Starting phenix.real_space_refine on Sat Aug 8 06:57:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y9v_72713/08_2026/9y9v_72713.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y9v_72713/08_2026/9y9v_72713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y9v_72713/08_2026/9y9v_72713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y9v_72713/08_2026/9y9v_72713.map" model { file = "/net/cci-nas-00/data/ceres_data/9y9v_72713/08_2026/9y9v_72713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y9v_72713/08_2026/9y9v_72713.cif" } resolution = 2.98 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= 0.008 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 141 5.16 5 C 16227 2.51 5 N 4278 2.21 5 O 5295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25941 Number of models: 1 Model: "" Number of chains: 60 Chain: "B" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1018 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "G" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "H" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 841 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 106} Chain: "L" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 799 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Chain: "h" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1026 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "l" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "C" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1018 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "A" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "D" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 841 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 106} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 799 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Chain: "d" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1026 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "e" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "J" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1018 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "I" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "K" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 841 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 106} Chain: "M" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 799 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Chain: "k" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1026 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "m" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "3" 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 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: "n" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "4" 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "1" 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: "2" 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.86, per 1000 atoms: 0.23 Number of scatterers: 25941 At special positions: 0 Unit cell: (186.092, 183.218, 153.041, 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 141 16.00 O 5295 8.00 N 4278 7.00 C 16227 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.05 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.05 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 92 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS A 501 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.05 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS d 22 " - pdb=" SG CYS d 92 " distance=2.03 Simple disulfide: pdb=" SG CYS e 23 " - pdb=" SG CYS e 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 605 " - pdb=" SG CYS I 501 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.04 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.04 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.04 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS k 22 " - pdb=" SG CYS k 92 " distance=2.03 Simple disulfide: pdb=" SG CYS m 23 " - pdb=" SG CYS m 88 " 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 ALPHA1-2 " MAN 0 4 " - " MAN 0 5 " " MAN 0 5 " - " MAN 0 6 " " MAN O 4 " - " MAN O 5 " " MAN O 5 " - " MAN O 6 " " MAN p 4 " - " MAN p 5 " " MAN p 5 " - " MAN p 6 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " MAN 0 7 " - " MAN 0 8 " " BMA O 3 " - " MAN O 4 " " MAN O 7 " - " MAN O 8 " " BMA U 3 " - " MAN U 4 " " BMA f 3 " - " MAN f 4 " " BMA p 3 " - " MAN p 4 " " MAN p 7 " - " MAN p 8 " " BMA v 3 " - " MAN v 4 " ALPHA1-6 " BMA 0 3 " - " MAN 0 7 " " MAN 0 7 " - " MAN 0 9 " " BMA O 3 " - " MAN O 7 " " MAN O 7 " - " MAN O 9 " " BMA Y 3 " - " MAN Y 4 " " BMA n 3 " - " MAN n 4 " " BMA p 3 " - " MAN p 7 " " MAN p 7 " - " MAN p 9 " " BMA z 3 " - " MAN z 4 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " 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 a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " NAG-ASN " NAG 0 1 " - " ASN I 332 " " NAG 1 1 " - " ASN I 448 " " NAG 2 1 " - " ASN I 276 " " NAG 3 1 " - " ASN G 197 " " NAG 4 1 " - " ASN A 197 " " NAG 5 1 " - " ASN I 197 " " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 137 " " NAG A 603 " - " ASN A 133 " " NAG A 604 " - " ASN A 462 " " NAG A 605 " - " ASN A 234 " " NAG A 606 " - " ASN A 339 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 137 " " NAG G 603 " - " ASN G 133 " " NAG G 604 " - " ASN G 462 " " NAG G 605 " - " ASN G 234 " " NAG G 606 " - " ASN G 339 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 137 " " NAG I 603 " - " ASN I 133 " " NAG I 604 " - " ASN I 462 " " NAG I 605 " - " ASN I 234 " " NAG I 606 " - " ASN I 339 " " NAG N 1 " - " ASN A 392 " " NAG O 1 " - " ASN A 332 " " NAG P 1 " - " ASN A 448 " " NAG Q 1 " - " ASN A 276 " " NAG R 1 " - " ASN I 156 " " NAG S 1 " - " ASN I 160 " " NAG T 1 " - " ASN I 355 " " NAG U 1 " - " ASN I 262 " " NAG V 1 " - " ASN I 295 " " NAG W 1 " - " ASN I 301 " " NAG X 1 " - " ASN I 363 " " NAG Y 1 " - " ASN I 386 " " NAG Z 1 " - " ASN I 392 " " NAG a 1 " - " ASN G 156 " " NAG b 1 " - " ASN G 160 " " NAG c 1 " - " ASN G 355 " " NAG f 1 " - " ASN G 262 " " NAG g 1 " - " ASN G 295 " " NAG i 1 " - " ASN G 301 " " NAG j 1 " - " ASN G 363 " " NAG n 1 " - " ASN G 386 " " NAG o 1 " - " ASN G 392 " " NAG p 1 " - " ASN G 332 " " NAG q 1 " - " ASN G 448 " " NAG r 1 " - " ASN G 276 " " NAG s 1 " - " ASN A 156 " " NAG t 1 " - " ASN A 160 " " NAG u 1 " - " ASN A 355 " " NAG v 1 " - " ASN A 262 " " NAG w 1 " - " ASN A 295 " " NAG x 1 " - " ASN A 301 " " NAG y 1 " - " ASN A 363 " " NAG z 1 " - " ASN A 386 " Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 997.1 milliseconds 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5718 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 63 sheets defined 16.2% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'B' and resid 515 through 520 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 570 through 595 removed outlier: 4.313A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B 594 " --> pdb=" O GLN B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 640 through 663 removed outlier: 3.945A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 63 removed outlier: 4.368A pdb=" N THR G 63 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 116 removed outlier: 3.596A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.533A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 122 through 126' Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 335 through 354 removed outlier: 4.467A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.734A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.535A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 425 through 429' Processing helix chain 'G' and resid 476 through 481 removed outlier: 3.730A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.936A pdb=" N SER L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'l' and resid 79 through 83 removed outlier: 3.666A pdb=" N ASP l 82 " --> pdb=" O GLU l 79 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU l 83 " --> pdb=" O ALA l 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 79 through 83' Processing helix chain 'C' and resid 516 through 520 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 570 through 595 removed outlier: 3.822A pdb=" N LYS C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP C 589 " --> pdb=" O ARG C 585 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 593 " --> pdb=" O ASP C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 622 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 640 through 663 removed outlier: 3.562A pdb=" N GLY C 644 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU C 648 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 660 " --> pdb=" O ASN C 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 63 removed outlier: 4.174A pdb=" N TYR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 116 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.626A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 335 through 354 removed outlier: 4.117A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.671A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.543A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.795A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.948A pdb=" N SER E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 100D through 100H Processing helix chain 'e' and resid 79 through 83 removed outlier: 3.661A pdb=" N ASP e 82 " --> pdb=" O GLU e 79 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU e 83 " --> pdb=" O ALA e 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 79 through 83' Processing helix chain 'J' and resid 516 through 520 Processing helix chain 'J' and resid 523 through 527 removed outlier: 4.610A pdb=" N GLY J 527 " --> pdb=" O GLY J 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 570 through 596 removed outlier: 3.839A pdb=" N LYS J 574 " --> pdb=" O VAL J 570 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP J 589 " --> pdb=" O ARG J 585 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU J 593 " --> pdb=" O ASP J 589 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP J 596 " --> pdb=" O LEU J 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 640 through 663 removed outlier: 3.706A pdb=" N GLY J 644 " --> pdb=" O GLN J 640 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN J 651 " --> pdb=" O GLU J 647 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU J 660 " --> pdb=" O ASN J 656 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 63 removed outlier: 3.974A pdb=" N TYR I 61 " --> pdb=" O ASP I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 116 Processing helix chain 'I' and resid 122 through 126 removed outlier: 3.544A pdb=" N LEU I 125 " --> pdb=" O LEU I 122 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N CYS I 126 " --> pdb=" O THR I 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 122 through 126' Processing helix chain 'I' and resid 335 through 354 removed outlier: 4.224A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.593A pdb=" N THR I 373 " --> pdb=" O LEU I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.518A pdb=" N GLN I 428 " --> pdb=" O ASN I 425 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG I 429 " --> pdb=" O MET I 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 425 through 429' Processing helix chain 'I' and resid 476 through 481 removed outlier: 3.796A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.951A pdb=" N SER M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'k' and resid 100D through 100H Processing helix chain 'm' and resid 79 through 83 removed outlier: 3.690A pdb=" N ASP m 82 " --> pdb=" O GLU m 79 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU m 83 " --> pdb=" O ALA m 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 609 removed outlier: 5.109A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.664A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 75 through 76 removed outlier: 7.081A pdb=" N CYS G 54 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS G 216 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 91 through 94 removed outlier: 4.032A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 169 through 177 removed outlier: 3.684A pdb=" N SER G 158 " --> pdb=" O GLN G 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 200 through 203 removed outlier: 3.705A pdb=" N ALA G 433 " --> pdb=" O ALA G 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.501A pdb=" N LEU G 285 " --> pdb=" O ARG G 273 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR G 297 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 315 through 322 removed outlier: 6.854A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 12.506A pdb=" N ILE G 284 " --> pdb=" O ASP G 457 " (cutoff:3.500A) removed outlier: 11.101A pdb=" N ASP G 457 " --> pdb=" O ILE G 284 " (cutoff:3.500A) removed outlier: 11.392A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 11.307A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 12.370A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 12.015A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.911A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR G 467 " --> pdb=" O ASP G 457 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.805A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N CYS H 22 " --> pdb=" O PHE H 78 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASP H 72 " --> pdb=" O GLN H 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.842A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TRP H 35 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER H 95 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS H 35A" --> pdb=" O ALA H 93 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.507A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.781A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU L 33 " --> pdb=" O PHE L 49 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N PHE L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.781A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'h' and resid 4 through 7 removed outlier: 4.381A pdb=" N GLN h 77 " --> pdb=" O ASP h 72 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASP h 72 " --> pdb=" O GLN h 77 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'h' and resid 46 through 51 removed outlier: 7.043A pdb=" N TRP h 36 " --> pdb=" O ILE h 48 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR h 50 " --> pdb=" O TRP h 34 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP h 34 " --> pdb=" O TYR h 50 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR h 100O" --> pdb=" O LEU h 96 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'h' and resid 88 through 90 Processing sheet with id=AB8, first strand: chain 'h' and resid 100 through 100A Processing sheet with id=AB9, first strand: chain 'l' and resid 9 through 13 removed outlier: 5.710A pdb=" N ILE l 9 " --> pdb=" O THR l 103 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N THR l 105 " --> pdb=" O ILE l 9 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE l 11 " --> pdb=" O THR l 105 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'l' and resid 21 through 23 removed outlier: 4.309A pdb=" N ALA l 71 " --> pdb=" O CYS l 23 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'l' and resid 42 through 48 removed outlier: 7.044A pdb=" N ARG l 39 " --> pdb=" O PRO l 44 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LEU l 46 " --> pdb=" O GLN l 37 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN l 37 " --> pdb=" O LEU l 46 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 603 through 609 removed outlier: 5.044A pdb=" N VAL A 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.587A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AC6, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.938A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AC8, first strand: chain 'A' and resid 200 through 203 removed outlier: 3.690A pdb=" N ALA A 433 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.602A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 297 " --> pdb=" O HIS A 330 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 376 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 315 through 322 removed outlier: 6.839A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 12.300A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 11.054A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 11.353A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.333A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.346A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.050A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.887A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.818A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 17 through 18 Processing sheet with id=AD4, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.842A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE D 50 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TRP D 35 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER D 95 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 70 through 72 removed outlier: 3.509A pdb=" N SER D 70 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP D 72 " --> pdb=" O GLN D 77 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AD7, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.765A pdb=" N LEU E 11 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU E 33 " --> pdb=" O PHE E 49 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N PHE E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.765A pdb=" N LEU E 11 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'd' and resid 4 through 7 removed outlier: 4.266A pdb=" N GLN d 77 " --> pdb=" O ASP d 72 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP d 72 " --> pdb=" O GLN d 77 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'd' and resid 46 through 51 removed outlier: 6.832A pdb=" N TRP d 36 " --> pdb=" O ILE d 48 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR d 50 " --> pdb=" O TRP d 34 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP d 34 " --> pdb=" O TYR d 50 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR d 100O" --> pdb=" O LEU d 96 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'd' and resid 88 through 90 Processing sheet with id=AE3, first strand: chain 'd' and resid 100 through 100A Processing sheet with id=AE4, first strand: chain 'e' and resid 9 through 13 removed outlier: 5.696A pdb=" N ILE e 9 " --> pdb=" O THR e 103 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N THR e 105 " --> pdb=" O ILE e 9 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE e 11 " --> pdb=" O THR e 105 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'e' and resid 19 through 23 removed outlier: 3.621A pdb=" N ALA e 19 " --> pdb=" O ILE e 75 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE e 75 " --> pdb=" O ALA e 19 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA e 71 " --> pdb=" O CYS e 23 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'e' and resid 42 through 48 removed outlier: 4.978A pdb=" N ALA e 43 " --> pdb=" O ARG e 39 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ARG e 39 " --> pdb=" O ALA e 43 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TRP e 35 " --> pdb=" O ILE e 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 603 through 609 removed outlier: 5.063A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA I 497 " --> pdb=" O THR I 37 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.627A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AF1, first strand: chain 'I' and resid 66 through 67 removed outlier: 7.153A pdb=" N HIS I 66 " --> pdb=" O SER I 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'I' and resid 91 through 94 removed outlier: 4.120A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=AF4, first strand: chain 'I' and resid 200 through 203 removed outlier: 6.302A pdb=" N ALA I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N TYR I 435 " --> pdb=" O ALA I 200 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 271 through 273 removed outlier: 7.580A pdb=" N GLN I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER I 334 " --> pdb=" O GLN I 293 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR I 297 " --> pdb=" O HIS I 330 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU I 381 " --> pdb=" O CYS I 378 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 315 through 322 removed outlier: 6.881A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 12.344A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 10.946A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 11.404A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 11.275A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 12.388A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 12.036A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.885A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR I 467 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N PHE I 468 " --> pdb=" O ILE I 358 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER I 393 " --> pdb=" O PHE I 361 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.823A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N CYS K 22 " --> pdb=" O PHE K 78 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP K 72 " --> pdb=" O GLN K 77 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR K 68 " --> pdb=" O THR K 81 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 57 through 59 removed outlier: 6.799A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE K 50 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TRP K 35 " --> pdb=" O PHE K 50 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER K 95 " --> pdb=" O TYR K 34 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AG1, first strand: chain 'M' and resid 10 through 12 removed outlier: 7.156A pdb=" N LEU M 33 " --> pdb=" O PHE M 49 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N PHE M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.613A pdb=" N THR M 97 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'k' and resid 4 through 7 removed outlier: 4.224A pdb=" N GLN k 77 " --> pdb=" O ASP k 72 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASP k 72 " --> pdb=" O GLN k 77 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'k' and resid 46 through 51 removed outlier: 7.037A pdb=" N TRP k 36 " --> pdb=" O ILE k 48 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TYR k 50 " --> pdb=" O TRP k 34 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TRP k 34 " --> pdb=" O TYR k 50 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR k 33 " --> pdb=" O THR k 95 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR k 100O" --> pdb=" O LEU k 96 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'k' and resid 88 through 90 Processing sheet with id=AG6, first strand: chain 'k' and resid 100 through 100A Processing sheet with id=AG7, first strand: chain 'm' and resid 9 through 13 removed outlier: 5.651A pdb=" N ILE m 9 " --> pdb=" O THR m 103 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR m 105 " --> pdb=" O ILE m 9 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE m 11 " --> pdb=" O THR m 105 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'm' and resid 19 through 23 removed outlier: 3.670A pdb=" N ALA m 19 " --> pdb=" O ILE m 75 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE m 75 " --> pdb=" O ALA m 19 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA m 71 " --> pdb=" O CYS m 23 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'm' and resid 42 through 48 removed outlier: 6.961A pdb=" N ARG m 39 " --> pdb=" O PRO m 44 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU m 46 " --> pdb=" O GLN m 37 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLN m 37 " --> pdb=" O LEU m 46 " (cutoff:3.500A) 747 hydrogen bonds defined for protein. 1959 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: 5.65 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8059 1.35 - 1.48: 7146 1.48 - 1.61: 11084 1.61 - 1.73: 0 1.73 - 1.86: 192 Bond restraints: 26481 Sorted by residual: bond pdb=" N VAL A 101 " pdb=" CA VAL A 101 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.39e+00 bond pdb=" N PHE M 96 " pdb=" CA PHE M 96 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.26e-02 6.30e+03 6.12e+00 bond pdb=" N SER M 93 " pdb=" CA SER M 93 " ideal model delta sigma weight residual 1.462 1.484 -0.022 1.22e-02 6.72e+03 3.40e+00 bond pdb=" CB CYS G 331 " pdb=" SG CYS G 331 " ideal model delta sigma weight residual 1.808 1.863 -0.055 3.30e-02 9.18e+02 2.78e+00 bond pdb=" CB CYS I 331 " pdb=" SG CYS I 331 " ideal model delta sigma weight residual 1.808 1.860 -0.052 3.30e-02 9.18e+02 2.47e+00 ... (remaining 26476 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 35478 2.50 - 5.01: 442 5.01 - 7.51: 52 7.51 - 10.02: 7 10.02 - 12.52: 3 Bond angle restraints: 35982 Sorted by residual: angle pdb=" C LEU E 94 " pdb=" CA LEU E 94 " pdb=" CB LEU E 94 " ideal model delta sigma weight residual 116.54 110.80 5.74 1.15e+00 7.56e-01 2.49e+01 angle pdb=" CB MET A 150 " pdb=" CG MET A 150 " pdb=" SD MET A 150 " ideal model delta sigma weight residual 112.70 125.22 -12.52 3.00e+00 1.11e-01 1.74e+01 angle pdb=" CA CYS G 296 " pdb=" CB CYS G 296 " pdb=" SG CYS G 296 " ideal model delta sigma weight residual 114.40 123.77 -9.37 2.30e+00 1.89e-01 1.66e+01 angle pdb=" CA CYS I 296 " pdb=" CB CYS I 296 " pdb=" SG CYS I 296 " ideal model delta sigma weight residual 114.40 123.17 -8.77 2.30e+00 1.89e-01 1.45e+01 angle pdb=" CB MET I 161 " pdb=" CG MET I 161 " pdb=" SD MET I 161 " ideal model delta sigma weight residual 112.70 124.08 -11.38 3.00e+00 1.11e-01 1.44e+01 ... (remaining 35977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.07: 15673 24.07 - 48.15: 1362 48.15 - 72.22: 320 72.22 - 96.30: 69 96.30 - 120.37: 18 Dihedral angle restraints: 17442 sinusoidal: 8529 harmonic: 8913 Sorted by residual: dihedral pdb=" CB CYS M 23 " pdb=" SG CYS M 23 " pdb=" SG CYS M 88 " pdb=" CB CYS M 88 " ideal model delta sinusoidal sigma weight residual 93.00 4.15 88.85 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual -86.00 -13.55 -72.45 1 1.00e+01 1.00e-02 6.71e+01 dihedral pdb=" CB CYS G 131 " pdb=" SG CYS G 131 " pdb=" SG CYS G 157 " pdb=" CB CYS G 157 " ideal model delta sinusoidal sigma weight residual -86.00 -14.77 -71.23 1 1.00e+01 1.00e-02 6.51e+01 ... (remaining 17439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3639 0.056 - 0.111: 636 0.111 - 0.167: 118 0.167 - 0.222: 14 0.222 - 0.278: 6 Chirality restraints: 4413 Sorted by residual: chirality pdb=" C3 NAG z 2 " pdb=" C2 NAG z 2 " pdb=" C4 NAG z 2 " pdb=" O3 NAG z 2 " both_signs ideal model delta sigma weight residual False 2.45 2.17 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C3 NAG n 2 " pdb=" C2 NAG n 2 " pdb=" C4 NAG n 2 " pdb=" O3 NAG n 2 " both_signs ideal model delta sigma weight residual False 2.45 2.18 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C3 NAG Y 2 " pdb=" C2 NAG Y 2 " pdb=" C4 NAG Y 2 " pdb=" O3 NAG Y 2 " both_signs ideal model delta sigma weight residual False 2.45 2.18 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 4410 not shown) Planarity restraints: 4449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 88 " -0.002 2.00e-02 2.50e+03 2.71e-02 9.16e+00 pdb=" CG ASN A 88 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN A 88 " -0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN A 88 " 0.032 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 386 " -0.000 2.00e-02 2.50e+03 2.28e-02 6.52e+00 pdb=" CG ASN A 386 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN A 386 " -0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN A 386 " 0.027 2.00e-02 2.50e+03 pdb=" C1 NAG z 1 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 88 " 0.004 2.00e-02 2.50e+03 1.50e-02 2.80e+00 pdb=" CG ASN I 88 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN I 88 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN I 88 " -0.010 2.00e-02 2.50e+03 pdb=" C1 NAG I 601 " 0.012 2.00e-02 2.50e+03 ... (remaining 4446 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 12282 2.96 - 3.44: 23093 3.44 - 3.93: 40099 3.93 - 4.41: 44389 4.41 - 4.90: 76045 Nonbonded interactions: 195908 Sorted by model distance: nonbonded pdb=" O2 MAN p 9 " pdb=" O3 MAN p 9 " model vdw 2.470 2.432 nonbonded pdb=" O2 MAN O 9 " pdb=" O3 MAN O 9 " model vdw 2.471 2.432 nonbonded pdb=" O2 MAN 0 9 " pdb=" O3 MAN 0 9 " model vdw 2.471 2.432 nonbonded pdb=" O5 MAN v 4 " pdb=" O6 MAN v 4 " model vdw 2.477 2.432 nonbonded pdb=" O5 MAN U 4 " pdb=" O6 MAN U 4 " model vdw 2.485 2.432 ... (remaining 195903 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 '0' selection = chain 'O' selection = chain 'p' } ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'g' selection = chain 'i' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'w' selection = chain 'x' } ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'U' selection = chain 'Y' selection = chain 'f' selection = chain 'n' selection = chain 'v' selection = chain 'z' } ncs_group { reference = chain 'X' selection = chain 'j' selection = chain 'y' } ncs_group { reference = chain 'd' selection = chain 'h' selection = chain 'k' } ncs_group { reference = chain 'e' selection = chain 'l' selection = chain 'm' } 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: 10.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.790 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.610 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.130 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:9.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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 0.055 26658 Z= 0.138 Angle : 0.754 12.671 36468 Z= 0.358 Chirality : 0.045 0.278 4413 Planarity : 0.004 0.032 4392 Dihedral : 18.296 120.373 11589 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.66 % Favored : 94.24 % Rotamer: Outliers : 3.98 % Allowed : 31.77 % Favored : 64.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.52 (0.15), residues: 3054 helix: -1.16 (0.26), residues: 336 sheet: -0.26 (0.18), residues: 864 loop : -1.38 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 66 TYR 0.017 0.001 TYR l 49 PHE 0.014 0.001 PHE G 288 TRP 0.028 0.001 TRP J 631 HIS 0.006 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (26481) covalent geometry : angle 0.68039 / 0.34 (35982) SS BOND : bond 0.00706 / 0.47 ( 45) SS BOND : angle 2.56624 / 1.60 ( 90) hydrogen bonds : bond 0.25651 / 17.22 ( 739) hydrogen bonds : angle 9.48331 / 6.58 ( 1959) link_ALPHA1-2 : bond 0.00376 / 0.20 ( 6) link_ALPHA1-2 : angle 1.42687 / 1.01 ( 18) link_ALPHA1-3 : bond 0.00897 / 0.48 ( 9) link_ALPHA1-3 : angle 1.39586 / 0.97 ( 27) link_ALPHA1-6 : bond 0.00557 / 0.28 ( 9) link_ALPHA1-6 : angle 1.38918 / 0.93 ( 27) link_BETA1-4 : bond 0.00925 / 0.69 ( 51) link_BETA1-4 : angle 2.71496 / 2.03 ( 153) link_NAG-ASN : bond 0.00369 / 0.28 ( 57) link_NAG-ASN : angle 3.58896 / 2.55 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 301 time to evaluate : 0.990 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: B 542 ARG cc_start: 0.7805 (ptt-90) cc_final: 0.7383 (ptm160) REVERT: B 627 THR cc_start: 0.7647 (OUTLIER) cc_final: 0.7221 (p) REVERT: B 638 TYR cc_start: 0.4177 (p90) cc_final: 0.3842 (p90) REVERT: B 658 GLN cc_start: 0.3561 (OUTLIER) cc_final: 0.2932 (tp40) REVERT: G 49 GLU cc_start: 0.8092 (pm20) cc_final: 0.7562 (mt-10) REVERT: G 63 THR cc_start: 0.2651 (OUTLIER) cc_final: 0.2337 (p) REVERT: G 130 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8147 (tp40) REVERT: G 189 LYS cc_start: 0.7581 (mmtm) cc_final: 0.7059 (mmmt) REVERT: G 190 GLU cc_start: 0.8774 (mp0) cc_final: 0.8319 (mm-30) REVERT: G 201 ILE cc_start: 0.8731 (mt) cc_final: 0.8437 (tt) REVERT: G 278 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8503 (p) REVERT: G 347 LYS cc_start: 0.8455 (tttt) cc_final: 0.8065 (ttpt) REVERT: G 350 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.5892 (mtp85) REVERT: G 426 MET cc_start: 0.7059 (ptt) cc_final: 0.6784 (ptt) REVERT: H 20 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.6934 (mp) REVERT: H 35 HIS cc_start: 0.7136 (OUTLIER) cc_final: 0.5897 (p90) REVERT: l 28 LEU cc_start: 0.6195 (OUTLIER) cc_final: 0.5405 (mt) REVERT: l 35 TRP cc_start: 0.6952 (OUTLIER) cc_final: 0.6388 (m-10) REVERT: l 96 TRP cc_start: 0.8693 (m100) cc_final: 0.8276 (m100) REVERT: C 535 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.7585 (mpp) REVERT: C 542 ARG cc_start: 0.7927 (ptt-90) cc_final: 0.7557 (ptm-80) REVERT: A 49 GLU cc_start: 0.8182 (pm20) cc_final: 0.7814 (pt0) REVERT: A 75 VAL cc_start: 0.7980 (p) cc_final: 0.7771 (m) REVERT: A 114 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8818 (pt0) REVERT: A 117 LYS cc_start: 0.8522 (mmmm) cc_final: 0.8299 (mmmt) REVERT: A 130 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8453 (tp40) REVERT: A 189 LYS cc_start: 0.7667 (mmtm) cc_final: 0.7214 (mmmt) REVERT: A 211 GLU cc_start: 0.8008 (pm20) cc_final: 0.7744 (pt0) REVERT: A 347 LYS cc_start: 0.8309 (tttt) cc_final: 0.7856 (ttpt) REVERT: A 416 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8076 (mt) REVERT: A 465 THR cc_start: 0.8686 (p) cc_final: 0.8418 (m) REVERT: A 475 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.7094 (mpp) REVERT: A 502 LYS cc_start: 0.7897 (tttt) cc_final: 0.7597 (tttt) REVERT: D 20 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.6802 (mp) REVERT: D 35 HIS cc_start: 0.7145 (OUTLIER) cc_final: 0.6617 (p90) REVERT: D 43 LYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6725 (ttpp) REVERT: e 28 LEU cc_start: 0.6132 (OUTLIER) cc_final: 0.5298 (mt) REVERT: e 35 TRP cc_start: 0.7182 (OUTLIER) cc_final: 0.6668 (m-10) REVERT: e 94 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.6789 (mmm160) REVERT: e 96 TRP cc_start: 0.8335 (m-10) cc_final: 0.7971 (m100) REVERT: J 545 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8135 (tt) REVERT: J 618 ASN cc_start: 0.7249 (m-40) cc_final: 0.7044 (m-40) REVERT: J 627 THR cc_start: 0.7318 (OUTLIER) cc_final: 0.6744 (p) REVERT: I 49 GLU cc_start: 0.8392 (pm20) cc_final: 0.8019 (pt0) REVERT: I 87 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7255 (pm20) REVERT: I 95 MET cc_start: 0.8240 (ptm) cc_final: 0.7959 (ttm) REVERT: I 130 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8530 (mm110) REVERT: I 189 LYS cc_start: 0.7535 (mmtm) cc_final: 0.7077 (mmmt) REVERT: I 205 CYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6419 (m) REVERT: I 288 PHE cc_start: 0.7606 (OUTLIER) cc_final: 0.6957 (p90) REVERT: I 347 LYS cc_start: 0.8434 (tttt) cc_final: 0.8049 (ttpt) REVERT: I 465 THR cc_start: 0.8760 (p) cc_final: 0.8450 (m) REVERT: K 35 HIS cc_start: 0.7104 (OUTLIER) cc_final: 0.6326 (p90) REVERT: K 82 MET cc_start: 0.5100 (mmm) cc_final: 0.2493 (tmm) REVERT: M 60 SER cc_start: 0.8514 (OUTLIER) cc_final: 0.8081 (t) REVERT: k 100 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7597 (mt-10) REVERT: m 28 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5374 (mt) REVERT: m 96 TRP cc_start: 0.8759 (m100) cc_final: 0.8209 (m100) outliers start: 107 outliers final: 66 residues processed: 386 average time/residue: 0.5048 time to fit residues: 234.3896 Evaluate side-chains 383 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 287 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 350 ARG Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain l residue 11 ILE Chi-restraints excluded: chain l residue 28 LEU Chi-restraints excluded: chain l residue 35 TRP Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain d residue 95 THR Chi-restraints excluded: chain d residue 108 THR Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 28 LEU Chi-restraints excluded: chain e residue 35 TRP Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 94 ARG Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 130 GLN Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 288 PHE Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain I residue 505 VAL Chi-restraints excluded: chain K residue 23 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 35 HIS Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain k residue 45 LEU Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain k residue 100 GLU Chi-restraints excluded: chain k residue 100 VAL Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain m residue 11 ILE Chi-restraints excluded: chain m residue 28 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 540 GLN ** G 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN h 97 HIS A 103 GLN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN E 38 GLN I 103 GLN I 356 ASN M 38 GLN k 97 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.205614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.157449 restraints weight = 33987.999| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 3.78 r_work: 0.3636 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26658 Z= 0.131 Angle : 0.727 12.416 36468 Z= 0.339 Chirality : 0.046 0.292 4413 Planarity : 0.004 0.030 4392 Dihedral : 12.189 100.331 6191 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.96 % Favored : 93.94 % Rotamer: Outliers : 8.06 % Allowed : 27.02 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.06 (0.15), residues: 3054 helix: 0.19 (0.29), residues: 336 sheet: 0.12 (0.18), residues: 867 loop : -1.32 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 456 TYR 0.013 0.001 TYR H 91 PHE 0.018 0.002 PHE I 288 TRP 0.017 0.001 TRP C 631 HIS 0.006 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (26481) covalent geometry : angle 0.66379 / 0.32 (35982) SS BOND : bond 0.00597 / 0.40 ( 45) SS BOND : angle 1.84601 / 1.24 ( 90) hydrogen bonds : bond 0.04976 / 3.25 ( 739) hydrogen bonds : angle 6.62688 / 4.65 ( 1959) link_ALPHA1-2 : bond 0.00679 / 0.34 ( 6) link_ALPHA1-2 : angle 1.90339 / 1.44 ( 18) link_ALPHA1-3 : bond 0.00842 / 0.46 ( 9) link_ALPHA1-3 : angle 1.44073 / 0.98 ( 27) link_ALPHA1-6 : bond 0.00686 / 0.36 ( 9) link_ALPHA1-6 : angle 2.02971 / 1.24 ( 27) link_BETA1-4 : bond 0.00928 / 0.69 ( 51) link_BETA1-4 : angle 2.70091 / 2.03 ( 153) link_NAG-ASN : bond 0.00338 / 0.26 ( 57) link_NAG-ASN : angle 3.19931 / 2.29 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 323 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 535 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.7904 (mpp) REVERT: B 542 ARG cc_start: 0.7773 (ptt-90) cc_final: 0.7354 (ptm160) REVERT: B 627 THR cc_start: 0.7668 (m) cc_final: 0.7245 (p) REVERT: B 638 TYR cc_start: 0.3944 (p90) cc_final: 0.3612 (p90) REVERT: B 658 GLN cc_start: 0.3591 (OUTLIER) cc_final: 0.2984 (tp40) REVERT: G 49 GLU cc_start: 0.8151 (pm20) cc_final: 0.7782 (pt0) REVERT: G 63 THR cc_start: 0.2651 (OUTLIER) cc_final: 0.2324 (p) REVERT: G 130 GLN cc_start: 0.8687 (tp40) cc_final: 0.8458 (mm110) REVERT: G 189 LYS cc_start: 0.7594 (mmtm) cc_final: 0.7102 (mmmt) REVERT: G 201 ILE cc_start: 0.8752 (mt) cc_final: 0.8516 (tt) REVERT: G 205 CYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6577 (m) REVERT: G 288 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7158 (p90) REVERT: G 347 LYS cc_start: 0.8454 (tttt) cc_final: 0.8126 (ttpt) REVERT: H 20 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6826 (mp) REVERT: H 35 HIS cc_start: 0.7142 (OUTLIER) cc_final: 0.6088 (p90) REVERT: h 48 ILE cc_start: 0.7217 (pt) cc_final: 0.6960 (mp) REVERT: h 63 LEU cc_start: 0.5673 (OUTLIER) cc_final: 0.5445 (pp) REVERT: l 28 LEU cc_start: 0.6278 (OUTLIER) cc_final: 0.5438 (mt) REVERT: l 35 TRP cc_start: 0.6906 (OUTLIER) cc_final: 0.6247 (m-10) REVERT: l 96 TRP cc_start: 0.8716 (m100) cc_final: 0.8302 (m100) REVERT: C 540 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7047 (mp-120) REVERT: C 542 ARG cc_start: 0.7864 (ptt180) cc_final: 0.7382 (ptp-110) REVERT: C 631 TRP cc_start: 0.7302 (OUTLIER) cc_final: 0.6854 (t-100) REVERT: A 49 GLU cc_start: 0.8204 (pm20) cc_final: 0.7804 (pt0) REVERT: A 75 VAL cc_start: 0.7964 (OUTLIER) cc_final: 0.7754 (m) REVERT: A 117 LYS cc_start: 0.8317 (mmmm) cc_final: 0.8111 (mmmt) REVERT: A 130 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8273 (mm110) REVERT: A 189 LYS cc_start: 0.7663 (mmtm) cc_final: 0.7210 (mmmt) REVERT: A 205 CYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7207 (m) REVERT: A 211 GLU cc_start: 0.7991 (pm20) cc_final: 0.7736 (pt0) REVERT: A 347 LYS cc_start: 0.8383 (tttt) cc_final: 0.8003 (ttpt) REVERT: A 465 THR cc_start: 0.8652 (p) cc_final: 0.8381 (m) REVERT: A 475 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7191 (mpp) REVERT: A 502 LYS cc_start: 0.7815 (tttt) cc_final: 0.7503 (tttt) REVERT: e 28 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5280 (mt) REVERT: e 35 TRP cc_start: 0.6960 (OUTLIER) cc_final: 0.6295 (m-10) REVERT: e 94 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.6943 (mmm160) REVERT: e 96 TRP cc_start: 0.8383 (m-10) cc_final: 0.8057 (m100) REVERT: J 535 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7698 (mpp) REVERT: J 545 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8172 (tt) REVERT: J 618 ASN cc_start: 0.7261 (m-40) cc_final: 0.7047 (m-40) REVERT: J 627 THR cc_start: 0.7198 (OUTLIER) cc_final: 0.6505 (p) REVERT: J 631 TRP cc_start: 0.7194 (m100) cc_final: 0.6825 (t-100) REVERT: J 634 GLU cc_start: 0.6200 (tt0) cc_final: 0.5962 (mt-10) REVERT: J 652 GLN cc_start: 0.6712 (OUTLIER) cc_final: 0.6319 (tt0) REVERT: I 49 GLU cc_start: 0.8426 (pm20) cc_final: 0.7992 (pt0) REVERT: I 95 MET cc_start: 0.8352 (ptm) cc_final: 0.8078 (ttm) REVERT: I 189 LYS cc_start: 0.7513 (mmtm) cc_final: 0.7046 (mmmt) REVERT: I 211 GLU cc_start: 0.7982 (pt0) cc_final: 0.7141 (mm-30) REVERT: I 288 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.6970 (p90) REVERT: I 347 LYS cc_start: 0.8404 (tttt) cc_final: 0.8094 (ttpt) REVERT: K 35 HIS cc_start: 0.7266 (OUTLIER) cc_final: 0.6524 (p90) REVERT: K 82 MET cc_start: 0.5077 (mmm) cc_final: 0.2542 (tmm) REVERT: K 86 ASP cc_start: 0.6749 (m-30) cc_final: 0.6396 (m-30) REVERT: M 21 MET cc_start: 0.5293 (mmt) cc_final: 0.4888 (mmt) REVERT: M 56 THR cc_start: 0.6699 (OUTLIER) cc_final: 0.6423 (t) REVERT: k 100 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.7758 (mt-10) REVERT: m 28 LEU cc_start: 0.6186 (OUTLIER) cc_final: 0.5300 (mt) REVERT: m 94 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.6517 (mmm160) REVERT: m 96 TRP cc_start: 0.8752 (m100) cc_final: 0.8191 (m100) outliers start: 217 outliers final: 82 residues processed: 488 average time/residue: 0.4476 time to fit residues: 264.0085 Evaluate side-chains 407 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 296 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 276 ASN Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 288 PHE Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain h residue 7 SER Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain l residue 28 LEU Chi-restraints excluded: chain l residue 35 TRP Chi-restraints excluded: chain l residue 104 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 631 TRP Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 95 THR Chi-restraints excluded: chain d residue 108 THR Chi-restraints excluded: chain e residue 28 LEU Chi-restraints excluded: chain e residue 35 TRP Chi-restraints excluded: chain e residue 94 ARG Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain J residue 535 MET Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 599 SER Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 652 GLN Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 288 PHE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 35 HIS Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 91 TYR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 45 LEU Chi-restraints excluded: chain k residue 100 GLU Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain m residue 28 LEU Chi-restraints excluded: chain m residue 94 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 46 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 283 optimal weight: 10.0000 chunk 236 optimal weight: 0.0070 chunk 152 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 chunk 213 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 226 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 overall best weight: 0.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 540 GLN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN A 302 ASN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 103 GLN I 130 GLN ** I 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.205713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.157751 restraints weight = 34078.741| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 3.90 r_work: 0.3640 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26658 Z= 0.126 Angle : 0.721 12.508 36468 Z= 0.331 Chirality : 0.046 0.302 4413 Planarity : 0.003 0.031 4392 Dihedral : 11.411 90.251 6115 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.86 % Favored : 94.04 % Rotamer: Outliers : 7.25 % Allowed : 27.80 % Favored : 64.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.15), residues: 3054 helix: 0.63 (0.30), residues: 333 sheet: 0.17 (0.18), residues: 870 loop : -1.33 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 66 TYR 0.014 0.001 TYR K 91 PHE 0.018 0.001 PHE I 288 TRP 0.012 0.001 TRP C 631 HIS 0.007 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (26481) covalent geometry : angle 0.65408 / 0.31 (35982) SS BOND : bond 0.00523 / 0.35 ( 45) SS BOND : angle 1.99189 / 1.39 ( 90) hydrogen bonds : bond 0.04534 / 2.98 ( 739) hydrogen bonds : angle 6.11559 / 4.30 ( 1959) link_ALPHA1-2 : bond 0.00776 / 0.39 ( 6) link_ALPHA1-2 : angle 2.13306 / 1.64 ( 18) link_ALPHA1-3 : bond 0.00790 / 0.44 ( 9) link_ALPHA1-3 : angle 1.49639 / 1.02 ( 27) link_ALPHA1-6 : bond 0.00716 / 0.39 ( 9) link_ALPHA1-6 : angle 2.23503 / 1.34 ( 27) link_BETA1-4 : bond 0.00951 / 0.70 ( 51) link_BETA1-4 : angle 2.72541 / 2.05 ( 153) link_NAG-ASN : bond 0.00375 / 0.27 ( 57) link_NAG-ASN : angle 3.21828 / 2.33 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 311 time to evaluate : 0.943 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: B 535 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.7881 (mpp) REVERT: B 542 ARG cc_start: 0.7795 (ptt-90) cc_final: 0.7396 (ptm160) REVERT: B 627 THR cc_start: 0.7689 (m) cc_final: 0.7261 (p) REVERT: B 638 TYR cc_start: 0.3871 (p90) cc_final: 0.3541 (p90) REVERT: B 658 GLN cc_start: 0.3492 (OUTLIER) cc_final: 0.2948 (tp40) REVERT: G 49 GLU cc_start: 0.8164 (pm20) cc_final: 0.7790 (pt0) REVERT: G 63 THR cc_start: 0.2629 (OUTLIER) cc_final: 0.2318 (p) REVERT: G 130 GLN cc_start: 0.8689 (tp40) cc_final: 0.8485 (mm110) REVERT: G 189 LYS cc_start: 0.7607 (mmtm) cc_final: 0.7117 (mmmt) REVERT: G 211 GLU cc_start: 0.8034 (pt0) cc_final: 0.7049 (mm-30) REVERT: G 347 LYS cc_start: 0.8427 (tttt) cc_final: 0.8098 (ttpt) REVERT: H 35 HIS cc_start: 0.7103 (OUTLIER) cc_final: 0.5936 (p90) REVERT: h 48 ILE cc_start: 0.7222 (pt) cc_final: 0.6977 (mp) REVERT: h 63 LEU cc_start: 0.5595 (OUTLIER) cc_final: 0.5385 (pp) REVERT: l 28 LEU cc_start: 0.6308 (OUTLIER) cc_final: 0.5491 (mt) REVERT: l 35 TRP cc_start: 0.6827 (OUTLIER) cc_final: 0.6303 (m-10) REVERT: l 96 TRP cc_start: 0.8718 (m100) cc_final: 0.8346 (m100) REVERT: C 535 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.7462 (mpp) REVERT: C 540 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.6849 (mp-120) REVERT: C 542 ARG cc_start: 0.7813 (ptt180) cc_final: 0.7380 (ptp-110) REVERT: C 621 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7576 (pp20) REVERT: C 631 TRP cc_start: 0.7362 (m100) cc_final: 0.6802 (t-100) REVERT: C 638 TYR cc_start: 0.3434 (p90) cc_final: 0.3033 (p90) REVERT: A 49 GLU cc_start: 0.8146 (pm20) cc_final: 0.7715 (pt0) REVERT: A 130 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8277 (mm110) REVERT: A 189 LYS cc_start: 0.7664 (mmtm) cc_final: 0.7251 (mmmt) REVERT: A 347 LYS cc_start: 0.8392 (tttt) cc_final: 0.8057 (ttpt) REVERT: A 465 THR cc_start: 0.8660 (p) cc_final: 0.8388 (m) REVERT: A 475 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.7178 (mpp) REVERT: A 502 LYS cc_start: 0.7763 (tttt) cc_final: 0.7463 (tttt) REVERT: d 4 LEU cc_start: 0.5771 (OUTLIER) cc_final: 0.5464 (mm) REVERT: e 28 LEU cc_start: 0.6177 (OUTLIER) cc_final: 0.5320 (mt) REVERT: e 35 TRP cc_start: 0.7022 (OUTLIER) cc_final: 0.6544 (m-10) REVERT: e 94 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7119 (mmm160) REVERT: e 96 TRP cc_start: 0.8390 (m100) cc_final: 0.8122 (m100) REVERT: J 535 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7720 (mpp) REVERT: J 545 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8194 (tt) REVERT: J 631 TRP cc_start: 0.7248 (m100) cc_final: 0.6821 (t-100) REVERT: J 634 GLU cc_start: 0.6139 (tt0) cc_final: 0.5919 (mt-10) REVERT: J 652 GLN cc_start: 0.6670 (OUTLIER) cc_final: 0.6344 (tt0) REVERT: I 49 GLU cc_start: 0.8426 (pm20) cc_final: 0.8197 (pp20) REVERT: I 87 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7259 (pm20) REVERT: I 189 LYS cc_start: 0.7570 (mmtm) cc_final: 0.7116 (mmmt) REVERT: I 211 GLU cc_start: 0.7969 (pt0) cc_final: 0.7213 (mm-30) REVERT: I 288 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.6972 (p90) REVERT: I 347 LYS cc_start: 0.8419 (tttt) cc_final: 0.8103 (ttpt) REVERT: I 350 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.5328 (mtp85) REVERT: I 465 THR cc_start: 0.8689 (p) cc_final: 0.8397 (m) REVERT: K 20 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6829 (mp) REVERT: K 35 HIS cc_start: 0.7285 (OUTLIER) cc_final: 0.6524 (p90) REVERT: K 82 MET cc_start: 0.4940 (mmm) cc_final: 0.2505 (tmm) REVERT: M 21 MET cc_start: 0.5462 (mmt) cc_final: 0.5162 (mmt) REVERT: M 56 THR cc_start: 0.6702 (OUTLIER) cc_final: 0.6443 (t) REVERT: k 48 ILE cc_start: 0.7353 (OUTLIER) cc_final: 0.6975 (mp) REVERT: m 28 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.5431 (mt) REVERT: m 94 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.6509 (mmm160) REVERT: m 96 TRP cc_start: 0.8754 (m100) cc_final: 0.8229 (m100) outliers start: 195 outliers final: 90 residues processed: 462 average time/residue: 0.4722 time to fit residues: 264.5983 Evaluate side-chains 404 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 287 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain l residue 28 LEU Chi-restraints excluded: chain l residue 35 TRP Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 104 LEU Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 621 GLU Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 95 THR Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 108 THR Chi-restraints excluded: chain e residue 28 LEU Chi-restraints excluded: chain e residue 35 TRP Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 94 ARG Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain J residue 535 MET Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 599 SER Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain J residue 652 GLN Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 72 HIS Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 288 PHE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 350 ARG Chi-restraints excluded: chain I residue 418 CYS Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 35 HIS Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 91 TYR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain k residue 45 LEU Chi-restraints excluded: chain k residue 48 ILE Chi-restraints excluded: chain k residue 100 GLU Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain m residue 28 LEU Chi-restraints excluded: chain m residue 94 ARG Chi-restraints excluded: chain m residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 120 optimal weight: 2.9990 chunk 302 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 chunk 287 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 540 GLN G 72 HIS G 203 GLN G 478 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN A 103 GLN A 203 GLN A 478 ASN D 60 ASN E 38 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 103 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 97 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.199479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.144124 restraints weight = 33433.865| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 3.39 r_work: 0.3517 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 26658 Z= 0.232 Angle : 0.876 16.711 36468 Z= 0.402 Chirality : 0.051 0.330 4413 Planarity : 0.004 0.047 4392 Dihedral : 11.303 87.965 6107 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.11 % Favored : 92.76 % Rotamer: Outliers : 9.81 % Allowed : 25.98 % Favored : 64.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.15 (0.15), residues: 3054 helix: 0.32 (0.29), residues: 351 sheet: 0.06 (0.18), residues: 888 loop : -1.47 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 500 TYR 0.023 0.002 TYR H 91 PHE 0.040 0.002 PHE I 288 TRP 0.024 0.002 TRP m 35 HIS 0.009 0.002 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.23 (26481) covalent geometry : angle 0.79430 / 0.38 (35982) SS BOND : bond 0.00919 / 0.66 ( 45) SS BOND : angle 2.80195 / 1.94 ( 90) hydrogen bonds : bond 0.05587 / 3.71 ( 739) hydrogen bonds : angle 6.00229 / 4.22 ( 1959) link_ALPHA1-2 : bond 0.00761 / 0.37 ( 6) link_ALPHA1-2 : angle 2.34715 / 1.79 ( 18) link_ALPHA1-3 : bond 0.00615 / 0.33 ( 9) link_ALPHA1-3 : angle 1.67482 / 1.12 ( 27) link_ALPHA1-6 : bond 0.00567 / 0.32 ( 9) link_ALPHA1-6 : angle 2.48243 / 1.49 ( 27) link_BETA1-4 : bond 0.00863 / 0.64 ( 51) link_BETA1-4 : angle 2.97790 / 2.21 ( 153) link_NAG-ASN : bond 0.00541 / 0.40 ( 57) link_NAG-ASN : angle 4.09831 / 2.99 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 264 poor density : 282 time to evaluate : 0.756 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: B 542 ARG cc_start: 0.8040 (ptt-90) cc_final: 0.7596 (ptm160) REVERT: B 658 GLN cc_start: 0.3743 (OUTLIER) cc_final: 0.3200 (tp40) REVERT: G 63 THR cc_start: 0.2525 (OUTLIER) cc_final: 0.2189 (p) REVERT: G 130 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8523 (mm110) REVERT: G 136 ASN cc_start: 0.6998 (t0) cc_final: 0.6681 (p0) REVERT: G 189 LYS cc_start: 0.7723 (mmtm) cc_final: 0.7237 (mmmt) REVERT: G 190 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8423 (mm-30) REVERT: G 201 ILE cc_start: 0.8716 (mp) cc_final: 0.8403 (tt) REVERT: G 211 GLU cc_start: 0.8015 (pt0) cc_final: 0.7128 (mm-30) REVERT: G 288 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7482 (p90) REVERT: G 347 LYS cc_start: 0.8511 (tttt) cc_final: 0.8083 (ttpt) REVERT: G 423 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8558 (pt) REVERT: H 20 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6827 (mp) REVERT: H 35 HIS cc_start: 0.7326 (OUTLIER) cc_final: 0.5849 (p90) REVERT: l 35 TRP cc_start: 0.6914 (OUTLIER) cc_final: 0.6236 (m-10) REVERT: l 94 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.6476 (mmm160) REVERT: l 96 TRP cc_start: 0.8849 (m100) cc_final: 0.8315 (m100) REVERT: C 535 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.7644 (mpp) REVERT: C 542 ARG cc_start: 0.8009 (ptt180) cc_final: 0.7513 (ptp-110) REVERT: C 590 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7557 (mp10) REVERT: C 621 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7564 (pp20) REVERT: C 631 TRP cc_start: 0.7387 (OUTLIER) cc_final: 0.6978 (t-100) REVERT: C 634 GLU cc_start: 0.6562 (tt0) cc_final: 0.6257 (mt-10) REVERT: A 49 GLU cc_start: 0.8358 (pm20) cc_final: 0.8072 (pm20) REVERT: A 117 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7741 (mmmt) REVERT: A 130 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8098 (mm110) REVERT: A 136 ASN cc_start: 0.7087 (t0) cc_final: 0.6771 (p0) REVERT: A 190 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8023 (mm-30) REVERT: A 347 LYS cc_start: 0.8454 (tttt) cc_final: 0.8043 (ttpt) REVERT: A 494 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8375 (mp) REVERT: A 502 LYS cc_start: 0.7919 (tttt) cc_final: 0.7510 (tttt) REVERT: d 100 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.7486 (mt-10) REVERT: e 35 TRP cc_start: 0.7099 (OUTLIER) cc_final: 0.6275 (m-10) REVERT: e 52 GLN cc_start: 0.7593 (mm110) cc_final: 0.7381 (mm110) REVERT: e 94 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7196 (mmm160) REVERT: J 631 TRP cc_start: 0.7349 (m100) cc_final: 0.6882 (t-100) REVERT: J 652 GLN cc_start: 0.6803 (OUTLIER) cc_final: 0.6481 (tt0) REVERT: I 87 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7053 (mp0) REVERT: I 189 LYS cc_start: 0.7632 (mmtm) cc_final: 0.7143 (mmmt) REVERT: I 211 GLU cc_start: 0.8051 (pt0) cc_final: 0.7244 (mm-30) REVERT: I 276 ASN cc_start: 0.6073 (OUTLIER) cc_final: 0.5791 (t0) REVERT: I 288 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7169 (p90) REVERT: I 347 LYS cc_start: 0.8520 (tttt) cc_final: 0.8147 (ttpt) REVERT: K 20 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6813 (mp) REVERT: K 82 MET cc_start: 0.5037 (mmm) cc_final: 0.2553 (tmm) REVERT: M 21 MET cc_start: 0.5432 (OUTLIER) cc_final: 0.5139 (mmt) REVERT: M 56 THR cc_start: 0.6863 (OUTLIER) cc_final: 0.6598 (t) REVERT: m 94 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.6746 (mmm160) REVERT: m 96 TRP cc_start: 0.8811 (m100) cc_final: 0.8245 (m100) outliers start: 264 outliers final: 141 residues processed: 487 average time/residue: 0.4300 time to fit residues: 254.7374 Evaluate side-chains 436 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 269 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 288 PHE Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 478 ASN Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain l residue 28 LEU Chi-restraints excluded: chain l residue 35 TRP Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 590 GLN Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 621 GLU Chi-restraints excluded: chain C residue 631 TRP Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 95 THR Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 108 THR Chi-restraints excluded: chain e residue 28 LEU Chi-restraints excluded: chain e residue 35 TRP Chi-restraints excluded: chain e residue 47 ILE Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 94 ARG Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 599 SER Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 652 GLN Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 72 HIS Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 276 ASN Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 288 PHE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 35 HIS Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 91 TYR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 45 LEU Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain k residue 100 GLU Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain m residue 28 LEU Chi-restraints excluded: chain m residue 94 ARG Chi-restraints excluded: chain m residue 95 VAL Chi-restraints excluded: chain m residue 95 THR Chi-restraints excluded: chain m residue 104 LEU Chi-restraints excluded: chain m residue 106 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 23 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 283 optimal weight: 9.9990 chunk 191 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 213 optimal weight: 0.7980 chunk 214 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 chunk 233 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 ASN I 103 GLN I 302 ASN ** I 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.200883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.142858 restraints weight = 33298.250| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.25 r_work: 0.3563 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26658 Z= 0.152 Angle : 0.781 14.119 36468 Z= 0.356 Chirality : 0.047 0.284 4413 Planarity : 0.004 0.037 4392 Dihedral : 10.290 83.351 6105 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.19 % Favored : 93.68 % Rotamer: Outliers : 7.77 % Allowed : 28.13 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.07 (0.15), residues: 3054 helix: 0.48 (0.30), residues: 351 sheet: 0.12 (0.18), residues: 888 loop : -1.44 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 53 TYR 0.017 0.001 TYR H 91 PHE 0.023 0.002 PHE I 288 TRP 0.014 0.001 TRP d 34 HIS 0.006 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (26481) covalent geometry : angle 0.70419 / 0.34 (35982) SS BOND : bond 0.00725 / 0.50 ( 45) SS BOND : angle 2.45463 / 1.65 ( 90) hydrogen bonds : bond 0.04487 / 2.97 ( 739) hydrogen bonds : angle 5.71153 / 4.03 ( 1959) link_ALPHA1-2 : bond 0.01257 / 0.62 ( 6) link_ALPHA1-2 : angle 1.84660 / 1.35 ( 18) link_ALPHA1-3 : bond 0.00733 / 0.40 ( 9) link_ALPHA1-3 : angle 1.54465 / 1.02 ( 27) link_ALPHA1-6 : bond 0.00909 / 0.53 ( 9) link_ALPHA1-6 : angle 2.23272 / 1.32 ( 27) link_BETA1-4 : bond 0.00927 / 0.69 ( 51) link_BETA1-4 : angle 3.01099 / 2.27 ( 153) link_NAG-ASN : bond 0.00367 / 0.28 ( 57) link_NAG-ASN : angle 3.61208 / 2.64 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 290 time to evaluate : 0.903 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: B 535 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.7871 (mpp) REVERT: B 542 ARG cc_start: 0.7875 (ptt-90) cc_final: 0.7470 (ptm160) REVERT: B 617 ARG cc_start: 0.5998 (mtp180) cc_final: 0.5550 (mtt90) REVERT: B 621 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7487 (pp20) REVERT: B 627 THR cc_start: 0.7651 (OUTLIER) cc_final: 0.7174 (p) REVERT: B 638 TYR cc_start: 0.3932 (p90) cc_final: 0.3604 (p90) REVERT: B 658 GLN cc_start: 0.3791 (OUTLIER) cc_final: 0.3232 (tp40) REVERT: G 49 GLU cc_start: 0.7997 (pm20) cc_final: 0.7481 (mt-10) REVERT: G 63 THR cc_start: 0.2682 (OUTLIER) cc_final: 0.2361 (p) REVERT: G 130 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8494 (mm110) REVERT: G 189 LYS cc_start: 0.7678 (mmtm) cc_final: 0.7159 (mmmt) REVERT: G 190 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8431 (mm-30) REVERT: G 201 ILE cc_start: 0.8770 (mp) cc_final: 0.8412 (tt) REVERT: G 211 GLU cc_start: 0.7971 (pt0) cc_final: 0.7052 (mm-30) REVERT: G 347 LYS cc_start: 0.8483 (tttt) cc_final: 0.8052 (ttpt) REVERT: G 426 MET cc_start: 0.7513 (ptt) cc_final: 0.7182 (ptt) REVERT: H 20 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6825 (mp) REVERT: H 35 HIS cc_start: 0.7248 (OUTLIER) cc_final: 0.6201 (p90) REVERT: L 21 MET cc_start: 0.5313 (OUTLIER) cc_final: 0.5110 (mtt) REVERT: l 35 TRP cc_start: 0.6852 (OUTLIER) cc_final: 0.6326 (m-10) REVERT: l 96 TRP cc_start: 0.8834 (m100) cc_final: 0.8332 (m100) REVERT: C 535 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.7572 (mpp) REVERT: C 542 ARG cc_start: 0.7865 (ptt180) cc_final: 0.7364 (ptp-110) REVERT: C 590 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.7324 (mp10) REVERT: C 621 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7529 (pp20) REVERT: C 631 TRP cc_start: 0.7430 (OUTLIER) cc_final: 0.6741 (t-100) REVERT: C 634 GLU cc_start: 0.6504 (tt0) cc_final: 0.6188 (mt-10) REVERT: A 49 GLU cc_start: 0.8305 (pm20) cc_final: 0.7809 (pt0) REVERT: A 100 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8202 (ptm) REVERT: A 130 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8362 (mm110) REVERT: A 136 ASN cc_start: 0.6980 (t0) cc_final: 0.6712 (p0) REVERT: A 347 LYS cc_start: 0.8441 (tttt) cc_final: 0.8000 (ttpt) REVERT: A 502 LYS cc_start: 0.7843 (tttt) cc_final: 0.7412 (tttt) REVERT: E 63 SER cc_start: 0.7151 (OUTLIER) cc_final: 0.6670 (t) REVERT: d 100 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8621 (mp0) REVERT: e 35 TRP cc_start: 0.7043 (OUTLIER) cc_final: 0.6270 (m-10) REVERT: e 52 GLN cc_start: 0.7529 (mm110) cc_final: 0.7277 (mm110) REVERT: e 94 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7154 (mmm160) REVERT: J 631 TRP cc_start: 0.7283 (m100) cc_final: 0.6901 (t-100) REVERT: J 652 GLN cc_start: 0.6647 (OUTLIER) cc_final: 0.6344 (tt0) REVERT: I 49 GLU cc_start: 0.8268 (pm20) cc_final: 0.7891 (pt0) REVERT: I 87 GLU cc_start: 0.7659 (tm-30) cc_final: 0.6968 (mp0) REVERT: I 189 LYS cc_start: 0.7577 (mmtm) cc_final: 0.6989 (mmmt) REVERT: I 211 GLU cc_start: 0.7981 (pt0) cc_final: 0.7143 (mm-30) REVERT: I 276 ASN cc_start: 0.5953 (OUTLIER) cc_final: 0.5650 (t0) REVERT: I 288 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7021 (p90) REVERT: I 347 LYS cc_start: 0.8501 (tttt) cc_final: 0.8111 (ttpt) REVERT: I 350 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.5525 (mtp85) REVERT: K 20 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6783 (mp) REVERT: K 35 HIS cc_start: 0.7417 (OUTLIER) cc_final: 0.6427 (p90) REVERT: K 82 MET cc_start: 0.4911 (mmm) cc_final: 0.2504 (tmm) REVERT: M 21 MET cc_start: 0.5335 (mmt) cc_final: 0.5081 (mmt) REVERT: M 56 THR cc_start: 0.6853 (OUTLIER) cc_final: 0.6585 (t) REVERT: m 94 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.6322 (mmm160) REVERT: m 96 TRP cc_start: 0.8787 (m100) cc_final: 0.8237 (m100) outliers start: 209 outliers final: 118 residues processed: 452 average time/residue: 0.4491 time to fit residues: 246.6853 Evaluate side-chains 420 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 274 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain h residue 7 SER Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain l residue 28 LEU Chi-restraints excluded: chain l residue 35 TRP Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 590 GLN Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 621 GLU Chi-restraints excluded: chain C residue 631 TRP Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 95 THR Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 108 THR Chi-restraints excluded: chain e residue 28 LEU Chi-restraints excluded: chain e residue 35 TRP Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 94 ARG Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 599 SER Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 652 GLN Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 72 HIS Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain I residue 276 ASN Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 288 PHE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 350 ARG Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 35 HIS Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 45 LEU Chi-restraints excluded: chain k residue 100 GLU Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain m residue 28 LEU Chi-restraints excluded: chain m residue 94 ARG Chi-restraints excluded: chain m residue 95 VAL Chi-restraints excluded: chain m residue 104 LEU Chi-restraints excluded: chain m residue 106 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 231 optimal weight: 6.9990 chunk 213 optimal weight: 0.6980 chunk 169 optimal weight: 0.0770 chunk 67 optimal weight: 3.9990 chunk 229 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 247 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 97 HIS A 103 GLN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.204193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.149955 restraints weight = 34161.171| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 3.33 r_work: 0.3552 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26658 Z= 0.128 Angle : 0.739 13.261 36468 Z= 0.338 Chirality : 0.046 0.262 4413 Planarity : 0.003 0.036 4392 Dihedral : 9.657 81.056 6105 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.22 % Favored : 93.65 % Rotamer: Outliers : 7.73 % Allowed : 28.65 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.15), residues: 3054 helix: 0.80 (0.31), residues: 333 sheet: 0.17 (0.18), residues: 849 loop : -1.38 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 456 TYR 0.016 0.001 TYR K 91 PHE 0.019 0.001 PHE I 288 TRP 0.013 0.001 TRP d 34 HIS 0.007 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (26481) covalent geometry : angle 0.66420 / 0.32 (35982) SS BOND : bond 0.00611 / 0.41 ( 45) SS BOND : angle 2.29563 / 1.55 ( 90) hydrogen bonds : bond 0.03973 / 2.62 ( 739) hydrogen bonds : angle 5.54878 / 3.91 ( 1959) link_ALPHA1-2 : bond 0.00911 / 0.45 ( 6) link_ALPHA1-2 : angle 1.56817 / 1.02 ( 18) link_ALPHA1-3 : bond 0.00709 / 0.38 ( 9) link_ALPHA1-3 : angle 1.53862 / 1.03 ( 27) link_ALPHA1-6 : bond 0.00952 / 0.54 ( 9) link_ALPHA1-6 : angle 2.13467 / 1.27 ( 27) link_BETA1-4 : bond 0.00894 / 0.66 ( 51) link_BETA1-4 : angle 2.93114 / 2.23 ( 153) link_NAG-ASN : bond 0.00397 / 0.28 ( 57) link_NAG-ASN : angle 3.44457 / 2.53 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 276 time to evaluate : 0.998 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: B 535 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7903 (mpp) REVERT: B 542 ARG cc_start: 0.7909 (ptt-90) cc_final: 0.7483 (ptm160) REVERT: B 617 ARG cc_start: 0.6042 (mtp180) cc_final: 0.5629 (mtt90) REVERT: B 627 THR cc_start: 0.7602 (OUTLIER) cc_final: 0.7116 (p) REVERT: B 638 TYR cc_start: 0.3994 (p90) cc_final: 0.3658 (p90) REVERT: B 658 GLN cc_start: 0.3807 (OUTLIER) cc_final: 0.3293 (tp40) REVERT: G 49 GLU cc_start: 0.8125 (pm20) cc_final: 0.7823 (pt0) REVERT: G 63 THR cc_start: 0.2649 (OUTLIER) cc_final: 0.2322 (p) REVERT: G 130 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8559 (mm110) REVERT: G 189 LYS cc_start: 0.7690 (mmtm) cc_final: 0.7142 (mmmt) REVERT: G 190 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8622 (mt-10) REVERT: G 211 GLU cc_start: 0.7982 (pt0) cc_final: 0.7101 (mm-30) REVERT: G 288 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.7180 (p90) REVERT: G 347 LYS cc_start: 0.8498 (tttt) cc_final: 0.8080 (ttpt) REVERT: G 426 MET cc_start: 0.7458 (ptt) cc_final: 0.7150 (ptt) REVERT: H 20 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6802 (mp) REVERT: H 35 HIS cc_start: 0.7222 (OUTLIER) cc_final: 0.6213 (p90) REVERT: h 45 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7061 (pt) REVERT: h 100 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8667 (mp0) REVERT: l 35 TRP cc_start: 0.6863 (OUTLIER) cc_final: 0.6404 (m-10) REVERT: l 94 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7555 (mmt90) REVERT: l 96 TRP cc_start: 0.8838 (m100) cc_final: 0.8316 (m100) REVERT: C 535 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.7596 (mpp) REVERT: C 542 ARG cc_start: 0.7902 (ptt-90) cc_final: 0.7388 (ptp-110) REVERT: C 631 TRP cc_start: 0.7456 (OUTLIER) cc_final: 0.6703 (t-100) REVERT: C 634 GLU cc_start: 0.6513 (tt0) cc_final: 0.6261 (mt-10) REVERT: A 49 GLU cc_start: 0.8277 (pm20) cc_final: 0.7749 (pt0) REVERT: A 130 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8145 (tp40) REVERT: A 136 ASN cc_start: 0.7008 (t0) cc_final: 0.6803 (p0) REVERT: A 190 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8073 (mm-30) REVERT: A 211 GLU cc_start: 0.8059 (pt0) cc_final: 0.7124 (mm-30) REVERT: A 347 LYS cc_start: 0.8436 (tttt) cc_final: 0.8031 (ttpt) REVERT: A 502 LYS cc_start: 0.7810 (tttt) cc_final: 0.7422 (tttt) REVERT: e 35 TRP cc_start: 0.7099 (OUTLIER) cc_final: 0.6629 (m-10) REVERT: e 52 GLN cc_start: 0.7471 (mm110) cc_final: 0.7256 (mm110) REVERT: J 631 TRP cc_start: 0.7243 (m100) cc_final: 0.6897 (t-100) REVERT: J 652 GLN cc_start: 0.6592 (OUTLIER) cc_final: 0.6329 (tt0) REVERT: I 49 GLU cc_start: 0.8291 (pm20) cc_final: 0.7865 (pt0) REVERT: I 87 GLU cc_start: 0.7693 (tm-30) cc_final: 0.6904 (mp0) REVERT: I 189 LYS cc_start: 0.7612 (mmtm) cc_final: 0.7060 (mmmt) REVERT: I 211 GLU cc_start: 0.8010 (pt0) cc_final: 0.7174 (mm-30) REVERT: I 243 SER cc_start: 0.8251 (OUTLIER) cc_final: 0.7993 (p) REVERT: I 276 ASN cc_start: 0.6027 (OUTLIER) cc_final: 0.5734 (t0) REVERT: I 288 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.6937 (p90) REVERT: I 347 LYS cc_start: 0.8507 (tttt) cc_final: 0.8123 (ttpt) REVERT: I 350 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.5323 (mtp85) REVERT: K 20 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6763 (mp) REVERT: K 35 HIS cc_start: 0.7382 (OUTLIER) cc_final: 0.6549 (p90) REVERT: K 82 MET cc_start: 0.4884 (mmm) cc_final: 0.2465 (tmm) REVERT: M 21 MET cc_start: 0.5275 (OUTLIER) cc_final: 0.4970 (mmt) REVERT: M 56 THR cc_start: 0.6844 (OUTLIER) cc_final: 0.6566 (t) REVERT: m 94 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.6297 (mmm160) REVERT: m 96 TRP cc_start: 0.8791 (m100) cc_final: 0.8231 (m100) outliers start: 208 outliers final: 118 residues processed: 435 average time/residue: 0.4780 time to fit residues: 251.0615 Evaluate side-chains 411 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 267 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 288 PHE Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 350 ARG Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain h residue 7 SER Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 100 GLU Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain l residue 28 LEU Chi-restraints excluded: chain l residue 35 TRP Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 631 TRP Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 95 THR Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 108 THR Chi-restraints excluded: chain e residue 28 LEU Chi-restraints excluded: chain e residue 35 TRP Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 652 GLN Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 72 HIS Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 276 ASN Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 288 PHE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 350 ARG Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 35 HIS Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 45 LEU Chi-restraints excluded: chain k residue 100 GLU Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain m residue 28 LEU Chi-restraints excluded: chain m residue 94 ARG Chi-restraints excluded: chain m residue 95 VAL Chi-restraints excluded: chain m residue 95 THR Chi-restraints excluded: chain m residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 50 optimal weight: 0.1980 chunk 239 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 205 optimal weight: 0.7980 chunk 291 optimal weight: 3.9990 chunk 294 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 238 optimal weight: 1.9990 chunk 255 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN A 103 GLN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 651 ASN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.203806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.155853 restraints weight = 33880.350| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 3.84 r_work: 0.3592 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26658 Z= 0.127 Angle : 0.720 13.143 36468 Z= 0.330 Chirality : 0.045 0.246 4413 Planarity : 0.003 0.035 4392 Dihedral : 9.156 80.088 6098 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.86 % Favored : 94.01 % Rotamer: Outliers : 7.92 % Allowed : 28.28 % Favored : 63.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.15), residues: 3054 helix: 0.90 (0.31), residues: 333 sheet: 0.12 (0.17), residues: 894 loop : -1.33 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 53 TYR 0.015 0.001 TYR H 91 PHE 0.019 0.001 PHE I 288 TRP 0.016 0.001 TRP k 34 HIS 0.005 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 (26481) covalent geometry : angle 0.64846 / 0.31 (35982) SS BOND : bond 0.00632 / 0.44 ( 45) SS BOND : angle 2.17171 / 1.50 ( 90) hydrogen bonds : bond 0.03848 / 2.54 ( 739) hydrogen bonds : angle 5.36376 / 3.78 ( 1959) link_ALPHA1-2 : bond 0.00728 / 0.37 ( 6) link_ALPHA1-2 : angle 1.57355 / 1.05 ( 18) link_ALPHA1-3 : bond 0.00737 / 0.40 ( 9) link_ALPHA1-3 : angle 1.52677 / 1.02 ( 27) link_ALPHA1-6 : bond 0.00912 / 0.52 ( 9) link_ALPHA1-6 : angle 2.00161 / 1.22 ( 27) link_BETA1-4 : bond 0.00794 / 0.58 ( 51) link_BETA1-4 : angle 2.80326 / 2.11 ( 153) link_NAG-ASN : bond 0.00368 / 0.27 ( 57) link_NAG-ASN : angle 3.36466 / 2.47 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 283 time to evaluate : 0.978 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: B 542 ARG cc_start: 0.7891 (ptt-90) cc_final: 0.7465 (ptm160) REVERT: B 617 ARG cc_start: 0.6030 (mtp180) cc_final: 0.5640 (mtt90) REVERT: B 627 THR cc_start: 0.7566 (OUTLIER) cc_final: 0.7141 (p) REVERT: B 638 TYR cc_start: 0.3873 (p90) cc_final: 0.3594 (p90) REVERT: B 658 GLN cc_start: 0.3627 (OUTLIER) cc_final: 0.3320 (tp40) REVERT: G 49 GLU cc_start: 0.8083 (pm20) cc_final: 0.7820 (pt0) REVERT: G 63 THR cc_start: 0.2694 (OUTLIER) cc_final: 0.2380 (p) REVERT: G 130 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8508 (mm110) REVERT: G 189 LYS cc_start: 0.7662 (mmtm) cc_final: 0.7178 (mmmt) REVERT: G 190 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8499 (mt-10) REVERT: G 205 CYS cc_start: 0.7316 (OUTLIER) cc_final: 0.6667 (m) REVERT: G 211 GLU cc_start: 0.7925 (pt0) cc_final: 0.7143 (mm-30) REVERT: G 304 ARG cc_start: 0.8529 (ttm170) cc_final: 0.8312 (ttm170) REVERT: G 347 LYS cc_start: 0.8430 (tttt) cc_final: 0.8086 (ttpt) REVERT: G 426 MET cc_start: 0.7420 (ptt) cc_final: 0.7143 (ptt) REVERT: H 20 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6833 (mp) REVERT: H 35 HIS cc_start: 0.7176 (OUTLIER) cc_final: 0.6220 (p90) REVERT: h 45 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7166 (pt) REVERT: l 35 TRP cc_start: 0.6843 (OUTLIER) cc_final: 0.6348 (m-10) REVERT: l 94 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7603 (mmt90) REVERT: l 96 TRP cc_start: 0.8859 (m100) cc_final: 0.8380 (m100) REVERT: C 535 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.7613 (mpp) REVERT: C 542 ARG cc_start: 0.7877 (ptt-90) cc_final: 0.7491 (ptm-80) REVERT: C 585 ARG cc_start: 0.8818 (mtp-110) cc_final: 0.8576 (mmm-85) REVERT: C 631 TRP cc_start: 0.7459 (OUTLIER) cc_final: 0.6935 (t-100) REVERT: C 634 GLU cc_start: 0.6482 (tt0) cc_final: 0.6218 (mt-10) REVERT: A 49 GLU cc_start: 0.8230 (pm20) cc_final: 0.7723 (pt0) REVERT: A 100 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8151 (ptm) REVERT: A 130 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8211 (mm110) REVERT: A 190 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8429 (mm-30) REVERT: A 211 GLU cc_start: 0.7997 (pt0) cc_final: 0.7156 (mm-30) REVERT: A 347 LYS cc_start: 0.8384 (tttt) cc_final: 0.8053 (ttpt) REVERT: A 485 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7553 (ptmt) REVERT: A 502 LYS cc_start: 0.7814 (tttt) cc_final: 0.7473 (tttt) REVERT: E 63 SER cc_start: 0.7134 (OUTLIER) cc_final: 0.6672 (t) REVERT: e 35 TRP cc_start: 0.7182 (OUTLIER) cc_final: 0.6718 (m-10) REVERT: e 52 GLN cc_start: 0.7483 (mm110) cc_final: 0.7269 (mm110) REVERT: e 96 TRP cc_start: 0.8630 (m100) cc_final: 0.8170 (m100) REVERT: J 631 TRP cc_start: 0.7215 (OUTLIER) cc_final: 0.6963 (t-100) REVERT: J 652 GLN cc_start: 0.6634 (OUTLIER) cc_final: 0.6384 (tt0) REVERT: I 49 GLU cc_start: 0.8296 (pm20) cc_final: 0.7583 (mt-10) REVERT: I 87 GLU cc_start: 0.7700 (tm-30) cc_final: 0.6951 (mp0) REVERT: I 189 LYS cc_start: 0.7602 (mmtm) cc_final: 0.7107 (mmmt) REVERT: I 211 GLU cc_start: 0.7952 (pt0) cc_final: 0.7221 (mm-30) REVERT: I 243 SER cc_start: 0.8198 (OUTLIER) cc_final: 0.7968 (p) REVERT: I 288 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.6959 (p90) REVERT: I 347 LYS cc_start: 0.8414 (tttt) cc_final: 0.8125 (ttpt) REVERT: I 350 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.5275 (mtp85) REVERT: K 20 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6793 (mp) REVERT: K 35 HIS cc_start: 0.7329 (OUTLIER) cc_final: 0.6541 (p90) REVERT: K 82 MET cc_start: 0.4930 (mmm) cc_final: 0.2621 (tmm) REVERT: M 21 MET cc_start: 0.5345 (OUTLIER) cc_final: 0.5062 (mmt) REVERT: M 56 THR cc_start: 0.6840 (OUTLIER) cc_final: 0.6568 (t) REVERT: m 94 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.6314 (mmm160) REVERT: m 96 TRP cc_start: 0.8809 (m100) cc_final: 0.8284 (m100) outliers start: 213 outliers final: 125 residues processed: 448 average time/residue: 0.4719 time to fit residues: 256.4842 Evaluate side-chains 422 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 270 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain h residue 7 SER Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain l residue 28 LEU Chi-restraints excluded: chain l residue 35 TRP Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 631 TRP Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 95 THR Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 108 THR Chi-restraints excluded: chain e residue 28 LEU Chi-restraints excluded: chain e residue 35 TRP Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain J residue 599 SER Chi-restraints excluded: chain J residue 631 TRP Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 652 GLN Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 72 HIS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 288 PHE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 350 ARG Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 35 HIS Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 45 LEU Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain k residue 100 GLU Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain m residue 28 LEU Chi-restraints excluded: chain m residue 94 ARG Chi-restraints excluded: chain m residue 95 VAL Chi-restraints excluded: chain m residue 95 THR Chi-restraints excluded: chain m residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 67 optimal weight: 2.9990 chunk 218 optimal weight: 6.9990 chunk 125 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 199 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 274 optimal weight: 0.0870 chunk 159 optimal weight: 9.9990 chunk 241 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 264 optimal weight: 0.0270 overall best weight: 0.9418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 72 HIS ** G 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 97 HIS A 103 GLN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 97 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.203245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.155318 restraints weight = 33887.669| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 3.79 r_work: 0.3579 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26658 Z= 0.138 Angle : 0.733 13.372 36468 Z= 0.338 Chirality : 0.045 0.242 4413 Planarity : 0.003 0.033 4392 Dihedral : 9.055 80.528 6098 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.09 % Favored : 93.78 % Rotamer: Outliers : 7.66 % Allowed : 28.65 % Favored : 63.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.15), residues: 3054 helix: 0.92 (0.31), residues: 333 sheet: 0.15 (0.17), residues: 888 loop : -1.33 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 53 TYR 0.018 0.001 TYR K 91 PHE 0.022 0.001 PHE I 288 TRP 0.014 0.001 TRP k 34 HIS 0.005 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (26481) covalent geometry : angle 0.66161 / 0.32 (35982) SS BOND : bond 0.00738 / 0.52 ( 45) SS BOND : angle 2.40688 / 1.61 ( 90) hydrogen bonds : bond 0.03947 / 2.61 ( 739) hydrogen bonds : angle 5.33110 / 3.76 ( 1959) link_ALPHA1-2 : bond 0.00550 / 0.28 ( 6) link_ALPHA1-2 : angle 1.51251 / 1.00 ( 18) link_ALPHA1-3 : bond 0.00726 / 0.39 ( 9) link_ALPHA1-3 : angle 1.53348 / 1.02 ( 27) link_ALPHA1-6 : bond 0.00813 / 0.47 ( 9) link_ALPHA1-6 : angle 1.93692 / 1.20 ( 27) link_BETA1-4 : bond 0.00721 / 0.52 ( 51) link_BETA1-4 : angle 2.69126 / 1.99 ( 153) link_NAG-ASN : bond 0.00363 / 0.26 ( 57) link_NAG-ASN : angle 3.44127 / 2.52 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 277 time to evaluate : 1.237 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: B 535 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8095 (mpp) REVERT: B 542 ARG cc_start: 0.7914 (ptt-90) cc_final: 0.7490 (ptm160) REVERT: B 627 THR cc_start: 0.7573 (OUTLIER) cc_final: 0.7143 (p) REVERT: B 638 TYR cc_start: 0.3897 (p90) cc_final: 0.3620 (p90) REVERT: B 658 GLN cc_start: 0.3688 (OUTLIER) cc_final: 0.3264 (tp40) REVERT: G 49 GLU cc_start: 0.8100 (pm20) cc_final: 0.7835 (pt0) REVERT: G 63 THR cc_start: 0.2864 (OUTLIER) cc_final: 0.2527 (p) REVERT: G 130 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8529 (mm110) REVERT: G 189 LYS cc_start: 0.7667 (mmtm) cc_final: 0.7181 (mmmt) REVERT: G 190 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8545 (mt-10) REVERT: G 205 CYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6672 (m) REVERT: G 211 GLU cc_start: 0.7927 (pt0) cc_final: 0.7174 (mm-30) REVERT: G 265 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7718 (mt) REVERT: G 304 ARG cc_start: 0.8556 (ttm170) cc_final: 0.8343 (ttm170) REVERT: G 347 LYS cc_start: 0.8457 (tttt) cc_final: 0.8058 (ttpt) REVERT: G 426 MET cc_start: 0.7487 (ptt) cc_final: 0.7226 (ptt) REVERT: H 20 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6819 (mp) REVERT: H 35 HIS cc_start: 0.7181 (OUTLIER) cc_final: 0.6292 (p90) REVERT: h 45 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7165 (pt) REVERT: l 35 TRP cc_start: 0.6852 (OUTLIER) cc_final: 0.6367 (m-10) REVERT: l 94 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7658 (mmt90) REVERT: l 96 TRP cc_start: 0.8869 (m100) cc_final: 0.8436 (m100) REVERT: C 535 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.7566 (mpp) REVERT: C 542 ARG cc_start: 0.7891 (ptt-90) cc_final: 0.7458 (ptm-80) REVERT: C 585 ARG cc_start: 0.8817 (mtp-110) cc_final: 0.8572 (mmm-85) REVERT: C 631 TRP cc_start: 0.7441 (OUTLIER) cc_final: 0.6812 (t-100) REVERT: C 634 GLU cc_start: 0.6474 (tt0) cc_final: 0.6238 (mt-10) REVERT: A 49 GLU cc_start: 0.8228 (pm20) cc_final: 0.7713 (pt0) REVERT: A 102 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6800 (tp30) REVERT: A 130 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8291 (mm110) REVERT: A 190 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8460 (mm-30) REVERT: A 211 GLU cc_start: 0.7992 (pt0) cc_final: 0.7148 (mm-30) REVERT: A 347 LYS cc_start: 0.8400 (tttt) cc_final: 0.8068 (ttpt) REVERT: A 502 LYS cc_start: 0.7822 (tttt) cc_final: 0.7472 (tttt) REVERT: E 63 SER cc_start: 0.7149 (OUTLIER) cc_final: 0.6673 (t) REVERT: e 35 TRP cc_start: 0.7151 (OUTLIER) cc_final: 0.6736 (m-10) REVERT: e 52 GLN cc_start: 0.7490 (mm110) cc_final: 0.7275 (mm110) REVERT: e 61 ARG cc_start: 0.5702 (OUTLIER) cc_final: 0.5076 (ttp-110) REVERT: J 542 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7487 (ptp-110) REVERT: J 617 ARG cc_start: 0.6134 (mtp180) cc_final: 0.5623 (mtt90) REVERT: J 631 TRP cc_start: 0.7222 (OUTLIER) cc_final: 0.7005 (t-100) REVERT: J 652 GLN cc_start: 0.6653 (OUTLIER) cc_final: 0.6410 (tt0) REVERT: I 49 GLU cc_start: 0.8371 (pm20) cc_final: 0.7939 (pt0) REVERT: I 87 GLU cc_start: 0.7716 (tm-30) cc_final: 0.6934 (mp0) REVERT: I 102 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6897 (tp30) REVERT: I 189 LYS cc_start: 0.7625 (mmtm) cc_final: 0.7092 (mmmt) REVERT: I 211 GLU cc_start: 0.7947 (pt0) cc_final: 0.7279 (mm-30) REVERT: I 243 SER cc_start: 0.8224 (OUTLIER) cc_final: 0.7957 (p) REVERT: I 288 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.6980 (p90) REVERT: I 347 LYS cc_start: 0.8432 (tttt) cc_final: 0.8129 (ttpt) REVERT: I 350 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.5360 (mtp85) REVERT: K 20 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6832 (mp) REVERT: K 35 HIS cc_start: 0.7330 (OUTLIER) cc_final: 0.6431 (p90) REVERT: K 82 MET cc_start: 0.4928 (mmm) cc_final: 0.2604 (tmm) REVERT: M 21 MET cc_start: 0.5327 (OUTLIER) cc_final: 0.5028 (mmt) REVERT: M 56 THR cc_start: 0.6832 (OUTLIER) cc_final: 0.6557 (t) REVERT: m 94 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.6282 (mmm160) REVERT: m 96 TRP cc_start: 0.8809 (m100) cc_final: 0.8274 (m100) outliers start: 206 outliers final: 133 residues processed: 433 average time/residue: 0.5185 time to fit residues: 269.7159 Evaluate side-chains 437 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 273 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain h residue 7 SER Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain l residue 28 LEU Chi-restraints excluded: chain l residue 35 TRP Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 590 GLN Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 631 TRP Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 95 THR Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 108 THR Chi-restraints excluded: chain e residue 28 LEU Chi-restraints excluded: chain e residue 35 TRP Chi-restraints excluded: chain e residue 61 ARG Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain J residue 542 ARG Chi-restraints excluded: chain J residue 599 SER Chi-restraints excluded: chain J residue 631 TRP Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 652 GLN Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 72 HIS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 288 PHE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 350 ARG Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 35 HIS Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 45 LEU Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain k residue 100 GLU Chi-restraints excluded: chain k residue 100 VAL Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain m residue 28 LEU Chi-restraints excluded: chain m residue 94 ARG Chi-restraints excluded: chain m residue 95 VAL Chi-restraints excluded: chain m residue 95 THR Chi-restraints excluded: chain m residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 204 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 241 optimal weight: 0.0370 chunk 49 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 266 optimal weight: 1.9990 overall best weight: 1.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN A 103 GLN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 302 ASN ** I 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.202247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.153789 restraints weight = 33760.696| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 3.90 r_work: 0.3554 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26658 Z= 0.151 Angle : 0.753 14.104 36468 Z= 0.348 Chirality : 0.046 0.235 4413 Planarity : 0.004 0.032 4392 Dihedral : 9.036 81.684 6098 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.48 % Favored : 93.39 % Rotamer: Outliers : 7.06 % Allowed : 29.32 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.15), residues: 3054 helix: 0.90 (0.31), residues: 333 sheet: 0.17 (0.17), residues: 888 loop : -1.34 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 53 TYR 0.017 0.001 TYR H 91 PHE 0.025 0.002 PHE I 288 TRP 0.019 0.001 TRP k 34 HIS 0.006 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (26481) covalent geometry : angle 0.68257 / 0.33 (35982) SS BOND : bond 0.00770 / 0.54 ( 45) SS BOND : angle 2.43727 / 1.65 ( 90) hydrogen bonds : bond 0.04197 / 2.79 ( 739) hydrogen bonds : angle 5.32818 / 3.75 ( 1959) link_ALPHA1-2 : bond 0.00455 / 0.23 ( 6) link_ALPHA1-2 : angle 1.51872 / 1.00 ( 18) link_ALPHA1-3 : bond 0.00704 / 0.38 ( 9) link_ALPHA1-3 : angle 1.55277 / 1.04 ( 27) link_ALPHA1-6 : bond 0.00722 / 0.42 ( 9) link_ALPHA1-6 : angle 1.88717 / 1.20 ( 27) link_BETA1-4 : bond 0.00657 / 0.47 ( 51) link_BETA1-4 : angle 2.52865 / 1.82 ( 153) link_NAG-ASN : bond 0.00401 / 0.30 ( 57) link_NAG-ASN : angle 3.58074 / 2.63 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 276 time to evaluate : 1.654 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: B 535 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8050 (mpp) REVERT: B 542 ARG cc_start: 0.7930 (ptt-90) cc_final: 0.7518 (ptm160) REVERT: B 627 THR cc_start: 0.7664 (OUTLIER) cc_final: 0.7230 (p) REVERT: B 658 GLN cc_start: 0.3641 (OUTLIER) cc_final: 0.3311 (tp40) REVERT: G 49 GLU cc_start: 0.8180 (pm20) cc_final: 0.7844 (pt0) REVERT: G 63 THR cc_start: 0.2795 (OUTLIER) cc_final: 0.2483 (p) REVERT: G 130 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8584 (mm110) REVERT: G 150 MET cc_start: 0.3818 (tpt) cc_final: 0.1891 (pp-130) REVERT: G 189 LYS cc_start: 0.7699 (mmtm) cc_final: 0.7200 (mmmt) REVERT: G 211 GLU cc_start: 0.7912 (pt0) cc_final: 0.7168 (mm-30) REVERT: G 265 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7720 (mt) REVERT: G 347 LYS cc_start: 0.8493 (tttt) cc_final: 0.8090 (ttpt) REVERT: G 426 MET cc_start: 0.7547 (ptt) cc_final: 0.7262 (ptt) REVERT: H 20 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6829 (mp) REVERT: H 35 HIS cc_start: 0.7250 (OUTLIER) cc_final: 0.6197 (p90) REVERT: h 45 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7136 (pt) REVERT: l 35 TRP cc_start: 0.6867 (OUTLIER) cc_final: 0.6408 (m-10) REVERT: l 94 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.7629 (mmt90) REVERT: l 96 TRP cc_start: 0.8868 (m100) cc_final: 0.8402 (m100) REVERT: C 535 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.7592 (mpp) REVERT: C 542 ARG cc_start: 0.7883 (ptt-90) cc_final: 0.7477 (ptm-80) REVERT: C 585 ARG cc_start: 0.8830 (mtp-110) cc_final: 0.8588 (mmm-85) REVERT: C 590 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.7300 (mp10) REVERT: C 631 TRP cc_start: 0.7448 (OUTLIER) cc_final: 0.6831 (t-100) REVERT: C 634 GLU cc_start: 0.6414 (tt0) cc_final: 0.6175 (mt-10) REVERT: A 49 GLU cc_start: 0.8291 (pm20) cc_final: 0.7998 (pm20) REVERT: A 102 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6878 (tp30) REVERT: A 117 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7420 (mmmt) REVERT: A 130 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8289 (mm110) REVERT: A 190 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8466 (mm-30) REVERT: A 211 GLU cc_start: 0.8019 (pt0) cc_final: 0.7163 (mm-30) REVERT: A 347 LYS cc_start: 0.8432 (tttt) cc_final: 0.8089 (ttpt) REVERT: A 485 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7593 (ptmt) REVERT: A 502 LYS cc_start: 0.7848 (tttt) cc_final: 0.7477 (tttt) REVERT: E 63 SER cc_start: 0.7157 (OUTLIER) cc_final: 0.6675 (t) REVERT: E 97 THR cc_start: 0.8125 (m) cc_final: 0.7909 (m) REVERT: e 35 TRP cc_start: 0.7155 (OUTLIER) cc_final: 0.6716 (m-10) REVERT: e 52 GLN cc_start: 0.7524 (mm110) cc_final: 0.7308 (mm110) REVERT: e 96 TRP cc_start: 0.8649 (m100) cc_final: 0.8179 (m100) REVERT: J 542 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7728 (ptp-170) REVERT: J 652 GLN cc_start: 0.6679 (OUTLIER) cc_final: 0.6454 (tt0) REVERT: J 658 GLN cc_start: 0.3890 (OUTLIER) cc_final: 0.3166 (tp40) REVERT: I 49 GLU cc_start: 0.8458 (pm20) cc_final: 0.8032 (pt0) REVERT: I 87 GLU cc_start: 0.7722 (tm-30) cc_final: 0.6897 (mp0) REVERT: I 102 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6974 (tp30) REVERT: I 189 LYS cc_start: 0.7643 (mmtm) cc_final: 0.7114 (mmmt) REVERT: I 211 GLU cc_start: 0.7943 (pt0) cc_final: 0.7350 (mm-30) REVERT: I 288 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7077 (p90) REVERT: I 347 LYS cc_start: 0.8483 (tttt) cc_final: 0.8155 (ttpt) REVERT: I 350 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.5540 (mtp85) REVERT: K 20 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6840 (mp) REVERT: K 82 MET cc_start: 0.4912 (mmm) cc_final: 0.2609 (tmm) REVERT: M 21 MET cc_start: 0.5367 (OUTLIER) cc_final: 0.5063 (mmt) REVERT: M 56 THR cc_start: 0.6865 (OUTLIER) cc_final: 0.6583 (t) REVERT: m 94 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.6266 (mmm160) REVERT: m 96 TRP cc_start: 0.8801 (m100) cc_final: 0.8241 (m100) outliers start: 190 outliers final: 134 residues processed: 419 average time/residue: 0.4765 time to fit residues: 240.9674 Evaluate side-chains 434 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 270 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 276 ASN Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain h residue 7 SER Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain l residue 28 LEU Chi-restraints excluded: chain l residue 35 TRP Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 590 GLN Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 631 TRP Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 95 THR Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 108 THR Chi-restraints excluded: chain e residue 28 LEU Chi-restraints excluded: chain e residue 35 TRP Chi-restraints excluded: chain e residue 61 ARG Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain J residue 542 ARG Chi-restraints excluded: chain J residue 599 SER Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 652 GLN Chi-restraints excluded: chain J residue 658 GLN Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 72 HIS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 288 PHE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 350 ARG Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 35 HIS Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 45 LEU Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain k residue 100 GLU Chi-restraints excluded: chain k residue 100 VAL Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain m residue 28 LEU Chi-restraints excluded: chain m residue 94 ARG Chi-restraints excluded: chain m residue 95 VAL Chi-restraints excluded: chain m residue 95 THR Chi-restraints excluded: chain m residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 281 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 177 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 280 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 61 optimal weight: 0.1980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 543 ASN A 103 GLN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 97 HIS m 51 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.199890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.145014 restraints weight = 33722.343| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 3.39 r_work: 0.3532 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 26658 Z= 0.257 Angle : 0.937 55.835 36468 Z= 0.455 Chirality : 0.054 1.404 4413 Planarity : 0.004 0.100 4392 Dihedral : 9.135 83.969 6093 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.71 % Favored : 93.16 % Rotamer: Outliers : 6.69 % Allowed : 29.88 % Favored : 63.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.01 (0.15), residues: 3054 helix: 0.60 (0.30), residues: 351 sheet: 0.16 (0.17), residues: 894 loop : -1.42 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 542 TYR 0.019 0.002 TYR H 91 PHE 0.035 0.002 PHE G 288 TRP 0.018 0.002 TRP k 34 HIS 0.007 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.26 (26481) covalent geometry : angle 0.85663 / 0.44 (35982) SS BOND : bond 0.00985 / 0.71 ( 45) SS BOND : angle 2.84600 / 1.92 ( 90) hydrogen bonds : bond 0.04733 / 3.16 ( 739) hydrogen bonds : angle 5.40947 / 3.81 ( 1959) link_ALPHA1-2 : bond 0.00551 / 0.27 ( 6) link_ALPHA1-2 : angle 1.59567 / 1.00 ( 18) link_ALPHA1-3 : bond 0.00615 / 0.33 ( 9) link_ALPHA1-3 : angle 1.58341 / 1.05 ( 27) link_ALPHA1-6 : bond 0.00647 / 0.38 ( 9) link_ALPHA1-6 : angle 2.04653 / 1.30 ( 27) link_BETA1-4 : bond 0.00644 / 0.46 ( 51) link_BETA1-4 : angle 2.62994 / 1.87 ( 153) link_NAG-ASN : bond 0.00495 / 0.37 ( 57) link_NAG-ASN : angle 4.58646 / 3.38 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 267 time to evaluate : 1.013 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: B 535 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8025 (mpp) REVERT: B 542 ARG cc_start: 0.7965 (ptt-90) cc_final: 0.7559 (ptm160) REVERT: B 627 THR cc_start: 0.7701 (OUTLIER) cc_final: 0.7246 (p) REVERT: B 658 GLN cc_start: 0.3713 (OUTLIER) cc_final: 0.3399 (tp40) REVERT: G 49 GLU cc_start: 0.8178 (pm20) cc_final: 0.7904 (pt0) REVERT: G 63 THR cc_start: 0.2750 (OUTLIER) cc_final: 0.2418 (p) REVERT: G 102 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6990 (tp30) REVERT: G 130 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8513 (mm110) REVERT: G 150 MET cc_start: 0.3871 (tpt) cc_final: 0.1938 (pp-130) REVERT: G 189 LYS cc_start: 0.7773 (mmtm) cc_final: 0.7289 (mmmt) REVERT: G 190 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8435 (mm-30) REVERT: G 288 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7323 (p90) REVERT: G 347 LYS cc_start: 0.8503 (tttt) cc_final: 0.8099 (ttpt) REVERT: G 426 MET cc_start: 0.7648 (ptt) cc_final: 0.7383 (ptt) REVERT: H 20 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6846 (mp) REVERT: H 35 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.6027 (p90) REVERT: h 45 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7132 (pt) REVERT: l 35 TRP cc_start: 0.6866 (OUTLIER) cc_final: 0.6388 (m-10) REVERT: l 94 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7784 (mmt90) REVERT: l 96 TRP cc_start: 0.8881 (m100) cc_final: 0.8405 (m100) REVERT: C 535 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.7621 (mpp) REVERT: C 542 ARG cc_start: 0.7852 (ptt180) cc_final: 0.7587 (ptm-80) REVERT: C 590 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7370 (mp10) REVERT: C 631 TRP cc_start: 0.7447 (OUTLIER) cc_final: 0.6859 (t-100) REVERT: C 634 GLU cc_start: 0.6422 (tt0) cc_final: 0.6175 (mt-10) REVERT: A 102 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6992 (tp30) REVERT: A 112 TRP cc_start: 0.8100 (OUTLIER) cc_final: 0.7807 (t-100) REVERT: A 117 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7488 (mmmt) REVERT: A 129 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8769 (mt) REVERT: A 130 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8358 (mm110) REVERT: A 190 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8476 (mm-30) REVERT: A 211 GLU cc_start: 0.8025 (pt0) cc_final: 0.7160 (mm-30) REVERT: A 347 LYS cc_start: 0.8452 (tttt) cc_final: 0.8076 (ttpt) REVERT: A 502 LYS cc_start: 0.7896 (tttt) cc_final: 0.7509 (tttt) REVERT: E 63 SER cc_start: 0.7078 (OUTLIER) cc_final: 0.6598 (t) REVERT: E 97 THR cc_start: 0.8164 (m) cc_final: 0.7939 (m) REVERT: e 35 TRP cc_start: 0.7220 (OUTLIER) cc_final: 0.6488 (m-10) REVERT: e 52 GLN cc_start: 0.7595 (mm110) cc_final: 0.7385 (mm110) REVERT: e 96 TRP cc_start: 0.8650 (m100) cc_final: 0.8131 (m100) REVERT: J 542 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7762 (ptp-170) REVERT: J 652 GLN cc_start: 0.6714 (OUTLIER) cc_final: 0.6485 (tt0) REVERT: J 658 GLN cc_start: 0.3911 (OUTLIER) cc_final: 0.3187 (tp40) REVERT: I 49 GLU cc_start: 0.8482 (pm20) cc_final: 0.8049 (pt0) REVERT: I 87 GLU cc_start: 0.7753 (tm-30) cc_final: 0.6854 (mp0) REVERT: I 102 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7057 (tp30) REVERT: I 150 MET cc_start: 0.3876 (tpt) cc_final: 0.1970 (pp-130) REVERT: I 189 LYS cc_start: 0.7655 (mmtm) cc_final: 0.7134 (mmmt) REVERT: I 211 GLU cc_start: 0.7957 (pt0) cc_final: 0.7359 (mm-30) REVERT: I 288 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.6860 (p90) REVERT: I 347 LYS cc_start: 0.8495 (tttt) cc_final: 0.8164 (ttpt) REVERT: I 350 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.5611 (mtp85) REVERT: K 20 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6844 (mp) REVERT: K 82 MET cc_start: 0.4964 (mmm) cc_final: 0.2683 (tmm) REVERT: M 21 MET cc_start: 0.5346 (OUTLIER) cc_final: 0.5037 (mmt) REVERT: M 56 THR cc_start: 0.6865 (OUTLIER) cc_final: 0.6587 (t) REVERT: m 94 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.6528 (mmm160) REVERT: m 96 TRP cc_start: 0.8805 (m100) cc_final: 0.8238 (m100) outliers start: 180 outliers final: 133 residues processed: 407 average time/residue: 0.4412 time to fit residues: 216.5648 Evaluate side-chains 426 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 261 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 276 ASN Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 288 PHE Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain h residue 7 SER Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain h residue 108 THR Chi-restraints excluded: chain l residue 28 LEU Chi-restraints excluded: chain l residue 35 TRP Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 590 GLN Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain C residue 631 TRP Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 95 THR Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 108 THR Chi-restraints excluded: chain e residue 28 LEU Chi-restraints excluded: chain e residue 35 TRP Chi-restraints excluded: chain e residue 61 ARG Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain J residue 542 ARG Chi-restraints excluded: chain J residue 599 SER Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 652 GLN Chi-restraints excluded: chain J residue 658 GLN Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 72 HIS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 288 PHE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 350 ARG Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 35 HIS Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 45 LEU Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain k residue 100 GLU Chi-restraints excluded: chain k residue 100 VAL Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain m residue 28 LEU Chi-restraints excluded: chain m residue 94 ARG Chi-restraints excluded: chain m residue 95 VAL Chi-restraints excluded: chain m residue 95 THR Chi-restraints excluded: chain m residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 110 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 231 optimal weight: 7.9990 chunk 294 optimal weight: 10.0000 chunk 291 optimal weight: 1.9990 chunk 239 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.200340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.145437 restraints weight = 33513.009| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 3.44 r_work: 0.3539 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 26658 Z= 0.227 Angle : 0.936 59.200 36468 Z= 0.451 Chirality : 0.052 1.320 4413 Planarity : 0.004 0.073 4392 Dihedral : 9.135 83.981 6093 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.75 % Favored : 93.12 % Rotamer: Outliers : 6.87 % Allowed : 29.65 % Favored : 63.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.03 (0.15), residues: 3054 helix: 0.59 (0.30), residues: 351 sheet: 0.18 (0.18), residues: 858 loop : -1.42 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 542 TYR 0.018 0.002 TYR H 91 PHE 0.035 0.002 PHE G 288 TRP 0.015 0.002 TRP h 34 HIS 0.006 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.22 (26481) covalent geometry : angle 0.85299 / 0.43 (35982) SS BOND : bond 0.01611 / 1.01 ( 45) SS BOND : angle 3.20265 / 2.24 ( 90) hydrogen bonds : bond 0.04598 / 3.06 ( 739) hydrogen bonds : angle 5.40568 / 3.81 ( 1959) link_ALPHA1-2 : bond 0.00527 / 0.26 ( 6) link_ALPHA1-2 : angle 1.58268 / 0.99 ( 18) link_ALPHA1-3 : bond 0.00625 / 0.33 ( 9) link_ALPHA1-3 : angle 1.58537 / 1.06 ( 27) link_ALPHA1-6 : bond 0.00638 / 0.39 ( 9) link_ALPHA1-6 : angle 2.04808 / 1.30 ( 27) link_BETA1-4 : bond 0.00621 / 0.44 ( 51) link_BETA1-4 : angle 2.61458 / 1.86 ( 153) link_NAG-ASN : bond 0.00499 / 0.36 ( 57) link_NAG-ASN : angle 4.58589 / 3.37 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9505.62 seconds wall clock time: 162 minutes 35.65 seconds (9755.65 seconds total)