERT: A 440 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8484 (mtmt) REVERT: A 514 SER cc_start: 0.8743 (OUTLIER) cc_final: 0.8381 (p) REVERT: A 546 LEU cc_start: 0.8455 (tp) cc_final: 0.8223 (tt) REVERT: A 586 ASP cc_start: 0.7973 (t0) cc_final: 0.7598 (m-30) REVERT: A 603 ASN cc_start: 0.8123 (t0) cc_final: 0.7785 (t0) REVERT: A 646 ARG cc_start: 0.7666 (ttp-110) cc_final: 0.7463 (ttp-110) REVERT: A 776 LYS cc_start: 0.8283 (ttpp) cc_final: 0.8012 (tttp) REVERT: A 780 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7371 (mt-10) REVERT: A 921 LYS cc_start: 0.8472 (mmmt) cc_final: 0.8118 (mmmt) REVERT: A 933 LYS cc_start: 0.8373 (mtmt) cc_final: 0.8148 (mtmt) REVERT: A 964 LYS cc_start: 0.8375 (tppt) cc_final: 0.7946 (mptt) REVERT: A 983 ARG cc_start: 0.8284 (ttm-80) cc_final: 0.7900 (ttm-80) REVERT: A 1005 GLN cc_start: 0.8186 (tp40) cc_final: 0.7781 (tp40) REVERT: A 1041 ASP cc_start: 0.8159 (t0) cc_final: 0.7874 (t0) REVERT: A 1084 ASP cc_start: 0.7616 (t0) cc_final: 0.7087 (t0) REVERT: I 47 TRP cc_start: 0.7519 (t60) cc_final: 0.7212 (t60) REVERT: I 92 VAL cc_start: 0.8943 (t) cc_final: 0.8728 (p) REVERT: M 3 GLN cc_start: 0.8039 (mp10) cc_final: 0.7771 (mp10) REVERT: M 24 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7467 (mtt90) REVERT: M 27 GLN cc_start: 0.7919 (pm20) cc_final: 0.7655 (pm20) REVERT: M 33 LEU cc_start: 0.8196 (tt) cc_final: 0.7858 (tt) REVERT: M 37 GLN cc_start: 0.7408 (tm-30) cc_final: 0.7176 (tp-100) REVERT: M 38 GLN cc_start: 0.7534 (tp40) cc_final: 0.7039 (tp40) REVERT: M 71 PHE cc_start: 0.6704 (m-80) cc_final: 0.6167 (m-10) REVERT: M 79 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7743 (mp10) REVERT: M 86 TYR cc_start: 0.8344 (m-10) cc_final: 0.8114 (m-10) REVERT: M 89 GLN cc_start: 0.6644 (OUTLIER) cc_final: 0.6436 (tp-100) REVERT: M 94 MET cc_start: 0.7038 (mmt) cc_final: 0.6644 (mmm) REVERT: M 119 PHE cc_start: 0.6637 (t80) cc_final: 0.6294 (t80) REVERT: M 141 TYR cc_start: 0.6322 (t80) cc_final: 0.5982 (t80) REVERT: J 19 ARG cc_start: 0.5863 (tpp80) cc_final: 0.5328 (tpp80) REVERT: J 34 MET cc_start: 0.7047 (mmm) cc_final: 0.6806 (mmm) REVERT: J 70 SER cc_start: 0.8110 (t) cc_final: 0.7760 (p) REVERT: J 78 LEU cc_start: 0.8157 (tp) cc_final: 0.7921 (tp) REVERT: J 92 VAL cc_start: 0.8935 (t) cc_final: 0.8581 (p) REVERT: J 105 TYR cc_start: 0.8204 (p90) cc_final: 0.7888 (p90) REVERT: J 128 PHE cc_start: 0.5839 (m-80) cc_final: 0.5498 (m-80) REVERT: N 14 SER cc_start: 0.8209 (m) cc_final: 0.7872 (p) REVERT: N 33 LEU cc_start: 0.8114 (tt) cc_final: 0.7853 (tt) REVERT: N 79 GLN cc_start: 0.7850 (mp10) cc_final: 0.7161 (mp10) REVERT: N 85 THR cc_start: 0.7039 (m) cc_final: 0.6727 (p) REVERT: N 86 TYR cc_start: 0.8243 (m-80) cc_final: 0.7996 (m-10) REVERT: N 94 MET cc_start: 0.6892 (mmt) cc_final: 0.6553 (mmm) REVERT: N 106 GLU cc_start: 0.5625 (tm-30) cc_final: 0.4830 (tm-30) outliers start: 201 outliers final: 140 residues processed: 1008 average time/residue: 0.2121 time to fit residues: 343.8959 Evaluate side-chains 1010 residues out of total 3725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 857 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 150 LYS Chi-restraints excluded: chain M residue 174 TYR Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 195 CYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain N residue 174 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 411 optimal weight: 2.9990 chunk 296 optimal weight: 0.8980 chunk 181 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 49 optimal weight: 0.8980 chunk 272 optimal weight: 0.8980 chunk 189 optimal weight: 0.3980 chunk 180 optimal weight: 0.0570 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 HIS C 532 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 901 GLN B 914 ASN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 955 ASN A1119 ASN M 89 GLN N 37 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.163953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.127825 restraints weight = 58553.539| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.83 r_work: 0.3492 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 35185 Z= 0.201 Angle : 0.712 12.831 48020 Z= 0.354 Chirality : 0.049 0.481 5616 Planarity : 0.005 0.080 6041 Dihedral : 7.450 68.398 6234 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 5.53 % Allowed : 15.44 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.13), residues: 4205 helix: 0.99 (0.20), residues: 636 sheet: -0.44 (0.15), residues: 1192 loop : -1.72 (0.12), residues: 2377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 357 TYR 0.030 0.002 TYR H 105 PHE 0.050 0.002 PHE I 152 TRP 0.015 0.002 TRP L 149 HIS 0.010 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00465 (35056) covalent geometry : angle 0.68224 (47687) SS BOND : bond 0.00541 ( 54) SS BOND : angle 2.45831 ( 108) hydrogen bonds : bond 0.04238 ( 1215) hydrogen bonds : angle 6.17287 ( 3249) link_BETA1-4 : bond 0.00741 ( 36) link_BETA1-4 : angle 2.40691 ( 108) link_NAG-ASN : bond 0.00428 ( 39) link_NAG-ASN : angle 2.70524 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 3725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 868 time to evaluate : 1.257 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: H 34 MET cc_start: 0.7552 (mmm) cc_final: 0.7096 (mmm) REVERT: H 70 SER cc_start: 0.8282 (t) cc_final: 0.7871 (p) REVERT: H 92 VAL cc_start: 0.8850 (t) cc_final: 0.8603 (p) REVERT: H 108 LEU cc_start: 0.7802 (tp) cc_final: 0.7507 (tp) REVERT: L 4 MET cc_start: 0.7292 (mmm) cc_final: 0.7016 (mmm) REVERT: L 33 LEU cc_start: 0.8204 (tt) cc_final: 0.7879 (tt) REVERT: L 71 PHE cc_start: 0.6516 (m-80) cc_final: 0.5975 (m-10) REVERT: L 79 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7226 (mp10) REVERT: L 89 GLN cc_start: 0.5899 (tt0) cc_final: 0.5549 (tt0) REVERT: L 141 TYR cc_start: 0.7656 (t80) cc_final: 0.7102 (t80) REVERT: L 196 GLU cc_start: 0.5840 (tm-30) cc_final: 0.5528 (tm-30) REVERT: C 96 GLU cc_start: 0.6787 (mm-30) cc_final: 0.6549 (mm-30) REVERT: C 105 ILE cc_start: 0.7940 (mm) cc_final: 0.7568 (tt) REVERT: C 196 ASN cc_start: 0.7546 (t0) cc_final: 0.7277 (t0) REVERT: C 210 ILE cc_start: 0.7403 (OUTLIER) cc_final: 0.7188 (pt) REVERT: C 239 GLN cc_start: 0.8000 (tt0) cc_final: 0.7729 (pt0) REVERT: C 246 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.6144 (ppt90) REVERT: C 310 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8337 (ttpt) REVERT: C 409 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6383 (tp-100) REVERT: C 424 LYS cc_start: 0.8090 (tttt) cc_final: 0.7818 (tttt) REVERT: C 428 ASP cc_start: 0.8075 (p0) cc_final: 0.7704 (p0) REVERT: C 559 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.8135 (t80) REVERT: C 586 ASP cc_start: 0.7861 (m-30) cc_final: 0.7554 (m-30) REVERT: C 603 ASN cc_start: 0.8333 (t0) cc_final: 0.8062 (t0) REVERT: C 703 ASN cc_start: 0.8726 (t0) cc_final: 0.8386 (t0) REVERT: C 776 LYS cc_start: 0.8177 (ttpp) cc_final: 0.7974 (tttm) REVERT: C 856 ASN cc_start: 0.8380 (p0) cc_final: 0.8110 (p0) REVERT: C 937 SER cc_start: 0.8041 (m) cc_final: 0.7791 (t) REVERT: C 955 ASN cc_start: 0.7668 (m110) cc_final: 0.7231 (m110) REVERT: C 1014 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7845 (mtp180) REVERT: C 1086 LYS cc_start: 0.8402 (ptpt) cc_final: 0.8071 (ptpp) REVERT: C 1118 ASP cc_start: 0.7789 (t0) cc_final: 0.7440 (t0) REVERT: C 1128 VAL cc_start: 0.8581 (m) cc_final: 0.8239 (p) REVERT: C 1139 ASP cc_start: 0.7846 (t0) cc_final: 0.7558 (t0) REVERT: C 1141 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7729 (pp) REVERT: B 51 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8297 (p) REVERT: B 133 PHE cc_start: 0.4801 (OUTLIER) cc_final: 0.4377 (p90) REVERT: B 134 GLN cc_start: 0.6687 (tp40) cc_final: 0.6428 (tp40) REVERT: B 135 PHE cc_start: 0.6975 (OUTLIER) cc_final: 0.6721 (m-80) REVERT: B 266 TYR cc_start: 0.8045 (m-80) cc_final: 0.7668 (m-80) REVERT: B 281 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7295 (pp20) REVERT: B 312 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8233 (tt) REVERT: B 346 THR cc_start: 0.8314 (m) cc_final: 0.7952 (p) REVERT: B 386 LYS cc_start: 0.8529 (mmmm) cc_final: 0.7726 (mtpp) REVERT: B 390 LEU cc_start: 0.8733 (mm) cc_final: 0.8375 (mm) REVERT: B 428 ASP cc_start: 0.7886 (p0) cc_final: 0.7579 (p0) REVERT: B 453 TYR cc_start: 0.6674 (p90) cc_final: 0.5578 (p90) REVERT: B 558 LYS cc_start: 0.8038 (tptm) cc_final: 0.7716 (tptm) REVERT: B 646 ARG cc_start: 0.7997 (mtp180) cc_final: 0.7736 (mtp180) REVERT: B 751 ASN cc_start: 0.7914 (p0) cc_final: 0.7646 (p0) REVERT: B 759 PHE cc_start: 0.7609 (t80) cc_final: 0.7172 (t80) REVERT: B 764 LYS cc_start: 0.7984 (tppp) cc_final: 0.7572 (tppp) REVERT: B 776 LYS cc_start: 0.8345 (ttpt) cc_final: 0.7924 (tttp) REVERT: B 780 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7761 (mt-10) REVERT: B 856 ASN cc_start: 0.7913 (p0) cc_final: 0.7537 (p0) REVERT: B 965 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7509 (mt0) REVERT: B 1017 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6882 (mm-30) REVERT: B 1073 LYS cc_start: 0.8400 (mtmt) cc_final: 0.8097 (mtpp) REVERT: A 28 TYR cc_start: 0.7131 (m-80) cc_final: 0.6747 (m-80) REVERT: A 133 PHE cc_start: 0.6960 (OUTLIER) cc_final: 0.6642 (p90) REVERT: A 138 ASP cc_start: 0.7596 (t0) cc_final: 0.7309 (t0) REVERT: A 153 MET cc_start: 0.7616 (mtm) cc_final: 0.7328 (mtm) REVERT: A 170 TYR cc_start: 0.7686 (t80) cc_final: 0.7308 (t80) REVERT: A 221 SER cc_start: 0.8328 (t) cc_final: 0.7874 (p) REVERT: A 237 ARG cc_start: 0.7843 (mtm110) cc_final: 0.7631 (mtp85) REVERT: A 244 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7170 (tm) REVERT: A 280 ASN cc_start: 0.7756 (m-40) cc_final: 0.7263 (m-40) REVERT: A 340 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7759 (mm-30) REVERT: A 347 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.8223 (t80) REVERT: A 355 ARG cc_start: 0.8191 (ttt-90) cc_final: 0.7905 (ttt-90) REVERT: A 365 TYR cc_start: 0.7429 (m-80) cc_final: 0.7160 (m-80) REVERT: A 386 LYS cc_start: 0.8534 (mttt) cc_final: 0.8127 (ptpp) REVERT: A 396 TYR cc_start: 0.7987 (m-80) cc_final: 0.7648 (m-80) REVERT: A 409 GLN cc_start: 0.6966 (OUTLIER) cc_final: 0.6604 (tt0) REVERT: A 439 ASN cc_start: 0.8040 (t0) cc_final: 0.7752 (t0) REVERT: A 440 LYS cc_start: 0.8805 (mtmt) cc_final: 0.8461 (mtmt) REVERT: A 451 TYR cc_start: 0.7058 (m-80) cc_final: 0.6847 (m-80) REVERT: A 514 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8406 (p) REVERT: A 546 LEU cc_start: 0.8436 (tp) cc_final: 0.8208 (tt) REVERT: A 586 ASP cc_start: 0.7969 (t0) cc_final: 0.7585 (m-30) REVERT: A 646 ARG cc_start: 0.7686 (ttp-110) cc_final: 0.7458 (ttp-110) REVERT: A 658 ASN cc_start: 0.7448 (OUTLIER) cc_final: 0.6796 (p0) REVERT: A 740 MET cc_start: 0.8125 (tpt) cc_final: 0.7868 (tpp) REVERT: A 759 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.6674 (m-10) REVERT: A 776 LYS cc_start: 0.8301 (ttpp) cc_final: 0.8061 (tttm) REVERT: A 780 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7424 (mt-10) REVERT: A 921 LYS cc_start: 0.8473 (mmmt) cc_final: 0.8094 (mmmt) REVERT: A 933 LYS cc_start: 0.8391 (mtmt) cc_final: 0.8165 (mtmt) REVERT: A 964 LYS cc_start: 0.8340 (tppt) cc_final: 0.7910 (mptt) REVERT: A 979 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7218 (m-30) REVERT: A 983 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.7933 (ttm-80) REVERT: A 1005 GLN cc_start: 0.8184 (tp40) cc_final: 0.7768 (tp40) REVERT: A 1014 ARG cc_start: 0.7912 (mtm-85) cc_final: 0.7594 (mtm-85) REVERT: A 1041 ASP cc_start: 0.8172 (t0) cc_final: 0.7863 (t0) REVERT: A 1084 ASP cc_start: 0.7635 (t0) cc_final: 0.7099 (t0) REVERT: I 34 MET cc_start: 0.7060 (mmm) cc_final: 0.6814 (mmm) REVERT: I 47 TRP cc_start: 0.7506 (t60) cc_final: 0.7168 (t60) REVERT: I 113 THR cc_start: 0.6208 (m) cc_final: 0.5986 (m) REVERT: M 3 GLN cc_start: 0.8024 (mp10) cc_final: 0.7772 (mp10) REVERT: M 33 LEU cc_start: 0.8210 (tt) cc_final: 0.7905 (tt) REVERT: M 38 GLN cc_start: 0.7603 (tp40) cc_final: 0.7048 (tp40) REVERT: M 71 PHE cc_start: 0.6589 (m-80) cc_final: 0.6141 (m-10) REVERT: M 86 TYR cc_start: 0.8285 (m-10) cc_final: 0.8079 (m-10) REVERT: M 94 MET cc_start: 0.7141 (mmt) cc_final: 0.6728 (mmm) REVERT: M 98 THR cc_start: 0.7682 (p) cc_final: 0.7435 (p) REVERT: M 119 PHE cc_start: 0.6671 (t80) cc_final: 0.6349 (t80) REVERT: M 141 TYR cc_start: 0.6309 (t80) cc_final: 0.6000 (t80) REVERT: J 19 ARG cc_start: 0.6144 (tpp80) cc_final: 0.5576 (tpp80) REVERT: J 70 SER cc_start: 0.8089 (t) cc_final: 0.7754 (p) REVERT: J 92 VAL cc_start: 0.8949 (t) cc_final: 0.8605 (p) REVERT: J 105 TYR cc_start: 0.8196 (p90) cc_final: 0.7881 (p90) REVERT: N 14 SER cc_start: 0.8177 (m) cc_final: 0.7833 (p) REVERT: N 33 LEU cc_start: 0.8074 (tt) cc_final: 0.7711 (tt) REVERT: N 71 PHE cc_start: 0.6458 (m-80) cc_final: 0.5867 (m-10) REVERT: N 85 THR cc_start: 0.7007 (m) cc_final: 0.6606 (p) REVERT: N 94 MET cc_start: 0.6965 (mmt) cc_final: 0.6625 (mmm) REVERT: N 104 ARG cc_start: 0.7206 (ttt90) cc_final: 0.6811 (ttt90) REVERT: N 106 GLU cc_start: 0.5630 (tm-30) cc_final: 0.4099 (tm-30) REVERT: N 126 LEU cc_start: 0.6353 (mt) cc_final: 0.6127 (mp) outliers start: 206 outliers final: 149 residues processed: 986 average time/residue: 0.2269 time to fit residues: 359.2437 Evaluate side-chains 1019 residues out of total 3725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 849 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 150 LYS Chi-restraints excluded: chain M residue 174 TYR Chi-restraints excluded: chain M residue 195 CYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 88 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 131 optimal weight: 0.9990 chunk 232 optimal weight: 0.3980 chunk 237 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 376 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 314 optimal weight: 0.9980 chunk 134 optimal weight: 0.4980 chunk 365 optimal weight: 10.0000 chunk 195 optimal weight: 0.0980 chunk 350 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 HIS C 532 ASN C 675 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 HIS B 360 ASN B 901 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.163388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.127590 restraints weight = 58329.619| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.80 r_work: 0.3488 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 35185 Z= 0.204 Angle : 0.716 12.813 48020 Z= 0.357 Chirality : 0.049 0.485 5616 Planarity : 0.005 0.074 6041 Dihedral : 7.318 68.435 6233 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 5.99 % Allowed : 15.79 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.13), residues: 4205 helix: 1.09 (0.21), residues: 630 sheet: -0.39 (0.15), residues: 1190 loop : -1.70 (0.12), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 19 TYR 0.031 0.002 TYR H 105 PHE 0.041 0.002 PHE A 643 TRP 0.031 0.002 TRP L 149 HIS 0.010 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00478 (35056) covalent geometry : angle 0.68686 (47687) SS BOND : bond 0.00548 ( 54) SS BOND : angle 2.35859 ( 108) hydrogen bonds : bond 0.04183 ( 1215) hydrogen bonds : angle 6.10878 ( 3249) link_BETA1-4 : bond 0.00753 ( 36) link_BETA1-4 : angle 2.31121 ( 108) link_NAG-ASN : bond 0.00411 ( 39) link_NAG-ASN : angle 2.79039 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 3725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 860 time to evaluate : 1.250 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: H 34 MET cc_start: 0.7564 (mmm) cc_final: 0.7117 (mmm) REVERT: H 70 SER cc_start: 0.8276 (t) cc_final: 0.7889 (p) REVERT: H 92 VAL cc_start: 0.8868 (t) cc_final: 0.8649 (p) REVERT: H 108 LEU cc_start: 0.7819 (tp) cc_final: 0.7524 (tp) REVERT: L 4 MET cc_start: 0.7281 (mmm) cc_final: 0.7018 (mmm) REVERT: L 33 LEU cc_start: 0.8209 (tt) cc_final: 0.7896 (tt) REVERT: L 71 PHE cc_start: 0.6529 (m-80) cc_final: 0.6006 (m-10) REVERT: L 79 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7317 (mp10) REVERT: L 89 GLN cc_start: 0.5870 (tt0) cc_final: 0.5497 (tt0) REVERT: L 94 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6692 (mtt) REVERT: L 141 TYR cc_start: 0.7621 (t80) cc_final: 0.7131 (t80) REVERT: L 180 LEU cc_start: 0.3231 (mt) cc_final: 0.2931 (tp) REVERT: L 196 GLU cc_start: 0.5789 (tm-30) cc_final: 0.5546 (tm-30) REVERT: L 210 PHE cc_start: 0.3700 (t80) cc_final: 0.3494 (t80) REVERT: C 44 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.7872 (mtt-85) REVERT: C 96 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6638 (mm-30) REVERT: C 105 ILE cc_start: 0.7964 (mm) cc_final: 0.7585 (tt) REVERT: C 129 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7541 (mtmm) REVERT: C 196 ASN cc_start: 0.7580 (t0) cc_final: 0.7318 (t0) REVERT: C 210 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.7203 (pt) REVERT: C 239 GLN cc_start: 0.7991 (tt0) cc_final: 0.7714 (pt0) REVERT: C 246 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.6146 (ppt90) REVERT: C 310 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8346 (ttpt) REVERT: C 409 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6663 (tp40) REVERT: C 424 LYS cc_start: 0.8090 (tttt) cc_final: 0.7832 (tttt) REVERT: C 559 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.8071 (t80) REVERT: C 586 ASP cc_start: 0.7857 (m-30) cc_final: 0.7544 (m-30) REVERT: C 603 ASN cc_start: 0.8350 (t0) cc_final: 0.8083 (t0) REVERT: C 707 TYR cc_start: 0.8094 (t80) cc_final: 0.7879 (t80) REVERT: C 740 MET cc_start: 0.7592 (ttp) cc_final: 0.7366 (ttp) REVERT: C 776 LYS cc_start: 0.8188 (ttpp) cc_final: 0.7976 (tttm) REVERT: C 937 SER cc_start: 0.8055 (m) cc_final: 0.7806 (t) REVERT: C 955 ASN cc_start: 0.7652 (m110) cc_final: 0.7204 (m110) REVERT: C 1014 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7844 (mtp180) REVERT: C 1086 LYS cc_start: 0.8400 (ptpt) cc_final: 0.8065 (ptpp) REVERT: C 1118 ASP cc_start: 0.7805 (t0) cc_final: 0.7432 (t0) REVERT: C 1128 VAL cc_start: 0.8598 (m) cc_final: 0.8236 (p) REVERT: C 1139 ASP cc_start: 0.7838 (t0) cc_final: 0.7552 (t0) REVERT: C 1141 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7757 (pp) REVERT: B 34 ARG cc_start: 0.7094 (mtp85) cc_final: 0.6730 (mtt-85) REVERT: B 51 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8290 (p) REVERT: B 133 PHE cc_start: 0.4976 (OUTLIER) cc_final: 0.4613 (p90) REVERT: B 134 GLN cc_start: 0.6729 (tp40) cc_final: 0.6487 (tp40) REVERT: B 135 PHE cc_start: 0.7008 (OUTLIER) cc_final: 0.6739 (m-80) REVERT: B 266 TYR cc_start: 0.8015 (m-80) cc_final: 0.7661 (m-80) REVERT: B 278 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8057 (ttpt) REVERT: B 281 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7294 (pp20) REVERT: B 312 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8236 (tt) REVERT: B 342 PHE cc_start: 0.8236 (m-80) cc_final: 0.8027 (m-80) REVERT: B 346 THR cc_start: 0.8341 (m) cc_final: 0.7989 (p) REVERT: B 386 LYS cc_start: 0.8548 (mmmm) cc_final: 0.7720 (mtpp) REVERT: B 390 LEU cc_start: 0.8728 (mm) cc_final: 0.8371 (mm) REVERT: B 428 ASP cc_start: 0.7879 (p0) cc_final: 0.7611 (p0) REVERT: B 453 TYR cc_start: 0.6865 (p90) cc_final: 0.5785 (p90) REVERT: B 454 ARG cc_start: 0.7574 (mmm-85) cc_final: 0.7126 (mmm-85) REVERT: B 493 GLN cc_start: 0.7093 (OUTLIER) cc_final: 0.6858 (pp30) REVERT: B 558 LYS cc_start: 0.8042 (tptm) cc_final: 0.7722 (tptm) REVERT: B 646 ARG cc_start: 0.7842 (mtp180) cc_final: 0.7611 (mtp180) REVERT: B 751 ASN cc_start: 0.7925 (p0) cc_final: 0.7557 (p0) REVERT: B 759 PHE cc_start: 0.7664 (t80) cc_final: 0.7238 (t80) REVERT: B 764 LYS cc_start: 0.7994 (tppp) cc_final: 0.7596 (tppp) REVERT: B 776 LYS cc_start: 0.8323 (ttpt) cc_final: 0.7918 (tttp) REVERT: B 780 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7740 (mt-10) REVERT: B 856 ASN cc_start: 0.7898 (p0) cc_final: 0.7484 (p0) REVERT: B 1017 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6896 (mm-30) REVERT: B 1073 LYS cc_start: 0.8408 (mtmt) cc_final: 0.8100 (mtpp) REVERT: A 28 TYR cc_start: 0.7121 (m-80) cc_final: 0.6720 (m-80) REVERT: A 51 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8333 (p) REVERT: A 138 ASP cc_start: 0.7541 (t0) cc_final: 0.7258 (t0) REVERT: A 153 MET cc_start: 0.7641 (mtm) cc_final: 0.7389 (mtm) REVERT: A 170 TYR cc_start: 0.7664 (t80) cc_final: 0.7332 (t80) REVERT: A 190 ARG cc_start: 0.7207 (mtp85) cc_final: 0.6876 (ptp-170) REVERT: A 221 SER cc_start: 0.8343 (t) cc_final: 0.7876 (p) REVERT: A 237 ARG cc_start: 0.7818 (mtm110) cc_final: 0.7616 (mtp85) REVERT: A 244 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7189 (tm) REVERT: A 280 ASN cc_start: 0.7768 (m-40) cc_final: 0.7310 (m-40) REVERT: A 340 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7740 (mm-30) REVERT: A 347 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.8237 (t80) REVERT: A 355 ARG cc_start: 0.8190 (ttt-90) cc_final: 0.7942 (ttt-90) REVERT: A 357 ARG cc_start: 0.7582 (ttm110) cc_final: 0.7341 (ttm110) REVERT: A 365 TYR cc_start: 0.7418 (m-80) cc_final: 0.7208 (m-80) REVERT: A 386 LYS cc_start: 0.8560 (mttt) cc_final: 0.8140 (ptpp) REVERT: A 396 TYR cc_start: 0.7973 (m-80) cc_final: 0.7647 (m-80) REVERT: A 409 GLN cc_start: 0.6989 (OUTLIER) cc_final: 0.6596 (tt0) REVERT: A 439 ASN cc_start: 0.8054 (t0) cc_final: 0.7772 (t0) REVERT: A 440 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8425 (mtmt) REVERT: A 451 TYR cc_start: 0.7087 (m-80) cc_final: 0.6873 (m-80) REVERT: A 514 SER cc_start: 0.8723 (OUTLIER) cc_final: 0.8366 (p) REVERT: A 546 LEU cc_start: 0.8438 (tp) cc_final: 0.8035 (tt) REVERT: A 565 PHE cc_start: 0.6897 (t80) cc_final: 0.6686 (t80) REVERT: A 586 ASP cc_start: 0.7943 (t0) cc_final: 0.7637 (m-30) REVERT: A 646 ARG cc_start: 0.7635 (ttp-110) cc_final: 0.7409 (ttp-110) REVERT: A 658 ASN cc_start: 0.7480 (OUTLIER) cc_final: 0.6774 (p0) REVERT: A 740 MET cc_start: 0.8212 (tpt) cc_final: 0.7919 (tpp) REVERT: A 776 LYS cc_start: 0.8288 (ttpp) cc_final: 0.8061 (tttp) REVERT: A 780 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7479 (mt-10) REVERT: A 921 LYS cc_start: 0.8489 (mmmt) cc_final: 0.8107 (mmmt) REVERT: A 933 LYS cc_start: 0.8385 (mtmt) cc_final: 0.8165 (mtmt) REVERT: A 964 LYS cc_start: 0.8370 (tppt) cc_final: 0.7937 (mptt) REVERT: A 979 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.7242 (m-30) REVERT: A 983 ARG cc_start: 0.8232 (ttm-80) cc_final: 0.7927 (ttm-80) REVERT: A 1005 GLN cc_start: 0.8186 (tp40) cc_final: 0.7764 (tp40) REVERT: A 1014 ARG cc_start: 0.7931 (mtm-85) cc_final: 0.7617 (mtm-85) REVERT: A 1041 ASP cc_start: 0.8184 (t0) cc_final: 0.7877 (t0) REVERT: A 1084 ASP cc_start: 0.7648 (t0) cc_final: 0.7109 (t0) REVERT: A 1094 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8215 (m) REVERT: I 34 MET cc_start: 0.7100 (mmm) cc_final: 0.6821 (mmm) REVERT: I 39 GLN cc_start: 0.7372 (tt0) cc_final: 0.6861 (tt0) REVERT: I 47 TRP cc_start: 0.7491 (t60) cc_final: 0.7161 (t60) REVERT: I 62 SER cc_start: 0.7706 (m) cc_final: 0.7493 (p) REVERT: I 113 THR cc_start: 0.6246 (m) cc_final: 0.6001 (m) REVERT: M 3 GLN cc_start: 0.8049 (mp10) cc_final: 0.7790 (mp10) REVERT: M 33 LEU cc_start: 0.8175 (tt) cc_final: 0.7890 (tt) REVERT: M 38 GLN cc_start: 0.7650 (tp40) cc_final: 0.7274 (tp40) REVERT: M 71 PHE cc_start: 0.6645 (m-80) cc_final: 0.6253 (m-80) REVERT: M 94 MET cc_start: 0.7144 (mmt) cc_final: 0.6654 (mmm) REVERT: M 119 PHE cc_start: 0.6821 (t80) cc_final: 0.6408 (t80) REVERT: M 141 TYR cc_start: 0.6399 (t80) cc_final: 0.6142 (t80) REVERT: J 19 ARG cc_start: 0.6260 (tpp80) cc_final: 0.5650 (tpp80) REVERT: J 70 SER cc_start: 0.8090 (t) cc_final: 0.7766 (p) REVERT: J 92 VAL cc_start: 0.8934 (t) cc_final: 0.8599 (p) REVERT: J 105 TYR cc_start: 0.8121 (p90) cc_final: 0.7769 (p90) REVERT: J 128 PHE cc_start: 0.5807 (m-80) cc_final: 0.5418 (m-80) REVERT: J 181 LEU cc_start: 0.7629 (mm) cc_final: 0.6911 (mm) REVERT: N 14 SER cc_start: 0.8174 (m) cc_final: 0.7820 (p) REVERT: N 33 LEU cc_start: 0.8065 (tt) cc_final: 0.7731 (tt) REVERT: N 71 PHE cc_start: 0.6492 (m-80) cc_final: 0.5912 (m-10) REVERT: N 85 THR cc_start: 0.7011 (m) cc_final: 0.6602 (p) REVERT: N 94 MET cc_start: 0.6942 (mmt) cc_final: 0.6620 (mmm) REVERT: N 104 ARG cc_start: 0.7190 (ttt90) cc_final: 0.6838 (ttt90) REVERT: N 106 GLU cc_start: 0.5587 (tm-30) cc_final: 0.4146 (tm-30) outliers start: 223 outliers final: 156 residues processed: 993 average time/residue: 0.2127 time to fit residues: 338.4776 Evaluate side-chains 1025 residues out of total 3725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 844 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 150 LYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 88 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 150 optimal weight: 1.9990 chunk 346 optimal weight: 4.9990 chunk 157 optimal weight: 0.2980 chunk 36 optimal weight: 0.0770 chunk 311 optimal weight: 0.7980 chunk 201 optimal weight: 0.9980 chunk 262 optimal weight: 1.9990 chunk 280 optimal weight: 0.9990 chunk 139 optimal weight: 0.6980 chunk 316 optimal weight: 0.4980 chunk 293 optimal weight: 0.9980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN C 334 ASN C 339 HIS C 360 ASN C 532 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A 125 ASN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 914 ASN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.162705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.126775 restraints weight = 58606.499| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.82 r_work: 0.3494 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 35185 Z= 0.192 Angle : 0.709 13.471 48020 Z= 0.353 Chirality : 0.048 0.488 5616 Planarity : 0.005 0.073 6041 Dihedral : 7.248 68.706 6233 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 5.58 % Allowed : 16.32 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.13), residues: 4205 helix: 1.13 (0.21), residues: 633 sheet: -0.31 (0.15), residues: 1198 loop : -1.66 (0.12), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1107 TYR 0.032 0.002 TYR H 105 PHE 0.034 0.002 PHE A 643 TRP 0.017 0.001 TRP L 149 HIS 0.010 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00447 (35056) covalent geometry : angle 0.68151 (47687) SS BOND : bond 0.00538 ( 54) SS BOND : angle 2.25798 ( 108) hydrogen bonds : bond 0.04051 ( 1215) hydrogen bonds : angle 6.03140 ( 3249) link_BETA1-4 : bond 0.00775 ( 36) link_BETA1-4 : angle 2.26461 ( 108) link_NAG-ASN : bond 0.00359 ( 39) link_NAG-ASN : angle 2.73416 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1070 residues out of total 3725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 862 time to evaluate : 1.317 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: H 7 SER cc_start: 0.6763 (t) cc_final: 0.6561 (m) REVERT: H 34 MET cc_start: 0.7577 (mmm) cc_final: 0.7129 (mmm) REVERT: H 70 SER cc_start: 0.8270 (t) cc_final: 0.7882 (p) REVERT: H 92 VAL cc_start: 0.8874 (t) cc_final: 0.8654 (p) REVERT: H 108 LEU cc_start: 0.7816 (tp) cc_final: 0.7525 (tp) REVERT: H 144 LEU cc_start: 0.6022 (OUTLIER) cc_final: 0.5648 (mt) REVERT: L 4 MET cc_start: 0.7304 (mmm) cc_final: 0.7071 (mmm) REVERT: L 71 PHE cc_start: 0.6617 (m-80) cc_final: 0.6128 (m-10) REVERT: L 79 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7422 (mp10) REVERT: L 89 GLN cc_start: 0.5946 (tt0) cc_final: 0.5532 (tt0) REVERT: L 94 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.6747 (mtt) REVERT: L 141 TYR cc_start: 0.7694 (t80) cc_final: 0.7157 (t80) REVERT: C 44 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.7866 (mtt-85) REVERT: C 105 ILE cc_start: 0.7949 (mm) cc_final: 0.7560 (tt) REVERT: C 129 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7514 (mtmm) REVERT: C 196 ASN cc_start: 0.7602 (t0) cc_final: 0.7330 (t0) REVERT: C 210 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.7213 (pt) REVERT: C 239 GLN cc_start: 0.7999 (tt0) cc_final: 0.7746 (pt0) REVERT: C 246 ARG cc_start: 0.6608 (OUTLIER) cc_final: 0.6129 (ppt90) REVERT: C 310 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8333 (ttpt) REVERT: C 409 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6581 (tp40) REVERT: C 424 LYS cc_start: 0.8101 (tttt) cc_final: 0.7869 (tttt) REVERT: C 428 ASP cc_start: 0.8040 (p0) cc_final: 0.7798 (p0) REVERT: C 559 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.8080 (t80) REVERT: C 586 ASP cc_start: 0.7893 (m-30) cc_final: 0.7555 (m-30) REVERT: C 603 ASN cc_start: 0.8366 (t0) cc_final: 0.8101 (t0) REVERT: C 663 ASP cc_start: 0.7387 (t0) cc_final: 0.7094 (t70) REVERT: C 703 ASN cc_start: 0.8727 (t0) cc_final: 0.8422 (t0) REVERT: C 707 TYR cc_start: 0.8131 (t80) cc_final: 0.7890 (t80) REVERT: C 740 MET cc_start: 0.7612 (ttp) cc_final: 0.7221 (tmm) REVERT: C 937 SER cc_start: 0.8002 (m) cc_final: 0.7751 (t) REVERT: C 955 ASN cc_start: 0.7669 (m110) cc_final: 0.7248 (m110) REVERT: C 1014 ARG cc_start: 0.8210 (ttp-170) cc_final: 0.7850 (mtp180) REVERT: C 1086 LYS cc_start: 0.8350 (ptpt) cc_final: 0.8003 (ptpp) REVERT: C 1118 ASP cc_start: 0.7793 (t0) cc_final: 0.7426 (t0) REVERT: C 1128 VAL cc_start: 0.8600 (m) cc_final: 0.8212 (p) REVERT: C 1139 ASP cc_start: 0.7856 (t0) cc_final: 0.7561 (t0) REVERT: C 1141 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7744 (pp) REVERT: B 51 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8272 (p) REVERT: B 133 PHE cc_start: 0.5269 (OUTLIER) cc_final: 0.4967 (p90) REVERT: B 134 GLN cc_start: 0.6825 (tp40) cc_final: 0.6576 (tp40) REVERT: B 135 PHE cc_start: 0.7050 (OUTLIER) cc_final: 0.6776 (m-80) REVERT: B 190 ARG cc_start: 0.7959 (mtp85) cc_final: 0.7671 (mtp180) REVERT: B 266 TYR cc_start: 0.8024 (m-80) cc_final: 0.7652 (m-80) REVERT: B 278 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8082 (ttpt) REVERT: B 281 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7311 (pp20) REVERT: B 312 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8212 (tt) REVERT: B 346 THR cc_start: 0.8343 (m) cc_final: 0.7998 (p) REVERT: B 386 LYS cc_start: 0.8570 (mmmm) cc_final: 0.7730 (mtpp) REVERT: B 390 LEU cc_start: 0.8753 (mm) cc_final: 0.8379 (mm) REVERT: B 428 ASP cc_start: 0.7907 (p0) cc_final: 0.7647 (p0) REVERT: B 453 TYR cc_start: 0.6825 (p90) cc_final: 0.5910 (p90) REVERT: B 454 ARG cc_start: 0.7585 (mmm-85) cc_final: 0.7131 (mmm-85) REVERT: B 493 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6856 (pp30) REVERT: B 558 LYS cc_start: 0.8055 (tptm) cc_final: 0.7706 (tptm) REVERT: B 588 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8436 (m) REVERT: B 620 VAL cc_start: 0.8508 (p) cc_final: 0.8288 (m) REVERT: B 759 PHE cc_start: 0.7695 (t80) cc_final: 0.7273 (t80) REVERT: B 764 LYS cc_start: 0.7981 (tppp) cc_final: 0.7566 (tppp) REVERT: B 776 LYS cc_start: 0.8294 (ttpt) cc_final: 0.7859 (tttp) REVERT: B 780 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7742 (mt-10) REVERT: B 856 ASN cc_start: 0.7902 (p0) cc_final: 0.7472 (p0) REVERT: B 918 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7755 (mt-10) REVERT: B 1017 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6895 (mm-30) REVERT: B 1073 LYS cc_start: 0.8416 (mtmt) cc_final: 0.8087 (mtpp) REVERT: B 1139 ASP cc_start: 0.7697 (t0) cc_final: 0.7477 (t0) REVERT: A 28 TYR cc_start: 0.7154 (m-80) cc_final: 0.6720 (m-80) REVERT: A 51 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8335 (p) REVERT: A 84 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6963 (mt) REVERT: A 138 ASP cc_start: 0.7554 (t0) cc_final: 0.7259 (t0) REVERT: A 170 TYR cc_start: 0.7666 (t80) cc_final: 0.7352 (t80) REVERT: A 190 ARG cc_start: 0.7213 (mtp85) cc_final: 0.6863 (ptp-170) REVERT: A 221 SER cc_start: 0.8343 (t) cc_final: 0.7890 (p) REVERT: A 237 ARG cc_start: 0.7830 (mtm110) cc_final: 0.7407 (mtp85) REVERT: A 244 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7202 (tm) REVERT: A 280 ASN cc_start: 0.7788 (m-40) cc_final: 0.7292 (m-40) REVERT: A 340 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7732 (mm-30) REVERT: A 347 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.8212 (t80) REVERT: A 357 ARG cc_start: 0.7541 (ttm110) cc_final: 0.7203 (ttm110) REVERT: A 386 LYS cc_start: 0.8613 (mttt) cc_final: 0.8162 (ptpp) REVERT: A 396 TYR cc_start: 0.7996 (m-80) cc_final: 0.7631 (m-80) REVERT: A 409 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6607 (tt0) REVERT: A 439 ASN cc_start: 0.8077 (t0) cc_final: 0.7785 (t0) REVERT: A 440 LYS cc_start: 0.8777 (mtmt) cc_final: 0.8414 (mtmt) REVERT: A 514 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8400 (p) REVERT: A 546 LEU cc_start: 0.8435 (tp) cc_final: 0.8057 (tt) REVERT: A 586 ASP cc_start: 0.7998 (t0) cc_final: 0.7643 (m-30) REVERT: A 646 ARG cc_start: 0.7642 (ttp-110) cc_final: 0.7441 (ttp-110) REVERT: A 658 ASN cc_start: 0.7486 (OUTLIER) cc_final: 0.6762 (p0) REVERT: A 740 MET cc_start: 0.8219 (tpt) cc_final: 0.7825 (tpp) REVERT: A 776 LYS cc_start: 0.8255 (ttpp) cc_final: 0.8018 (tttp) REVERT: A 780 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7502 (mt-10) REVERT: A 825 LYS cc_start: 0.8100 (ttmm) cc_final: 0.7891 (ttmm) REVERT: A 868 GLU cc_start: 0.7671 (mp0) cc_final: 0.7418 (mp0) REVERT: A 921 LYS cc_start: 0.8458 (mmmt) cc_final: 0.8069 (mmmt) REVERT: A 933 LYS cc_start: 0.8335 (mtmt) cc_final: 0.8094 (mtmt) REVERT: A 964 LYS cc_start: 0.8348 (tppt) cc_final: 0.7909 (mptt) REVERT: A 979 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7231 (m-30) REVERT: A 983 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7919 (ttm-80) REVERT: A 1005 GLN cc_start: 0.8194 (tp40) cc_final: 0.7772 (tp40) REVERT: A 1014 ARG cc_start: 0.7977 (mtm-85) cc_final: 0.7685 (mtm-85) REVERT: A 1041 ASP cc_start: 0.8223 (t0) cc_final: 0.7886 (t0) REVERT: A 1084 ASP cc_start: 0.7660 (t0) cc_final: 0.7108 (t0) REVERT: A 1094 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.8193 (m) REVERT: I 34 MET cc_start: 0.7220 (mmm) cc_final: 0.6885 (mmm) REVERT: I 39 GLN cc_start: 0.7435 (tt0) cc_final: 0.7007 (tt0) REVERT: I 47 TRP cc_start: 0.7514 (t60) cc_final: 0.7076 (t60) REVERT: I 62 SER cc_start: 0.7697 (m) cc_final: 0.7490 (p) REVERT: I 113 THR cc_start: 0.6209 (m) cc_final: 0.5957 (m) REVERT: I 181 LEU cc_start: 0.7885 (tp) cc_final: 0.7560 (tp) REVERT: M 3 GLN cc_start: 0.8039 (mp10) cc_final: 0.7778 (mp10) REVERT: M 27 GLN cc_start: 0.7946 (pm20) cc_final: 0.7706 (pm20) REVERT: M 33 LEU cc_start: 0.8131 (tt) cc_final: 0.7833 (tt) REVERT: M 38 GLN cc_start: 0.7745 (tp40) cc_final: 0.7209 (tp40) REVERT: M 71 PHE cc_start: 0.6719 (m-80) cc_final: 0.6298 (m-80) REVERT: M 79 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7787 (mp10) REVERT: M 94 MET cc_start: 0.7272 (mmt) cc_final: 0.6715 (mmm) REVERT: M 141 TYR cc_start: 0.6585 (t80) cc_final: 0.6309 (t80) REVERT: J 19 ARG cc_start: 0.6282 (tpp80) cc_final: 0.5626 (tpp80) REVERT: J 34 MET cc_start: 0.6937 (mmm) cc_final: 0.6648 (mmm) REVERT: J 70 SER cc_start: 0.8219 (t) cc_final: 0.7897 (p) REVERT: J 92 VAL cc_start: 0.8936 (t) cc_final: 0.8623 (p) REVERT: J 105 TYR cc_start: 0.8108 (p90) cc_final: 0.7767 (p90) REVERT: J 128 PHE cc_start: 0.5825 (m-80) cc_final: 0.5373 (m-80) REVERT: N 14 SER cc_start: 0.8211 (m) cc_final: 0.7855 (p) REVERT: N 33 LEU cc_start: 0.8006 (tt) cc_final: 0.7662 (tt) REVERT: N 71 PHE cc_start: 0.6532 (m-80) cc_final: 0.5948 (m-10) REVERT: N 79 GLN cc_start: 0.7923 (mp10) cc_final: 0.7441 (mp10) REVERT: N 85 THR cc_start: 0.7062 (m) cc_final: 0.6592 (p) REVERT: N 94 MET cc_start: 0.6950 (mmt) cc_final: 0.6573 (mmm) REVERT: N 104 ARG cc_start: 0.7292 (ttt90) cc_final: 0.6938 (ttt90) REVERT: N 106 GLU cc_start: 0.5654 (tm-30) cc_final: 0.4079 (tm-30) outliers start: 208 outliers final: 155 residues processed: 983 average time/residue: 0.2143 time to fit residues: 337.0953 Evaluate side-chains 1022 residues out of total 3725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 840 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 150 LYS Chi-restraints excluded: chain M residue 195 CYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 88 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 326 optimal weight: 0.9990 chunk 182 optimal weight: 10.0000 chunk 218 optimal weight: 0.8980 chunk 227 optimal weight: 0.6980 chunk 274 optimal weight: 0.7980 chunk 172 optimal weight: 0.5980 chunk 10 optimal weight: 0.2980 chunk 65 optimal weight: 0.2980 chunk 348 optimal weight: 1.9990 chunk 289 optimal weight: 1.9990 chunk 287 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 ASN C 339 HIS C 532 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A 125 ASN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 564 GLN A 914 ASN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.162165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.125950 restraints weight = 58282.677| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.85 r_work: 0.3486 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 35185 Z= 0.208 Angle : 0.729 13.998 48020 Z= 0.363 Chirality : 0.049 0.528 5616 Planarity : 0.005 0.075 6041 Dihedral : 7.262 68.797 6232 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 5.48 % Allowed : 16.78 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.13), residues: 4205 helix: 1.15 (0.21), residues: 633 sheet: -0.34 (0.15), residues: 1196 loop : -1.65 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 19 TYR 0.033 0.002 TYR I 105 PHE 0.035 0.002 PHE A 643 TRP 0.037 0.002 TRP L 149 HIS 0.010 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00485 (35056) covalent geometry : angle 0.70204 (47687) SS BOND : bond 0.00548 ( 54) SS BOND : angle 2.42938 ( 108) hydrogen bonds : bond 0.04085 ( 1215) hydrogen bonds : angle 5.99515 ( 3249) link_BETA1-4 : bond 0.00775 ( 36) link_BETA1-4 : angle 2.24457 ( 108) link_NAG-ASN : bond 0.00380 ( 39) link_NAG-ASN : angle 2.64571 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1054 residues out of total 3725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 850 time to evaluate : 1.264 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: H 34 MET cc_start: 0.7606 (mmm) cc_final: 0.7166 (mmm) REVERT: H 70 SER cc_start: 0.8227 (t) cc_final: 0.7860 (p) REVERT: H 92 VAL cc_start: 0.8847 (t) cc_final: 0.8635 (p) REVERT: H 108 LEU cc_start: 0.7812 (tp) cc_final: 0.7524 (tp) REVERT: H 144 LEU cc_start: 0.6002 (OUTLIER) cc_final: 0.5656 (mt) REVERT: L 4 MET cc_start: 0.7373 (mmm) cc_final: 0.7165 (mmm) REVERT: L 71 PHE cc_start: 0.6625 (m-80) cc_final: 0.6147 (m-10) REVERT: L 89 GLN cc_start: 0.6038 (tt0) cc_final: 0.5606 (tt0) REVERT: L 94 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6798 (mtt) REVERT: L 141 TYR cc_start: 0.7672 (t80) cc_final: 0.7119 (t80) REVERT: C 44 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.7825 (mtt180) REVERT: C 96 GLU cc_start: 0.7226 (pt0) cc_final: 0.7018 (pm20) REVERT: C 105 ILE cc_start: 0.7959 (mm) cc_final: 0.7569 (tt) REVERT: C 129 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7531 (mtmm) REVERT: C 196 ASN cc_start: 0.7626 (t0) cc_final: 0.7358 (t0) REVERT: C 210 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.7212 (pt) REVERT: C 239 GLN cc_start: 0.7994 (tt0) cc_final: 0.7724 (tt0) REVERT: C 246 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.6106 (ppt90) REVERT: C 310 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8353 (ttpt) REVERT: C 409 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6579 (tp-100) REVERT: C 424 LYS cc_start: 0.8114 (tttt) cc_final: 0.7872 (tttt) REVERT: C 428 ASP cc_start: 0.8045 (p0) cc_final: 0.7826 (p0) REVERT: C 442 ASP cc_start: 0.7256 (m-30) cc_final: 0.6964 (p0) REVERT: C 559 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.8022 (t80) REVERT: C 586 ASP cc_start: 0.7913 (m-30) cc_final: 0.7565 (m-30) REVERT: C 603 ASN cc_start: 0.8372 (t0) cc_final: 0.8111 (t0) REVERT: C 703 ASN cc_start: 0.8720 (t0) cc_final: 0.8421 (t0) REVERT: C 707 TYR cc_start: 0.8175 (t80) cc_final: 0.7925 (t80) REVERT: C 740 MET cc_start: 0.7625 (ttp) cc_final: 0.7261 (ttp) REVERT: C 937 SER cc_start: 0.8031 (m) cc_final: 0.7786 (t) REVERT: C 955 ASN cc_start: 0.7693 (m110) cc_final: 0.7274 (m110) REVERT: C 1014 ARG cc_start: 0.8216 (ttp-170) cc_final: 0.7853 (mtp180) REVERT: C 1086 LYS cc_start: 0.8334 (ptpt) cc_final: 0.7983 (ptpp) REVERT: C 1128 VAL cc_start: 0.8621 (m) cc_final: 0.8243 (p) REVERT: C 1139 ASP cc_start: 0.7859 (t0) cc_final: 0.7558 (t0) REVERT: C 1141 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7756 (pp) REVERT: B 51 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8276 (p) REVERT: B 133 PHE cc_start: 0.5467 (OUTLIER) cc_final: 0.5204 (p90) REVERT: B 134 GLN cc_start: 0.6871 (tp40) cc_final: 0.6629 (tp40) REVERT: B 190 ARG cc_start: 0.7969 (mtp85) cc_final: 0.7672 (mtp180) REVERT: B 213 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6591 (pm20) REVERT: B 237 ARG cc_start: 0.8017 (tpp80) cc_final: 0.7573 (mmm-85) REVERT: B 266 TYR cc_start: 0.8025 (m-80) cc_final: 0.7663 (m-80) REVERT: B 278 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8084 (ttpt) REVERT: B 281 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7350 (pp20) REVERT: B 312 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8209 (tt) REVERT: B 346 THR cc_start: 0.8371 (m) cc_final: 0.8018 (p) REVERT: B 386 LYS cc_start: 0.8569 (mmmm) cc_final: 0.7742 (mtpp) REVERT: B 390 LEU cc_start: 0.8770 (mm) cc_final: 0.8405 (mm) REVERT: B 428 ASP cc_start: 0.7908 (p0) cc_final: 0.7657 (p0) REVERT: B 436 TRP cc_start: 0.8178 (p90) cc_final: 0.7937 (p90) REVERT: B 454 ARG cc_start: 0.7587 (mmm-85) cc_final: 0.7302 (mmm-85) REVERT: B 558 LYS cc_start: 0.8050 (tptm) cc_final: 0.7707 (tptm) REVERT: B 588 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8438 (m) REVERT: B 620 VAL cc_start: 0.8467 (p) cc_final: 0.8250 (m) REVERT: B 759 PHE cc_start: 0.7736 (t80) cc_final: 0.7315 (t80) REVERT: B 764 LYS cc_start: 0.8006 (tppp) cc_final: 0.7595 (tppp) REVERT: B 776 LYS cc_start: 0.8272 (ttpt) cc_final: 0.7847 (tttp) REVERT: B 780 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7746 (mt-10) REVERT: B 856 ASN cc_start: 0.7905 (p0) cc_final: 0.7475 (p0) REVERT: B 918 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7771 (mt-10) REVERT: B 1017 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6925 (mm-30) REVERT: B 1073 LYS cc_start: 0.8427 (mtmt) cc_final: 0.8100 (mtpp) REVERT: A 28 TYR cc_start: 0.7129 (m-80) cc_final: 0.6705 (m-80) REVERT: A 51 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8326 (p) REVERT: A 138 ASP cc_start: 0.7563 (t0) cc_final: 0.7269 (t0) REVERT: A 170 TYR cc_start: 0.7693 (t80) cc_final: 0.7383 (t80) REVERT: A 190 ARG cc_start: 0.7230 (mtp85) cc_final: 0.6887 (ptp-170) REVERT: A 221 SER cc_start: 0.8361 (t) cc_final: 0.7907 (p) REVERT: A 237 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7472 (mtp85) REVERT: A 244 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7203 (tm) REVERT: A 280 ASN cc_start: 0.7801 (m-40) cc_final: 0.7282 (m-40) REVERT: A 340 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7728 (mm-30) REVERT: A 347 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.8198 (t80) REVERT: A 357 ARG cc_start: 0.7596 (ttm110) cc_final: 0.7290 (ttm110) REVERT: A 365 TYR cc_start: 0.7503 (m-80) cc_final: 0.7228 (m-80) REVERT: A 386 LYS cc_start: 0.8593 (mttt) cc_final: 0.8133 (ptpp) REVERT: A 396 TYR cc_start: 0.7975 (m-80) cc_final: 0.7643 (m-80) REVERT: A 409 GLN cc_start: 0.7053 (OUTLIER) cc_final: 0.6626 (tt0) REVERT: A 439 ASN cc_start: 0.8038 (t0) cc_final: 0.7761 (t0) REVERT: A 440 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8410 (mtmt) REVERT: A 514 SER cc_start: 0.8746 (OUTLIER) cc_final: 0.8319 (p) REVERT: A 546 LEU cc_start: 0.8348 (tp) cc_final: 0.8106 (tt) REVERT: A 586 ASP cc_start: 0.8003 (t0) cc_final: 0.7665 (m-30) REVERT: A 603 ASN cc_start: 0.8174 (t0) cc_final: 0.7870 (t0) REVERT: A 645 THR cc_start: 0.8202 (m) cc_final: 0.7967 (m) REVERT: A 646 ARG cc_start: 0.7694 (ttp-110) cc_final: 0.7440 (ttp-110) REVERT: A 658 ASN cc_start: 0.7482 (OUTLIER) cc_final: 0.6755 (p0) REVERT: A 740 MET cc_start: 0.8235 (tpt) cc_final: 0.7639 (tpp) REVERT: A 776 LYS cc_start: 0.8255 (ttpp) cc_final: 0.8010 (tttp) REVERT: A 780 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7506 (mt-10) REVERT: A 825 LYS cc_start: 0.8100 (ttmm) cc_final: 0.7881 (ttmm) REVERT: A 921 LYS cc_start: 0.8460 (mmmt) cc_final: 0.8071 (mmmt) REVERT: A 933 LYS cc_start: 0.8293 (mtmt) cc_final: 0.8060 (mtmt) REVERT: A 964 LYS cc_start: 0.8370 (tppt) cc_final: 0.7934 (mptt) REVERT: A 979 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7237 (m-30) REVERT: A 983 ARG cc_start: 0.8248 (ttm-80) cc_final: 0.7916 (ttm-80) REVERT: A 1005 GLN cc_start: 0.8199 (tp40) cc_final: 0.7717 (tp40) REVERT: A 1041 ASP cc_start: 0.8232 (t0) cc_final: 0.7882 (t0) REVERT: A 1084 ASP cc_start: 0.7676 (t0) cc_final: 0.7119 (t0) REVERT: A 1094 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8195 (m) REVERT: I 34 MET cc_start: 0.7261 (mmm) cc_final: 0.6880 (mmm) REVERT: I 39 GLN cc_start: 0.7381 (tt0) cc_final: 0.7032 (tt0) REVERT: I 47 TRP cc_start: 0.7525 (t60) cc_final: 0.7107 (t60) REVERT: I 113 THR cc_start: 0.6190 (m) cc_final: 0.5938 (m) REVERT: I 181 LEU cc_start: 0.7953 (tp) cc_final: 0.7628 (tp) REVERT: M 3 GLN cc_start: 0.8082 (mp10) cc_final: 0.7822 (mp10) REVERT: M 27 GLN cc_start: 0.7964 (pm20) cc_final: 0.7709 (pm20) REVERT: M 33 LEU cc_start: 0.8122 (tt) cc_final: 0.7792 (tt) REVERT: M 38 GLN cc_start: 0.7681 (tp40) cc_final: 0.7359 (tp40) REVERT: M 71 PHE cc_start: 0.6697 (m-80) cc_final: 0.6216 (m-10) REVERT: M 94 MET cc_start: 0.7361 (mmt) cc_final: 0.6999 (mmm) REVERT: J 34 MET cc_start: 0.6996 (mmm) cc_final: 0.6659 (mmm) REVERT: J 70 SER cc_start: 0.8178 (t) cc_final: 0.7872 (p) REVERT: J 92 VAL cc_start: 0.8961 (t) cc_final: 0.8633 (p) REVERT: J 105 TYR cc_start: 0.8106 (p90) cc_final: 0.7766 (p90) REVERT: N 14 SER cc_start: 0.8201 (m) cc_final: 0.7835 (p) REVERT: N 33 LEU cc_start: 0.8012 (tt) cc_final: 0.7679 (tt) REVERT: N 71 PHE cc_start: 0.6527 (m-80) cc_final: 0.5961 (m-10) REVERT: N 79 GLN cc_start: 0.7917 (mp10) cc_final: 0.7414 (mp10) REVERT: N 85 THR cc_start: 0.7055 (m) cc_final: 0.6554 (p) REVERT: N 94 MET cc_start: 0.7008 (mmt) cc_final: 0.6627 (mmm) REVERT: N 104 ARG cc_start: 0.7187 (ttt90) cc_final: 0.6845 (ttt90) REVERT: N 106 GLU cc_start: 0.5646 (tm-30) cc_final: 0.4125 (tm-30) outliers start: 204 outliers final: 152 residues processed: 972 average time/residue: 0.2308 time to fit residues: 357.8643 Evaluate side-chains 1011 residues out of total 3725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 834 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 150 LYS Chi-restraints excluded: chain M residue 195 CYS Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 88 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 216 optimal weight: 0.3980 chunk 287 optimal weight: 0.6980 chunk 172 optimal weight: 0.9980 chunk 269 optimal weight: 0.9980 chunk 185 optimal weight: 0.7980 chunk 308 optimal weight: 0.5980 chunk 387 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 110 optimal weight: 0.0970 chunk 156 optimal weight: 0.9990 chunk 288 optimal weight: 0.2980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 HIS C 360 ASN C 532 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A 280 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.162287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.126009 restraints weight = 58383.132| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.86 r_work: 0.3495 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 35185 Z= 0.179 Angle : 0.726 14.595 48020 Z= 0.362 Chirality : 0.048 0.479 5616 Planarity : 0.005 0.072 6041 Dihedral : 7.221 69.175 6232 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 5.10 % Allowed : 17.61 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.13), residues: 4205 helix: 1.21 (0.21), residues: 633 sheet: -0.28 (0.15), residues: 1173 loop : -1.63 (0.12), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 357 TYR 0.032 0.002 TYR H 105 PHE 0.037 0.002 PHE A 643 TRP 0.025 0.002 TRP L 149 HIS 0.011 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00419 (35056) covalent geometry : angle 0.70080 (47687) SS BOND : bond 0.00527 ( 54) SS BOND : angle 2.28363 ( 108) hydrogen bonds : bond 0.03950 ( 1215) hydrogen bonds : angle 5.93731 ( 3249) link_BETA1-4 : bond 0.00768 ( 36) link_BETA1-4 : angle 2.19473 ( 108) link_NAG-ASN : bond 0.00329 ( 39) link_NAG-ASN : angle 2.62625 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 3725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 834 time to evaluate : 1.354 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: H 34 MET cc_start: 0.7641 (mmm) cc_final: 0.7194 (mmm) REVERT: H 70 SER cc_start: 0.8179 (t) cc_final: 0.7821 (p) REVERT: H 108 LEU cc_start: 0.7797 (tp) cc_final: 0.7507 (tp) REVERT: H 144 LEU cc_start: 0.5877 (OUTLIER) cc_final: 0.5536 (mt) REVERT: L 4 MET cc_start: 0.7366 (mmm) cc_final: 0.7157 (mmm) REVERT: L 6 GLN cc_start: 0.6760 (mt0) cc_final: 0.6468 (pt0) REVERT: L 71 PHE cc_start: 0.6574 (m-80) cc_final: 0.6145 (m-10) REVERT: L 89 GLN cc_start: 0.5994 (tt0) cc_final: 0.5561 (tt0) REVERT: L 94 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.6923 (mtt) REVERT: C 34 ARG cc_start: 0.7308 (mtp85) cc_final: 0.6899 (mtt-85) REVERT: C 44 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.7825 (mtt-85) REVERT: C 105 ILE cc_start: 0.7947 (mm) cc_final: 0.7555 (tt) REVERT: C 129 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7514 (mtmm) REVERT: C 196 ASN cc_start: 0.7598 (t0) cc_final: 0.7299 (t0) REVERT: C 239 GLN cc_start: 0.7989 (tt0) cc_final: 0.7740 (tt0) REVERT: C 246 ARG cc_start: 0.6569 (OUTLIER) cc_final: 0.6101 (ppt90) REVERT: C 298 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: C 310 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8347 (ttpt) REVERT: C 406 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6602 (mm-30) REVERT: C 409 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6587 (tp-100) REVERT: C 424 LYS cc_start: 0.8099 (tttt) cc_final: 0.7868 (tttt) REVERT: C 428 ASP cc_start: 0.8057 (p0) cc_final: 0.7727 (p0) REVERT: C 442 ASP cc_start: 0.7254 (m-30) cc_final: 0.7012 (p0) REVERT: C 495 TYR cc_start: 0.6968 (t80) cc_final: 0.6555 (t80) REVERT: C 559 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8042 (t80) REVERT: C 586 ASP cc_start: 0.7908 (m-30) cc_final: 0.7544 (m-30) REVERT: C 603 ASN cc_start: 0.8356 (t0) cc_final: 0.8094 (t0) REVERT: C 702 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7148 (mm-30) REVERT: C 703 ASN cc_start: 0.8704 (t0) cc_final: 0.8363 (t0) REVERT: C 707 TYR cc_start: 0.8169 (t80) cc_final: 0.7939 (t80) REVERT: C 740 MET cc_start: 0.7611 (ttp) cc_final: 0.7235 (ttp) REVERT: C 937 SER cc_start: 0.7996 (m) cc_final: 0.7771 (t) REVERT: C 955 ASN cc_start: 0.7656 (m110) cc_final: 0.7224 (m110) REVERT: C 1014 ARG cc_start: 0.8249 (ttp-170) cc_final: 0.7887 (mtp180) REVERT: C 1086 LYS cc_start: 0.8300 (ptpt) cc_final: 0.7953 (ptpp) REVERT: C 1127 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7211 (t0) REVERT: C 1128 VAL cc_start: 0.8619 (m) cc_final: 0.8245 (p) REVERT: C 1139 ASP cc_start: 0.7877 (t0) cc_final: 0.7566 (t0) REVERT: C 1141 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7746 (pp) REVERT: B 51 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8272 (p) REVERT: B 133 PHE cc_start: 0.5481 (OUTLIER) cc_final: 0.5223 (p90) REVERT: B 134 GLN cc_start: 0.6890 (tp40) cc_final: 0.6640 (tp40) REVERT: B 190 ARG cc_start: 0.7968 (mtp85) cc_final: 0.7664 (mtp180) REVERT: B 213 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6599 (pm20) REVERT: B 237 ARG cc_start: 0.7996 (tpp80) cc_final: 0.7538 (mmm-85) REVERT: B 266 TYR cc_start: 0.8021 (m-80) cc_final: 0.7623 (m-80) REVERT: B 278 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8084 (ttpt) REVERT: B 281 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7315 (pp20) REVERT: B 312 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8198 (tt) REVERT: B 346 THR cc_start: 0.8375 (m) cc_final: 0.8067 (p) REVERT: B 353 TRP cc_start: 0.7936 (p90) cc_final: 0.7491 (p90) REVERT: B 386 LYS cc_start: 0.8583 (mmmm) cc_final: 0.7757 (mtpp) REVERT: B 390 LEU cc_start: 0.8750 (mm) cc_final: 0.8385 (mm) REVERT: B 428 ASP cc_start: 0.7886 (p0) cc_final: 0.7641 (p0) REVERT: B 454 ARG cc_start: 0.7574 (mmm-85) cc_final: 0.7283 (mmm-85) REVERT: B 508 TYR cc_start: 0.6982 (m-80) cc_final: 0.6514 (m-80) REVERT: B 558 LYS cc_start: 0.8035 (tptm) cc_final: 0.7697 (tptm) REVERT: B 588 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8432 (m) REVERT: B 751 ASN cc_start: 0.7909 (p0) cc_final: 0.7512 (p0) REVERT: B 759 PHE cc_start: 0.7708 (t80) cc_final: 0.7318 (t80) REVERT: B 764 LYS cc_start: 0.7988 (tppp) cc_final: 0.7583 (tppp) REVERT: B 776 LYS cc_start: 0.8291 (ttpt) cc_final: 0.7858 (tttp) REVERT: B 780 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7750 (mt-10) REVERT: B 856 ASN cc_start: 0.7896 (p0) cc_final: 0.7454 (p0) REVERT: B 918 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7743 (mt-10) REVERT: B 933 LYS cc_start: 0.8264 (mtmm) cc_final: 0.8062 (mtmm) REVERT: B 1017 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6901 (mm-30) REVERT: B 1073 LYS cc_start: 0.8420 (mtmt) cc_final: 0.8079 (mtpp) REVERT: B 1107 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7267 (mtp180) REVERT: A 28 TYR cc_start: 0.7113 (m-80) cc_final: 0.6669 (m-80) REVERT: A 51 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8323 (p) REVERT: A 84 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6981 (mt) REVERT: A 138 ASP cc_start: 0.7562 (t0) cc_final: 0.7270 (t0) REVERT: A 153 MET cc_start: 0.7678 (mtm) cc_final: 0.7390 (ttp) REVERT: A 170 TYR cc_start: 0.7671 (t80) cc_final: 0.7368 (t80) REVERT: A 190 ARG cc_start: 0.7218 (mtp85) cc_final: 0.6864 (ptp-170) REVERT: A 221 SER cc_start: 0.8356 (t) cc_final: 0.7912 (p) REVERT: A 237 ARG cc_start: 0.7797 (mtm110) cc_final: 0.7472 (mtp85) REVERT: A 244 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7157 (tm) REVERT: A 280 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.7416 (m110) REVERT: A 340 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7705 (mm-30) REVERT: A 347 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.8154 (t80) REVERT: A 357 ARG cc_start: 0.7583 (ttm110) cc_final: 0.7275 (ttm110) REVERT: A 365 TYR cc_start: 0.7470 (m-80) cc_final: 0.7167 (m-80) REVERT: A 386 LYS cc_start: 0.8589 (mttt) cc_final: 0.8110 (ptpp) REVERT: A 396 TYR cc_start: 0.7987 (m-80) cc_final: 0.7660 (m-80) REVERT: A 409 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.6599 (tt0) REVERT: A 439 ASN cc_start: 0.8056 (t0) cc_final: 0.7771 (t0) REVERT: A 440 LYS cc_start: 0.8759 (mtmt) cc_final: 0.8403 (mtmt) REVERT: A 514 SER cc_start: 0.8801 (OUTLIER) cc_final: 0.8391 (p) REVERT: A 542 ASN cc_start: 0.8265 (t0) cc_final: 0.8001 (t0) REVERT: A 546 LEU cc_start: 0.8343 (tp) cc_final: 0.8088 (tt) REVERT: A 586 ASP cc_start: 0.8012 (t0) cc_final: 0.7676 (m-30) REVERT: A 603 ASN cc_start: 0.8173 (t0) cc_final: 0.7870 (t0) REVERT: A 646 ARG cc_start: 0.7684 (ttp-110) cc_final: 0.7475 (ttp-110) REVERT: A 658 ASN cc_start: 0.7535 (OUTLIER) cc_final: 0.6788 (p0) REVERT: A 740 MET cc_start: 0.8212 (tpt) cc_final: 0.7628 (tpp) REVERT: A 825 LYS cc_start: 0.8086 (ttmm) cc_final: 0.7873 (ttmm) REVERT: A 868 GLU cc_start: 0.7651 (mp0) cc_final: 0.7428 (mp0) REVERT: A 902 MET cc_start: 0.8537 (tpt) cc_final: 0.8289 (mmt) REVERT: A 921 LYS cc_start: 0.8452 (mmmt) cc_final: 0.8065 (mmmt) REVERT: A 933 LYS cc_start: 0.8292 (mtmt) cc_final: 0.8048 (mtmt) REVERT: A 964 LYS cc_start: 0.8363 (tppt) cc_final: 0.7936 (mptt) REVERT: A 979 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7255 (m-30) REVERT: A 983 ARG cc_start: 0.8253 (ttm-80) cc_final: 0.7919 (ttm-80) REVERT: A 1005 GLN cc_start: 0.8198 (tp40) cc_final: 0.7777 (tp40) REVERT: A 1041 ASP cc_start: 0.8232 (t0) cc_final: 0.7893 (t0) REVERT: A 1084 ASP cc_start: 0.7673 (t0) cc_final: 0.7101 (t0) REVERT: A 1094 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8188 (m) REVERT: I 34 MET cc_start: 0.7264 (mmm) cc_final: 0.6897 (mmm) REVERT: I 39 GLN cc_start: 0.7339 (tt0) cc_final: 0.7030 (tt0) REVERT: I 47 TRP cc_start: 0.7527 (t60) cc_final: 0.7131 (t60) REVERT: I 113 THR cc_start: 0.6153 (m) cc_final: 0.5890 (m) REVERT: I 181 LEU cc_start: 0.8007 (tp) cc_final: 0.7691 (tp) REVERT: M 33 LEU cc_start: 0.8088 (tt) cc_final: 0.7869 (tt) REVERT: M 71 PHE cc_start: 0.6562 (m-80) cc_final: 0.6275 (m-80) REVERT: M 79 GLN cc_start: 0.6554 (mp10) cc_final: 0.6211 (mp10) REVERT: M 85 THR cc_start: 0.6916 (OUTLIER) cc_final: 0.6628 (t) REVERT: M 86 TYR cc_start: 0.8137 (m-10) cc_final: 0.7816 (m-10) REVERT: M 94 MET cc_start: 0.7341 (mmt) cc_final: 0.6992 (mmm) REVERT: J 34 MET cc_start: 0.6979 (mmm) cc_final: 0.6629 (mmm) REVERT: J 70 SER cc_start: 0.8188 (t) cc_final: 0.7877 (p) REVERT: J 92 VAL cc_start: 0.8960 (t) cc_final: 0.8631 (p) REVERT: J 105 TYR cc_start: 0.8111 (p90) cc_final: 0.7714 (p90) REVERT: J 128 PHE cc_start: 0.5492 (m-80) cc_final: 0.4882 (m-10) REVERT: N 14 SER cc_start: 0.8127 (m) cc_final: 0.7742 (p) REVERT: N 33 LEU cc_start: 0.7954 (tt) cc_final: 0.7637 (tt) REVERT: N 71 PHE cc_start: 0.6508 (m-80) cc_final: 0.5957 (m-10) REVERT: N 79 GLN cc_start: 0.7859 (mp10) cc_final: 0.7360 (mp10) REVERT: N 85 THR cc_start: 0.7055 (m) cc_final: 0.6601 (p) REVERT: N 94 MET cc_start: 0.7019 (mmt) cc_final: 0.6660 (mmm) REVERT: N 104 ARG cc_start: 0.7178 (ttt90) cc_final: 0.6854 (ttt90) REVERT: N 106 GLU cc_start: 0.5657 (tm-30) cc_final: 0.4249 (tm-30) outliers start: 190 outliers final: 144 residues processed: 948 average time/residue: 0.2318 time to fit residues: 350.1226 Evaluate side-chains 1003 residues out of total 3725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 829 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 150 LYS Chi-restraints excluded: chain M residue 195 CYS Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 88 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 174 optimal weight: 0.6980 chunk 144 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 203 optimal weight: 0.0970 chunk 155 optimal weight: 0.9990 chunk 286 optimal weight: 0.5980 chunk 213 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 282 optimal weight: 0.4980 chunk 271 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 HIS C 532 ASN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A 280 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN A 564 GLN A 907 ASN A 914 ASN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1119 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.162229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.125994 restraints weight = 58474.792| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.87 r_work: 0.3482 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 35185 Z= 0.200 Angle : 0.732 15.123 48020 Z= 0.366 Chirality : 0.048 0.462 5616 Planarity : 0.005 0.075 6041 Dihedral : 7.218 69.208 6230 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 5.05 % Allowed : 17.83 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.13), residues: 4205 helix: 1.23 (0.21), residues: 633 sheet: -0.35 (0.15), residues: 1184 loop : -1.62 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 357 TYR 0.039 0.002 TYR M 141 PHE 0.035 0.002 PHE A 643 TRP 0.026 0.002 TRP L 149 HIS 0.012 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00465 (35056) covalent geometry : angle 0.70767 (47687) SS BOND : bond 0.00545 ( 54) SS BOND : angle 2.24330 ( 108) hydrogen bonds : bond 0.03989 ( 1215) hydrogen bonds : angle 5.89971 ( 3249) link_BETA1-4 : bond 0.00753 ( 36) link_BETA1-4 : angle 2.18579 ( 108) link_NAG-ASN : bond 0.00362 ( 39) link_NAG-ASN : angle 2.59136 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 3725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 834 time to evaluate : 1.442 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: H 34 MET cc_start: 0.7658 (mmm) cc_final: 0.7215 (mmm) REVERT: H 70 SER cc_start: 0.8161 (t) cc_final: 0.7799 (p) REVERT: H 108 LEU cc_start: 0.7804 (tp) cc_final: 0.7519 (tp) REVERT: H 144 LEU cc_start: 0.5887 (OUTLIER) cc_final: 0.5566 (mt) REVERT: L 6 GLN cc_start: 0.6776 (mt0) cc_final: 0.6497 (pt0) REVERT: L 71 PHE cc_start: 0.6598 (m-80) cc_final: 0.6166 (m-10) REVERT: L 79 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7354 (mp10) REVERT: L 89 GLN cc_start: 0.6006 (tt0) cc_final: 0.5611 (tt0) REVERT: L 94 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.6819 (mtt) REVERT: C 44 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.7825 (mtt-85) REVERT: C 105 ILE cc_start: 0.7991 (mm) cc_final: 0.7601 (tt) REVERT: C 129 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7515 (mtmm) REVERT: C 196 ASN cc_start: 0.7628 (t0) cc_final: 0.7334 (t0) REVERT: C 221 SER cc_start: 0.8082 (m) cc_final: 0.7865 (p) REVERT: C 239 GLN cc_start: 0.7996 (tt0) cc_final: 0.7748 (tt0) REVERT: C 246 ARG cc_start: 0.6570 (OUTLIER) cc_final: 0.6091 (ppt90) REVERT: C 298 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: C 310 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8371 (ttpt) REVERT: C 321 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8408 (mm-40) REVERT: C 406 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6636 (mm-30) REVERT: C 409 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6602 (tp40) REVERT: C 424 LYS cc_start: 0.8105 (tttt) cc_final: 0.7865 (tttt) REVERT: C 428 ASP cc_start: 0.8090 (p0) cc_final: 0.7766 (p0) REVERT: C 442 ASP cc_start: 0.7251 (m-30) cc_final: 0.7019 (p0) REVERT: C 559 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8049 (t80) REVERT: C 586 ASP cc_start: 0.7916 (m-30) cc_final: 0.7554 (m-30) REVERT: C 603 ASN cc_start: 0.8377 (t0) cc_final: 0.8119 (t0) REVERT: C 703 ASN cc_start: 0.8703 (t0) cc_final: 0.8392 (t0) REVERT: C 707 TYR cc_start: 0.8185 (t80) cc_final: 0.7953 (t80) REVERT: C 740 MET cc_start: 0.7639 (ttp) cc_final: 0.7430 (ttt) REVERT: C 773 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7514 (tm-30) REVERT: C 937 SER cc_start: 0.7965 (m) cc_final: 0.7743 (t) REVERT: C 955 ASN cc_start: 0.7667 (m110) cc_final: 0.7208 (m110) REVERT: C 1014 ARG cc_start: 0.8247 (ttp-170) cc_final: 0.7869 (mtp180) REVERT: C 1086 LYS cc_start: 0.8293 (ptpt) cc_final: 0.7944 (ptpp) REVERT: C 1127 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7206 (t0) REVERT: C 1128 VAL cc_start: 0.8623 (m) cc_final: 0.8252 (p) REVERT: C 1139 ASP cc_start: 0.7880 (t0) cc_final: 0.7561 (t0) REVERT: C 1141 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7714 (pp) REVERT: B 51 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8275 (p) REVERT: B 133 PHE cc_start: 0.5666 (OUTLIER) cc_final: 0.5416 (p90) REVERT: B 134 GLN cc_start: 0.6923 (tp40) cc_final: 0.6682 (tp40) REVERT: B 190 ARG cc_start: 0.7968 (mtp85) cc_final: 0.7646 (mtp180) REVERT: B 213 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6583 (pm20) REVERT: B 237 ARG cc_start: 0.7991 (tpp80) cc_final: 0.7528 (mmm-85) REVERT: B 266 TYR cc_start: 0.7978 (m-80) cc_final: 0.7595 (m-80) REVERT: B 278 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8094 (ttpt) REVERT: B 281 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7379 (pp20) REVERT: B 312 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8203 (tt) REVERT: B 346 THR cc_start: 0.8389 (m) cc_final: 0.8091 (p) REVERT: B 386 LYS cc_start: 0.8592 (mmmm) cc_final: 0.7759 (mtpp) REVERT: B 390 LEU cc_start: 0.8763 (mm) cc_final: 0.8408 (mm) REVERT: B 428 ASP cc_start: 0.7907 (p0) cc_final: 0.7664 (p0) REVERT: B 454 ARG cc_start: 0.7575 (mmm-85) cc_final: 0.7288 (mmm-85) REVERT: B 508 TYR cc_start: 0.7110 (m-80) cc_final: 0.6533 (m-80) REVERT: B 558 LYS cc_start: 0.8033 (tptm) cc_final: 0.7687 (tptm) REVERT: B 588 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8434 (m) REVERT: B 759 PHE cc_start: 0.7726 (t80) cc_final: 0.7381 (t80) REVERT: B 764 LYS cc_start: 0.8000 (tppp) cc_final: 0.7592 (tppp) REVERT: B 776 LYS cc_start: 0.8286 (ttpt) cc_final: 0.7851 (tttp) REVERT: B 780 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7742 (mt-10) REVERT: B 856 ASN cc_start: 0.7891 (p0) cc_final: 0.7462 (p0) REVERT: B 868 GLU cc_start: 0.7720 (mp0) cc_final: 0.7418 (mp0) REVERT: B 918 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7743 (mt-10) REVERT: B 933 LYS cc_start: 0.8266 (mtmm) cc_final: 0.8057 (mtmm) REVERT: B 1017 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6907 (mm-30) REVERT: B 1073 LYS cc_start: 0.8418 (mtmt) cc_final: 0.8074 (mtpp) REVERT: B 1107 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7427 (mtt180) REVERT: B 1139 ASP cc_start: 0.7650 (t0) cc_final: 0.7427 (t0) REVERT: A 28 TYR cc_start: 0.7141 (m-80) cc_final: 0.6701 (m-80) REVERT: A 51 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8318 (p) REVERT: A 84 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6996 (mt) REVERT: A 138 ASP cc_start: 0.7578 (t0) cc_final: 0.7285 (t0) REVERT: A 170 TYR cc_start: 0.7676 (t80) cc_final: 0.7255 (t80) REVERT: A 190 ARG cc_start: 0.7224 (mtp85) cc_final: 0.6872 (ptp-170) REVERT: A 221 SER cc_start: 0.8318 (t) cc_final: 0.7877 (p) REVERT: A 237 ARG cc_start: 0.7824 (mtm110) cc_final: 0.7488 (mtp85) REVERT: A 244 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7103 (tm) REVERT: A 280 ASN cc_start: 0.7736 (OUTLIER) cc_final: 0.7392 (m110) REVERT: A 347 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.8148 (t80) REVERT: A 357 ARG cc_start: 0.7602 (ttm110) cc_final: 0.7300 (ttm110) REVERT: A 365 TYR cc_start: 0.7512 (m-80) cc_final: 0.7205 (m-80) REVERT: A 409 GLN cc_start: 0.7074 (OUTLIER) cc_final: 0.6641 (tt0) REVERT: A 439 ASN cc_start: 0.8113 (t0) cc_final: 0.7829 (t0) REVERT: A 440 LYS cc_start: 0.8779 (mtmt) cc_final: 0.8409 (mtmt) REVERT: A 514 SER cc_start: 0.8807 (OUTLIER) cc_final: 0.8388 (p) REVERT: A 542 ASN cc_start: 0.8271 (t0) cc_final: 0.8006 (t0) REVERT: A 546 LEU cc_start: 0.8358 (tp) cc_final: 0.8093 (tt) REVERT: A 563 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7659 (mm-40) REVERT: A 586 ASP cc_start: 0.8010 (t0) cc_final: 0.7674 (m-30) REVERT: A 603 ASN cc_start: 0.8168 (t0) cc_final: 0.7815 (t0) REVERT: A 646 ARG cc_start: 0.7680 (ttp-110) cc_final: 0.7472 (ttp-110) REVERT: A 658 ASN cc_start: 0.7571 (OUTLIER) cc_final: 0.6801 (p0) REVERT: A 740 MET cc_start: 0.8237 (tpt) cc_final: 0.7649 (tpp) REVERT: A 825 LYS cc_start: 0.8099 (ttmm) cc_final: 0.7870 (ttmm) REVERT: A 868 GLU cc_start: 0.7663 (mp0) cc_final: 0.7447 (mp0) REVERT: A 921 LYS cc_start: 0.8450 (mmmt) cc_final: 0.8063 (mmmt) REVERT: A 933 LYS cc_start: 0.8331 (mtmt) cc_final: 0.8092 (mtmt) REVERT: A 964 LYS cc_start: 0.8356 (tppt) cc_final: 0.7927 (mptt) REVERT: A 979 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7259 (m-30) REVERT: A 983 ARG cc_start: 0.8252 (ttm-80) cc_final: 0.7892 (ttm-80) REVERT: A 1005 GLN cc_start: 0.8198 (tp40) cc_final: 0.7768 (tp40) REVERT: A 1041 ASP cc_start: 0.8251 (t0) cc_final: 0.7915 (t0) REVERT: A 1084 ASP cc_start: 0.7695 (t0) cc_final: 0.7125 (t0) REVERT: A 1094 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.8180 (m) REVERT: I 34 MET cc_start: 0.7265 (mmm) cc_final: 0.7016 (mmm) REVERT: I 39 GLN cc_start: 0.7348 (tt0) cc_final: 0.7031 (tt0) REVERT: I 47 TRP cc_start: 0.7533 (t60) cc_final: 0.7054 (t60) REVERT: I 113 THR cc_start: 0.6181 (m) cc_final: 0.5910 (m) REVERT: I 181 LEU cc_start: 0.8103 (tp) cc_final: 0.7790 (tp) REVERT: M 33 LEU cc_start: 0.8074 (tt) cc_final: 0.7772 (tt) REVERT: M 71 PHE cc_start: 0.6588 (m-80) cc_final: 0.6304 (m-80) REVERT: M 94 MET cc_start: 0.7381 (mmt) cc_final: 0.7031 (mmm) REVERT: J 34 MET cc_start: 0.7000 (mmm) cc_final: 0.6632 (mmm) REVERT: J 92 VAL cc_start: 0.8963 (t) cc_final: 0.8632 (p) REVERT: J 105 TYR cc_start: 0.8097 (p90) cc_final: 0.7705 (p90) REVERT: J 128 PHE cc_start: 0.5577 (m-80) cc_final: 0.4975 (m-10) REVERT: N 33 LEU cc_start: 0.7946 (tt) cc_final: 0.7638 (tt) REVERT: N 71 PHE cc_start: 0.6539 (m-80) cc_final: 0.5991 (m-10) REVERT: N 79 GLN cc_start: 0.7873 (mp10) cc_final: 0.7377 (mp10) REVERT: N 85 THR cc_start: 0.7051 (m) cc_final: 0.6594 (p) REVERT: N 94 MET cc_start: 0.7036 (mmt) cc_final: 0.6676 (mmm) REVERT: N 106 GLU cc_start: 0.5662 (tm-30) cc_final: 0.5072 (tm-30) outliers start: 188 outliers final: 147 residues processed: 945 average time/residue: 0.2345 time to fit residues: 352.8749 Evaluate side-chains 996 residues out of total 3725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 818 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 440 LYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 150 LYS Chi-restraints excluded: chain M residue 195 CYS Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 151 TYR Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 88 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 216 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 187 optimal weight: 0.0060 chunk 156 optimal weight: 0.7980 chunk 174 optimal weight: 0.9980 chunk 223 optimal weight: 0.9990 chunk 289 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 HIS C 532 ASN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN A 564 GLN A 907 ASN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.162120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.125938 restraints weight = 58336.873| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.84 r_work: 0.3488 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.164 35185 Z= 0.256 Angle : 0.892 59.196 48020 Z= 0.491 Chirality : 0.049 0.651 5616 Planarity : 0.006 0.117 6041 Dihedral : 7.221 69.217 6230 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 5.13 % Allowed : 17.93 % Favored : 76.94 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.13), residues: 4205 helix: 1.22 (0.21), residues: 633 sheet: -0.35 (0.15), residues: 1184 loop : -1.63 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG M 109 TYR 0.081 0.002 TYR M 141 PHE 0.041 0.002 PHE M 119 TRP 0.022 0.002 TRP L 149 HIS 0.010 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00565 (35056) covalent geometry : angle 0.87338 (47687) SS BOND : bond 0.00512 ( 54) SS BOND : angle 2.17963 ( 108) hydrogen bonds : bond 0.04010 ( 1215) hydrogen bonds : angle 5.89805 ( 3249) link_BETA1-4 : bond 0.00733 ( 36) link_BETA1-4 : angle 2.19261 ( 108) link_NAG-ASN : bond 0.00371 ( 39) link_NAG-ASN : angle 2.58891 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11160.08 seconds wall clock time: 191 minutes 37.62 seconds (11497.62 seconds total)