Starting phenix.real_space_refine on Sat Aug 8 06:49:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q3x_72216/08_2026/9q3x_72216.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q3x_72216/08_2026/9q3x_72216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q3x_72216/08_2026/9q3x_72216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q3x_72216/08_2026/9q3x_72216.map" model { file = "/net/cci-nas-00/data/ceres_data/9q3x_72216/08_2026/9q3x_72216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q3x_72216/08_2026/9q3x_72216.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.027 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 135 5.16 5 C 16194 2.51 5 N 4263 2.21 5 O 5298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 25890 Number of models: 1 Model: "" Number of chains: 60 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: "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: "H" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 828 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "L" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 793 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 95} Chain: "h" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} 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: "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: "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: "D" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 828 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "E" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 793 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 95} Chain: "d" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} 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: "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: "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: "K" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 828 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "M" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 793 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 95} Chain: "k" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.03, per 1000 atoms: 0.19 Number of scatterers: 25890 At special positions: 0 Unit cell: (188.532, 186.753, 153.849, 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 135 16.00 O 5298 8.00 N 4263 7.00 C 16194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 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=2.03 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=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 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 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 A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " 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 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 I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.02 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " 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 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 Y 3 " - " MAN Y 4 " " BMA f 3 " - " MAN f 4 " " BMA n 3 " - " MAN n 4 " " BMA p 3 " - " MAN p 4 " " MAN p 7 " - " MAN p 8 " " BMA v 3 " - " MAN v 4 " " BMA z 3 " - " MAN z 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 5 " " BMA n 3 " - " MAN n 5 " " BMA p 3 " - " MAN p 7 " " MAN p 7 " - " MAN p 9 " " BMA z 3 " - " MAN z 5 " 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 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 A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 137 " " NAG A 603 " - " ASN A 133 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 462 " " NAG A 606 " - " ASN A 234 " " NAG A 607 " - " ASN A 339 " " NAG B 701 " - " ASN B 611 " " NAG C 701 " - " ASN C 611 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 137 " " NAG G 603 " - " ASN G 133 " " NAG G 604 " - " ASN G 197 " " NAG G 605 " - " ASN G 462 " " NAG G 606 " - " ASN G 234 " " NAG G 607 " - " 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 197 " " NAG I 605 " - " ASN I 462 " " NAG I 606 " - " ASN I 234 " " NAG I 607 " - " ASN I 339 " " NAG J 701 " - " ASN J 611 " " 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: 1.81 Conformation dependent library (CDL) restraints added in 843.5 milliseconds 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5694 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 58 sheets defined 15.3% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'G' and resid 102 through 115 removed outlier: 3.599A pdb=" N ASP G 113 " --> pdb=" O ILE G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.645A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 354 removed outlier: 3.923A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.521A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 3.635A 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 475 through 480 removed outlier: 3.696A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 520 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 571 through 595 Processing helix chain 'B' and resid 620 through 624 removed outlier: 4.040A pdb=" N TRP B 623 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 640 through 664 removed outlier: 3.513A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'h' and resid 83 through 87 removed outlier: 3.941A pdb=" N ASP h 86 " --> pdb=" O THR h 83 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER h 87 " --> pdb=" O ALA h 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 83 through 87' Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.989A pdb=" N TYR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR A 63 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 116 removed outlier: 3.767A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.660A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.888A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.567A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.707A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.701A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 520 Processing helix chain 'C' and resid 529 through 535 removed outlier: 3.540A pdb=" N MET C 535 " --> pdb=" O GLY C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 543 through 545 No H-bonds generated for 'chain 'C' and resid 543 through 545' Processing helix chain 'C' and resid 571 through 595 Processing helix chain 'C' and resid 627 through 636 Processing helix chain 'C' and resid 640 through 664 removed outlier: 3.785A pdb=" N GLY C 644 " --> pdb=" O GLN C 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.538A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 83 through 87 removed outlier: 3.966A pdb=" N ASP d 86 " --> pdb=" O THR d 83 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER d 87 " --> pdb=" O ALA d 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 83 through 87' Processing helix chain 'I' and resid 57 through 62 removed outlier: 3.965A pdb=" N TYR I 61 " --> pdb=" O ASP I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 116 removed outlier: 3.535A pdb=" N ASP I 113 " --> pdb=" O ILE I 109 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU I 116 " --> pdb=" O TRP I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 removed outlier: 3.600A pdb=" N CYS I 126 " --> pdb=" O THR I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 181 No H-bonds generated for 'chain 'I' and resid 179 through 181' Processing helix chain 'I' and resid 335 through 350 Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.501A pdb=" N THR I 373 " --> pdb=" O LEU I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.685A pdb=" N ARG I 429 " --> pdb=" O MET I 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 483 removed outlier: 3.630A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 516 through 520 Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 537 through 543 removed outlier: 4.124A pdb=" N ASN J 543 " --> pdb=" O VAL J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 571 through 595 Processing helix chain 'J' and resid 627 through 636 Processing helix chain 'J' and resid 640 through 664 removed outlier: 3.575A pdb=" N GLY J 644 " --> pdb=" O GLN J 640 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.563A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'k' and resid 61 through 64 removed outlier: 3.842A pdb=" N LYS k 64 " --> pdb=" O PRO k 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 61 through 64' Processing helix chain 'k' and resid 83 through 87 removed outlier: 3.978A pdb=" N ASP k 86 " --> pdb=" O THR k 83 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER k 87 " --> pdb=" O ALA k 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 83 through 87' Processing sheet with id=AA1, first strand: chain 'G' and resid 495 through 498 removed outlier: 5.633A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS B 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.039A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AA5, first strand: chain 'G' and resid 201 through 203 Processing sheet with id=AA6, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.614A pdb=" N LEU G 285 " --> pdb=" O ARG G 273 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 315 through 322 removed outlier: 6.781A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 11.120A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 12.429A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 11.721A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.740A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE G 294 " --> pdb=" O SER G 447 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.588A pdb=" N ASN H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR H 50 " --> pdb=" O ASN H 58 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TRP H 35 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.668A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.636A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'h' and resid 4 through 7 removed outlier: 3.537A pdb=" N THR h 21 " --> pdb=" O SER h 7 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLN h 77 " --> pdb=" O ASP h 72 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP h 72 " --> pdb=" O GLN h 77 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER h 79 " --> pdb=" O SER h 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'h' and resid 58 through 59 removed outlier: 3.871A pdb=" N ASN h 58 " --> pdb=" O TYR h 50 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR h 50 " --> pdb=" O ASN h 58 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TRP h 36 " --> pdb=" O ILE h 48 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR h 50 " --> pdb=" O TRP h 34 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TRP h 34 " --> pdb=" O TYR h 50 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR h 33 " --> pdb=" O THR h 95 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR h 100O" --> pdb=" O LEU h 96 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'h' and resid 58 through 59 removed outlier: 3.871A pdb=" N ASN h 58 " --> pdb=" O TYR h 50 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR h 50 " --> pdb=" O ASN h 58 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TRP h 36 " --> pdb=" O ILE h 48 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR h 50 " --> pdb=" O TRP h 34 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TRP h 34 " --> pdb=" O TYR h 50 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR h 33 " --> pdb=" O THR h 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR h 105 " --> pdb=" O TYR h 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'h' and resid 100 through 100A removed outlier: 3.600A pdb=" N PHE h 100K" --> pdb=" O ARG h 100 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'l' and resid 10 through 13 removed outlier: 6.201A pdb=" N ILE l 11 " --> pdb=" O THR l 105 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR l 102 " --> pdb=" O TYR l 86 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR l 86 " --> pdb=" O THR l 102 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE l 48 " --> pdb=" O TRP l 35 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLN l 37 " --> pdb=" O LEU l 46 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU l 46 " --> pdb=" O GLN l 37 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'l' and resid 19 through 23 removed outlier: 4.212A pdb=" N ALA l 71 " --> pdb=" O CYS l 23 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 495 through 499 removed outlier: 3.531A pdb=" N GLY A 495 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TRP A 35 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU A 34 " --> pdb=" O TRP C 610 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL A 36 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL C 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N VAL A 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N THR C 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AC4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'A' and resid 201 through 203 removed outlier: 3.658A pdb=" N TYR A 435 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.646A pdb=" N LEU A 285 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.646A pdb=" N LEU A 285 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 11.031A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.119A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.318A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.590A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.816A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE A 294 " --> pdb=" O SER A 447 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 302 through 312 removed outlier: 5.805A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'D' and resid 57 through 59 removed outlier: 3.560A pdb=" N TYR D 50 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D 89 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL D 107 " --> pdb=" O TYR D 90 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 67 through 72 removed outlier: 3.687A pdb=" N SER D 79 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP D 72 " --> pdb=" O GLN D 77 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.560A pdb=" N VAL E 19 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.667A pdb=" N ASP E 105 " --> pdb=" O LEU E 11 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.840A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'd' and resid 4 through 7 removed outlier: 4.413A pdb=" N GLN d 77 " --> pdb=" O ASP d 72 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP d 72 " --> pdb=" O GLN d 77 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER d 79 " --> pdb=" O SER d 70 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER d 70 " --> pdb=" O SER d 79 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'd' and resid 58 through 59 removed outlier: 3.851A pdb=" N ASN d 58 " --> pdb=" O TYR d 50 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR d 50 " --> pdb=" O ASN d 58 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TRP d 36 " --> pdb=" O ILE d 48 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TYR d 50 " --> pdb=" O TRP d 34 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TRP d 34 " --> pdb=" O TYR d 50 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR d 33 " --> pdb=" O THR d 95 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR d 100O" --> pdb=" O LEU d 96 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'd' and resid 58 through 59 removed outlier: 3.851A pdb=" N ASN d 58 " --> pdb=" O TYR d 50 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR d 50 " --> pdb=" O ASN d 58 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TRP d 36 " --> pdb=" O ILE d 48 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TYR d 50 " --> pdb=" O TRP d 34 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TRP d 34 " --> pdb=" O TYR d 50 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR d 33 " --> pdb=" O THR d 95 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR d 105 " --> pdb=" O TYR d 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'd' and resid 100 through 100A removed outlier: 3.511A pdb=" N PHE d 100K" --> pdb=" O ARG d 100 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'e' and resid 10 through 13 removed outlier: 6.200A pdb=" N ILE e 11 " --> pdb=" O THR e 105 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR e 102 " --> pdb=" O TYR e 86 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR e 86 " --> pdb=" O THR e 102 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE e 48 " --> pdb=" O TRP e 35 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLN e 37 " --> pdb=" O LEU e 46 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU e 46 " --> pdb=" O GLN e 37 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'e' and resid 19 through 23 removed outlier: 3.504A pdb=" N ALA e 19 " --> pdb=" O ILE e 75 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE e 21 " --> pdb=" O LEU e 73 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA e 71 " --> pdb=" O CYS e 23 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 495 through 498 removed outlier: 3.558A pdb=" N GLY I 495 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR J 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 45 through 47 Processing sheet with id=AE6, first strand: chain 'I' and resid 55 through 56 Processing sheet with id=AE7, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=AE8, first strand: chain 'I' and resid 201 through 203 Processing sheet with id=AE9, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.603A pdb=" N LEU I 285 " --> pdb=" O ARG I 273 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLN I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER I 334 " --> pdb=" O GLN I 293 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU I 381 " --> pdb=" O CYS I 378 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.603A pdb=" N LEU I 285 " --> pdb=" O ARG I 273 " (cutoff:3.500A) removed outlier: 10.684A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 11.101A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 12.330A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 11.586A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 11.063A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE I 294 " --> pdb=" O SER I 447 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 302 through 312 removed outlier: 6.070A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AF4, first strand: chain 'K' and resid 57 through 59 removed outlier: 3.508A pdb=" N ASN K 58 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR K 50 " --> pdb=" O ASN K 58 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR K 50 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TRP K 35 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE K 37 " --> pdb=" O TYR K 91 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN K 39 " --> pdb=" O VAL K 89 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL K 89 " --> pdb=" O GLN K 39 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR K 90 " --> pdb=" O VAL K 107 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL K 107 " --> pdb=" O TYR K 90 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 69 through 72 removed outlier: 3.606A pdb=" N SER K 79 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP K 72 " --> pdb=" O GLN K 77 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 5 through 7 Processing sheet with id=AF7, first strand: chain 'M' and resid 53 through 54 removed outlier: 6.531A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'k' and resid 4 through 7 removed outlier: 4.506A pdb=" N GLN k 77 " --> pdb=" O ASP k 72 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP k 72 " --> pdb=" O GLN k 77 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'k' and resid 58 through 59 removed outlier: 3.859A pdb=" N ASN k 58 " --> pdb=" O TYR k 50 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR k 50 " --> pdb=" O ASN k 58 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TRP k 36 " --> pdb=" O ILE k 48 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR k 50 " --> pdb=" O TRP k 34 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TRP k 34 " --> pdb=" O TYR k 50 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR k 33 " --> pdb=" O THR k 95 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR k 100O" --> pdb=" O LEU k 96 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'k' and resid 58 through 59 removed outlier: 3.859A pdb=" N ASN k 58 " --> pdb=" O TYR k 50 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR k 50 " --> pdb=" O ASN k 58 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TRP k 36 " --> pdb=" O ILE k 48 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR k 50 " --> pdb=" O TRP k 34 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TRP k 34 " --> pdb=" O TYR k 50 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR k 33 " --> pdb=" O THR k 95 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR k 105 " --> pdb=" O TYR k 90 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'k' and resid 100 through 100A removed outlier: 3.600A pdb=" N PHE k 100K" --> pdb=" O ARG k 100 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'm' and resid 10 through 13 removed outlier: 6.190A pdb=" N ILE m 11 " --> pdb=" O THR m 105 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR m 102 " --> pdb=" O TYR m 86 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'm' and resid 19 through 23 removed outlier: 3.527A pdb=" N ALA m 19 " --> pdb=" O ILE m 75 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE m 75 " --> pdb=" O ALA m 19 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE m 21 " --> pdb=" O LEU m 73 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA m 71 " --> pdb=" O CYS m 23 " (cutoff:3.500A) 733 hydrogen bonds defined for protein. 1956 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: 3.89 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7954 1.34 - 1.47: 7027 1.47 - 1.59: 11272 1.59 - 1.72: 0 1.72 - 1.84: 180 Bond restraints: 26433 Sorted by residual: bond pdb=" CB GLU B 621 " pdb=" CG GLU B 621 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" CA ASN I 356 " pdb=" CB ASN I 356 " ideal model delta sigma weight residual 1.536 1.588 -0.052 4.10e-02 5.95e+02 1.59e+00 bond pdb=" C ASN I 80 " pdb=" N PRO I 81 " ideal model delta sigma weight residual 1.330 1.345 -0.015 1.19e-02 7.06e+03 1.58e+00 bond pdb=" CB ASN A 197 " pdb=" CG ASN A 197 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.55e+00 bond pdb=" CA THR B 639 " pdb=" CB THR B 639 " ideal model delta sigma weight residual 1.534 1.551 -0.017 1.34e-02 5.57e+03 1.52e+00 ... (remaining 26428 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 35464 2.31 - 4.63: 412 4.63 - 6.94: 49 6.94 - 9.25: 2 9.25 - 11.57: 1 Bond angle restraints: 35928 Sorted by residual: angle pdb=" N LEU J 537 " pdb=" CA LEU J 537 " pdb=" C LEU J 537 " ideal model delta sigma weight residual 114.56 109.37 5.19 1.27e+00 6.20e-01 1.67e+01 angle pdb=" CB MET k 2 " pdb=" CG MET k 2 " pdb=" SD MET k 2 " ideal model delta sigma weight residual 112.70 124.27 -11.57 3.00e+00 1.11e-01 1.49e+01 angle pdb=" N ILE m 47 " pdb=" CA ILE m 47 " pdb=" C ILE m 47 " ideal model delta sigma weight residual 111.62 108.65 2.97 7.90e-01 1.60e+00 1.41e+01 angle pdb=" C VAL A 68 " pdb=" N TRP A 69 " pdb=" CA TRP A 69 " ideal model delta sigma weight residual 120.79 125.71 -4.92 1.39e+00 5.18e-01 1.25e+01 angle pdb=" C ASN G 67 " pdb=" N VAL G 68 " pdb=" CA VAL G 68 " ideal model delta sigma weight residual 121.97 115.64 6.33 1.80e+00 3.09e-01 1.24e+01 ... (remaining 35923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.37: 15942 25.37 - 50.74: 1289 50.74 - 76.11: 176 76.11 - 101.48: 38 101.48 - 126.85: 24 Dihedral angle restraints: 17469 sinusoidal: 8586 harmonic: 8883 Sorted by residual: dihedral pdb=" CB CYS I 218 " pdb=" SG CYS I 218 " pdb=" SG CYS I 247 " pdb=" CB CYS I 247 " ideal model delta sinusoidal sigma weight residual 93.00 17.51 75.49 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CB CYS I 54 " pdb=" SG CYS I 54 " pdb=" SG CYS I 74 " pdb=" CB CYS I 74 " ideal model delta sinusoidal sigma weight residual -86.00 -11.54 -74.46 1 1.00e+01 1.00e-02 7.03e+01 dihedral pdb=" CB CYS G 218 " pdb=" SG CYS G 218 " pdb=" SG CYS G 247 " pdb=" CB CYS G 247 " ideal model delta sinusoidal sigma weight residual 93.00 30.94 62.06 1 1.00e+01 1.00e-02 5.10e+01 ... (remaining 17466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 4000 0.080 - 0.160: 399 0.160 - 0.241: 8 0.241 - 0.321: 2 0.321 - 0.401: 1 Chirality restraints: 4410 Sorted by residual: chirality pdb=" C1 NAG G 606 " pdb=" ND2 ASN G 234 " pdb=" C2 NAG G 606 " pdb=" O5 NAG G 606 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" C1 NAG I 606 " pdb=" ND2 ASN I 234 " pdb=" C2 NAG I 606 " pdb=" O5 NAG I 606 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C1 NAG A 606 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A 606 " pdb=" O5 NAG A 606 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 4407 not shown) Planarity restraints: 4440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 640 " -0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" C GLN B 640 " 0.035 2.00e-02 2.50e+03 pdb=" O GLN B 640 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE B 641 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN J 640 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.64e+00 pdb=" C GLN J 640 " -0.028 2.00e-02 2.50e+03 pdb=" O GLN J 640 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE J 641 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL I 75 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO I 76 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO I 76 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO I 76 " -0.022 5.00e-02 4.00e+02 ... (remaining 4437 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 12748 2.97 - 3.45: 23348 3.45 - 3.94: 39263 3.94 - 4.42: 41926 4.42 - 4.90: 72543 Nonbonded interactions: 189828 Sorted by model distance: nonbonded pdb=" O ASN A 356 " pdb=" OD1 ASN A 356 " model vdw 2.491 3.040 nonbonded pdb=" C4 NAG x 1 " pdb=" O5 NAG x 2 " model vdw 2.509 2.776 nonbonded pdb=" C4 NAG W 1 " pdb=" O5 NAG W 2 " model vdw 2.516 2.776 nonbonded pdb=" N GLU B 621 " pdb=" OE1 GLU B 621 " model vdw 2.523 3.120 nonbonded pdb=" O ASN G 356 " pdb=" OD1 ASN G 356 " model vdw 2.543 3.040 ... (remaining 189823 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: 0.02 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'O' selection = chain 'p' } ncs_group { reference = chain '1' selection = chain '2' 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 'f' selection = chain 'v' } ncs_group { reference = chain 'X' selection = chain 'j' selection = chain 'y' } ncs_group { reference = chain 'Y' selection = chain 'n' selection = chain 'z' } 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 group one per residue 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: 3.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 19.460 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 0.052 26613 Z= 0.121 Angle : 0.666 13.159 36423 Z= 0.314 Chirality : 0.044 0.401 4410 Planarity : 0.003 0.039 4380 Dihedral : 17.556 126.848 11640 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.96 % Allowed : 27.32 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.22 (0.15), residues: 3039 helix: 1.60 (0.30), residues: 336 sheet: -0.59 (0.18), residues: 858 loop : -1.43 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG l 31 TYR 0.015 0.001 TYR k 100M PHE 0.014 0.001 PHE I 223 TRP 0.021 0.001 TRP e 96 HIS 0.002 0.001 HIS I 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (26433) covalent geometry : angle 0.59603 / 0.30 (35928) SS BOND : bond 0.00390 / 0.18 ( 45) SS BOND : angle 1.22044 / 0.84 ( 90) hydrogen bonds : bond 0.24012 / 16.12 ( 701) hydrogen bonds : angle 9.47896 / 6.56 ( 1956) link_ALPHA1-2 : bond 0.00437 / 0.21 ( 6) link_ALPHA1-2 : angle 1.44346 / 0.87 ( 18) link_ALPHA1-3 : bond 0.00969 / 0.53 ( 12) link_ALPHA1-3 : angle 1.36553 / 0.88 ( 36) link_ALPHA1-6 : bond 0.00693 / 0.39 ( 9) link_ALPHA1-6 : angle 1.42483 / 0.94 ( 27) link_BETA1-4 : bond 0.00867 / 0.46 ( 48) link_BETA1-4 : angle 2.45857 / 2.01 ( 144) link_NAG-ASN : bond 0.00581 / 0.40 ( 60) link_NAG-ASN : angle 3.53433 / 2.52 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 264 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 114 GLN cc_start: 0.8392 (tm-30) cc_final: 0.8068 (tt0) REVERT: G 190 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8120 (mt-10) REVERT: A 114 GLN cc_start: 0.8469 (tm-30) cc_final: 0.7862 (tm-30) REVERT: A 190 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7796 (mt-10) REVERT: C 544 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7595 (tp) REVERT: d 100 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: d 100 TYR cc_start: 0.6910 (p90) cc_final: 0.6400 (p90) REVERT: J 640 GLN cc_start: 0.6489 (tm-30) cc_final: 0.6145 (tm-30) outliers start: 106 outliers final: 90 residues processed: 348 average time/residue: 0.1351 time to fit residues: 80.3055 Evaluate side-chains 351 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 257 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 190 GLU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 228 CYS Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain d residue 45 LEU Chi-restraints excluded: chain d residue 95 THR Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 370 GLU Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 584 GLU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 36 TRP Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain m residue 50 ASN Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain m residue 95 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 67 ASN G 85 HIS ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN E 37 GLN ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN k 77 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.246812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.221226 restraints weight = 35431.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.213898 restraints weight = 58172.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.212765 restraints weight = 64031.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.212452 restraints weight = 60734.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.211988 restraints weight = 49377.264| |-----------------------------------------------------------------------------| r_work (final): 0.4492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 26613 Z= 0.208 Angle : 0.764 14.960 36423 Z= 0.353 Chirality : 0.047 0.290 4410 Planarity : 0.004 0.042 4380 Dihedral : 11.858 107.309 6245 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 8.81 % Allowed : 23.14 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.28 (0.15), residues: 3039 helix: 1.33 (0.30), residues: 336 sheet: -0.52 (0.18), residues: 879 loop : -1.48 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 53 TYR 0.023 0.002 TYR E 91 PHE 0.025 0.002 PHE I 376 TRP 0.020 0.001 TRP e 96 HIS 0.005 0.001 HIS I 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.21 (26433) covalent geometry : angle 0.68393 / 0.33 (35928) SS BOND : bond 0.00590 / 0.33 ( 45) SS BOND : angle 1.40439 / 0.98 ( 90) hydrogen bonds : bond 0.04451 / 2.92 ( 701) hydrogen bonds : angle 6.90557 / 4.80 ( 1956) link_ALPHA1-2 : bond 0.00802 / 0.45 ( 6) link_ALPHA1-2 : angle 2.02663 / 1.20 ( 18) link_ALPHA1-3 : bond 0.00996 / 0.58 ( 12) link_ALPHA1-3 : angle 1.95028 / 1.21 ( 36) link_ALPHA1-6 : bond 0.00712 / 0.41 ( 9) link_ALPHA1-6 : angle 2.27865 / 1.50 ( 27) link_BETA1-4 : bond 0.00707 / 0.38 ( 48) link_BETA1-4 : angle 2.57956 / 2.04 ( 144) link_NAG-ASN : bond 0.00644 / 0.44 ( 60) link_NAG-ASN : angle 4.04956 / 2.85 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 271 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 20 LEU cc_start: 0.6118 (OUTLIER) cc_final: 0.5682 (mm) REVERT: h 80 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6370 (mp) REVERT: A 114 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8037 (tm-30) REVERT: A 190 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8059 (mt-10) REVERT: A 322 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7901 (tt) REVERT: A 454 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7716 (mt) REVERT: C 544 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7545 (tp) REVERT: E 58 VAL cc_start: 0.6364 (OUTLIER) cc_final: 0.6138 (p) REVERT: d 100 TYR cc_start: 0.6660 (p90) cc_final: 0.6375 (p90) REVERT: I 190 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8554 (mt-10) REVERT: I 454 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7622 (mt) outliers start: 236 outliers final: 146 residues processed: 480 average time/residue: 0.1403 time to fit residues: 112.5222 Evaluate side-chains 408 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 253 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 228 CYS Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 283 ASN Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 358 ILE Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 575 GLN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain h residue 11 LEU Chi-restraints excluded: chain h residue 20 LEU Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 50 ASN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 95 LYS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 89 LYS Chi-restraints excluded: chain e residue 50 ASN Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 258 GLN Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 345 VAL Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 423 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 454 LEU Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 535 MET Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 584 GLU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 598 CYS Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 646 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 36 TRP Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain k residue 21 THR Chi-restraints excluded: chain k residue 89 LYS Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 20 optimal weight: 0.1980 chunk 150 optimal weight: 0.9980 chunk 4 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 137 optimal weight: 0.5980 chunk 295 optimal weight: 7.9990 chunk 239 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 67 ASN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN A 195 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 ASN M 37 GLN k 77 GLN m 37 GLN m 50 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.253157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.229352 restraints weight = 35626.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.222428 restraints weight = 48371.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.217507 restraints weight = 56542.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.216624 restraints weight = 56221.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.214292 restraints weight = 53248.861| |-----------------------------------------------------------------------------| r_work (final): 0.4494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26613 Z= 0.114 Angle : 0.672 13.093 36423 Z= 0.307 Chirality : 0.045 0.356 4410 Planarity : 0.003 0.040 4380 Dihedral : 10.497 104.538 6179 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 6.53 % Allowed : 25.35 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 3039 helix: 1.59 (0.30), residues: 342 sheet: -0.20 (0.18), residues: 849 loop : -1.45 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.012 0.001 TYR L 49 PHE 0.018 0.001 PHE I 223 TRP 0.017 0.001 TRP I 69 HIS 0.003 0.001 HIS G 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (26433) covalent geometry : angle 0.59863 / 0.29 (35928) SS BOND : bond 0.00541 / 0.29 ( 45) SS BOND : angle 1.42246 / 0.97 ( 90) hydrogen bonds : bond 0.03758 / 2.50 ( 701) hydrogen bonds : angle 6.11613 / 4.22 ( 1956) link_ALPHA1-2 : bond 0.01038 / 0.57 ( 6) link_ALPHA1-2 : angle 2.26086 / 1.30 ( 18) link_ALPHA1-3 : bond 0.01127 / 0.66 ( 12) link_ALPHA1-3 : angle 1.70798 / 1.08 ( 36) link_ALPHA1-6 : bond 0.00901 / 0.52 ( 9) link_ALPHA1-6 : angle 2.12783 / 1.41 ( 27) link_BETA1-4 : bond 0.00849 / 0.45 ( 48) link_BETA1-4 : angle 2.45162 / 2.00 ( 144) link_NAG-ASN : bond 0.00580 / 0.41 ( 60) link_NAG-ASN : angle 3.50916 / 2.50 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 275 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: h 20 LEU cc_start: 0.6264 (OUTLIER) cc_final: 0.5712 (mm) REVERT: h 80 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6093 (mp) REVERT: A 114 GLN cc_start: 0.8423 (tm-30) cc_final: 0.7843 (tm-30) REVERT: A 190 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: C 544 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7495 (tp) REVERT: E 58 VAL cc_start: 0.6278 (OUTLIER) cc_final: 0.6076 (p) REVERT: d 100 TYR cc_start: 0.6766 (p90) cc_final: 0.6524 (p90) REVERT: I 190 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8525 (mt-10) REVERT: J 603 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.8031 (tt) outliers start: 175 outliers final: 106 residues processed: 428 average time/residue: 0.1346 time to fit residues: 97.6052 Evaluate side-chains 376 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 263 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 228 CYS Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain h residue 11 LEU Chi-restraints excluded: chain h residue 20 LEU Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain l residue 50 ASN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 95 LYS Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 89 LYS Chi-restraints excluded: chain e residue 50 ASN Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 195 ASN Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 258 GLN Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 289 ASN Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 385 CYS Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 423 ILE Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 584 GLU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 598 CYS Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 646 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 36 TRP Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain k residue 80 LEU Chi-restraints excluded: chain k residue 89 LYS Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain m residue 50 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 247 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 242 optimal weight: 2.9990 chunk 288 optimal weight: 4.9990 chunk 182 optimal weight: 20.0000 chunk 120 optimal weight: 3.9990 chunk 250 optimal weight: 0.9980 chunk 212 optimal weight: 0.6980 chunk 11 optimal weight: 0.0670 chunk 1 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 67 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN A 302 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 ASN I 302 ASN ** J 540 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 = 0.4751 r_free = 0.4751 target = 0.246942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.222300 restraints weight = 35303.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.215503 restraints weight = 47463.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.212579 restraints weight = 58946.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.212860 restraints weight = 58554.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.211422 restraints weight = 47990.610| |-----------------------------------------------------------------------------| r_work (final): 0.4534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26613 Z= 0.123 Angle : 0.670 13.278 36423 Z= 0.304 Chirality : 0.044 0.300 4410 Planarity : 0.003 0.041 4380 Dihedral : 9.849 102.508 6163 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 7.24 % Allowed : 24.52 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 3039 helix: 1.64 (0.30), residues: 342 sheet: -0.11 (0.19), residues: 843 loop : -1.46 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG d 100 TYR 0.011 0.001 TYR L 91 PHE 0.017 0.001 PHE G 223 TRP 0.015 0.001 TRP I 69 HIS 0.003 0.001 HIS I 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (26433) covalent geometry : angle 0.59571 / 0.29 (35928) SS BOND : bond 0.00428 / 0.21 ( 45) SS BOND : angle 1.22538 / 0.87 ( 90) hydrogen bonds : bond 0.03464 / 2.30 ( 701) hydrogen bonds : angle 5.77197 / 3.98 ( 1956) link_ALPHA1-2 : bond 0.01231 / 0.69 ( 6) link_ALPHA1-2 : angle 2.22739 / 1.31 ( 18) link_ALPHA1-3 : bond 0.01084 / 0.64 ( 12) link_ALPHA1-3 : angle 1.75203 / 1.11 ( 36) link_ALPHA1-6 : bond 0.00962 / 0.56 ( 9) link_ALPHA1-6 : angle 2.06218 / 1.35 ( 27) link_BETA1-4 : bond 0.00789 / 0.42 ( 48) link_BETA1-4 : angle 2.44887 / 1.99 ( 144) link_NAG-ASN : bond 0.00587 / 0.41 ( 60) link_NAG-ASN : angle 3.57299 / 2.54 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 269 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 20 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5659 (mm) REVERT: h 80 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6221 (mp) REVERT: h 100 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: A 114 GLN cc_start: 0.8446 (tm-30) cc_final: 0.7856 (tm-30) REVERT: A 190 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8230 (mt-10) REVERT: A 376 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7295 (p90) REVERT: C 544 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7575 (tp) REVERT: d 100 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: I 190 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8540 (mt-10) REVERT: k 2 MET cc_start: 0.4034 (tpp) cc_final: 0.3760 (tpp) outliers start: 194 outliers final: 137 residues processed: 432 average time/residue: 0.1312 time to fit residues: 96.6774 Evaluate side-chains 402 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 257 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 283 ASN Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain h residue 11 LEU Chi-restraints excluded: chain h residue 20 LEU Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 100 GLU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 95 LYS Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain d residue 2 MET Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 95 THR Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain e residue 46 LEU Chi-restraints excluded: chain e residue 50 ASN Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 195 ASN Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 258 GLN Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 345 VAL Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 425 ASN Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 584 GLU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 629 LEU Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 646 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 36 TRP Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain k residue 89 LYS Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 255 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 182 optimal weight: 30.0000 chunk 70 optimal weight: 7.9990 chunk 257 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 288 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 146 optimal weight: 8.9990 chunk 123 optimal weight: 0.7980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 67 ASN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN A 302 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN I 302 ASN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN m 50 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.243678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.219183 restraints weight = 35164.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.211565 restraints weight = 47702.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.209255 restraints weight = 58800.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.208827 restraints weight = 55747.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.207265 restraints weight = 45468.518| |-----------------------------------------------------------------------------| r_work (final): 0.4463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 26613 Z= 0.203 Angle : 0.747 15.200 36423 Z= 0.343 Chirality : 0.047 0.292 4410 Planarity : 0.004 0.040 4380 Dihedral : 9.931 101.380 6160 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 8.21 % Allowed : 24.08 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 3039 helix: 1.39 (0.30), residues: 336 sheet: -0.19 (0.18), residues: 846 loop : -1.52 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 273 TYR 0.023 0.002 TYR M 91 PHE 0.029 0.002 PHE G 376 TRP 0.014 0.001 TRP m 96 HIS 0.007 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.20 (26433) covalent geometry : angle 0.66643 / 0.32 (35928) SS BOND : bond 0.00577 / 0.32 ( 45) SS BOND : angle 1.52551 / 1.09 ( 90) hydrogen bonds : bond 0.03940 / 2.61 ( 701) hydrogen bonds : angle 5.79997 / 4.02 ( 1956) link_ALPHA1-2 : bond 0.01210 / 0.70 ( 6) link_ALPHA1-2 : angle 1.96446 / 1.28 ( 18) link_ALPHA1-3 : bond 0.00995 / 0.57 ( 12) link_ALPHA1-3 : angle 1.81556 / 1.16 ( 36) link_ALPHA1-6 : bond 0.00963 / 0.56 ( 9) link_ALPHA1-6 : angle 1.80410 / 1.17 ( 27) link_BETA1-4 : bond 0.00731 / 0.40 ( 48) link_BETA1-4 : angle 2.58505 / 2.06 ( 144) link_NAG-ASN : bond 0.00633 / 0.44 ( 60) link_NAG-ASN : angle 4.01689 / 2.81 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 265 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 190 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8531 (mt-10) REVERT: G 454 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7610 (mt) REVERT: B 603 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.6948 (tt) REVERT: h 20 LEU cc_start: 0.6257 (OUTLIER) cc_final: 0.5726 (mm) REVERT: h 80 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6244 (mp) REVERT: A 114 GLN cc_start: 0.8580 (tm-30) cc_final: 0.7962 (tm-30) REVERT: A 376 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7584 (p90) REVERT: C 544 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7531 (tp) REVERT: C 626 MET cc_start: 0.5839 (mmt) cc_final: 0.5596 (mmt) REVERT: d 100 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: I 114 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8276 (tt0) REVERT: I 305 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7886 (pttt) REVERT: I 454 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7484 (mt) REVERT: J 577 GLN cc_start: 0.7510 (mt0) cc_final: 0.7180 (mm-40) REVERT: k 2 MET cc_start: 0.4153 (tpp) cc_final: 0.3941 (tpp) outliers start: 220 outliers final: 162 residues processed: 454 average time/residue: 0.1331 time to fit residues: 103.3862 Evaluate side-chains 425 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 253 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 190 GLU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 283 ASN Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain G residue 385 CYS Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 454 LEU Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain h residue 11 LEU Chi-restraints excluded: chain h residue 20 LEU Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 50 ASN Chi-restraints excluded: chain l residue 69 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 95 LYS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 577 GLN Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 95 THR Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain e residue 50 ASN Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 258 GLN Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 289 ASN Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 305 LYS Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 345 VAL Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 385 CYS Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 423 ILE Chi-restraints excluded: chain I residue 425 ASN Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 454 LEU Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 583 VAL Chi-restraints excluded: chain J residue 584 GLU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 598 CYS Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 629 LEU Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 646 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 36 TRP Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain k residue 21 THR Chi-restraints excluded: chain k residue 80 LEU Chi-restraints excluded: chain k residue 89 LYS Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 50 ASN Chi-restraints excluded: chain m residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 234 optimal weight: 0.6980 chunk 260 optimal weight: 7.9990 chunk 256 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 201 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 243 optimal weight: 0.5980 chunk 172 optimal weight: 0.0570 chunk 25 optimal weight: 1.9990 chunk 283 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 67 ASN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 ASN I 302 ASN I 425 ASN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.259375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.222879 restraints weight = 36350.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.206657 restraints weight = 54980.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.203695 restraints weight = 60955.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.203700 restraints weight = 49995.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.204184 restraints weight = 36929.213| |-----------------------------------------------------------------------------| r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26613 Z= 0.132 Angle : 0.684 13.897 36423 Z= 0.313 Chirality : 0.045 0.295 4410 Planarity : 0.003 0.039 4380 Dihedral : 9.670 100.359 6155 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 6.87 % Allowed : 25.46 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.05 (0.15), residues: 3039 helix: 1.51 (0.30), residues: 342 sheet: -0.11 (0.19), residues: 837 loop : -1.47 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 178 TYR 0.015 0.001 TYR h 91 PHE 0.019 0.002 PHE I 223 TRP 0.015 0.001 TRP m 96 HIS 0.003 0.001 HIS I 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (26433) covalent geometry : angle 0.60669 / 0.29 (35928) SS BOND : bond 0.00556 / 0.33 ( 45) SS BOND : angle 1.46859 / 0.93 ( 90) hydrogen bonds : bond 0.03419 / 2.26 ( 701) hydrogen bonds : angle 5.49437 / 3.80 ( 1956) link_ALPHA1-2 : bond 0.00945 / 0.53 ( 6) link_ALPHA1-2 : angle 1.79965 / 1.17 ( 18) link_ALPHA1-3 : bond 0.01083 / 0.63 ( 12) link_ALPHA1-3 : angle 1.74123 / 1.12 ( 36) link_ALPHA1-6 : bond 0.00942 / 0.54 ( 9) link_ALPHA1-6 : angle 1.61239 / 1.04 ( 27) link_BETA1-4 : bond 0.00765 / 0.41 ( 48) link_BETA1-4 : angle 2.50262 / 2.02 ( 144) link_NAG-ASN : bond 0.00598 / 0.42 ( 60) link_NAG-ASN : angle 3.72698 / 2.63 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 267 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 503 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.5550 (ptp-170) REVERT: B 603 ILE cc_start: 0.7103 (OUTLIER) cc_final: 0.6766 (tt) REVERT: h 80 LEU cc_start: 0.6733 (OUTLIER) cc_final: 0.5833 (mp) REVERT: A 114 GLN cc_start: 0.8529 (tm-30) cc_final: 0.7915 (tm-30) REVERT: A 376 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7501 (p90) REVERT: C 544 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7494 (tp) REVERT: d 100 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: I 114 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8182 (tt0) REVERT: J 625 ASN cc_start: 0.7418 (OUTLIER) cc_final: 0.7168 (p0) REVERT: k 2 MET cc_start: 0.4512 (tpp) cc_final: 0.4125 (tpp) outliers start: 184 outliers final: 151 residues processed: 423 average time/residue: 0.1289 time to fit residues: 92.1097 Evaluate side-chains 417 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 259 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 283 ASN Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain G residue 385 CYS Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain G residue 476 ARG Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain G residue 503 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain h residue 11 LEU Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 50 ASN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 95 LYS Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 95 THR Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain e residue 50 ASN Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 195 ASN Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 258 GLN Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain I residue 345 VAL Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 385 CYS Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 423 ILE Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 584 GLU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 598 CYS Chi-restraints excluded: chain J residue 601 LYS Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 629 LEU Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 646 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 36 TRP Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain k residue 21 THR Chi-restraints excluded: chain k residue 80 LEU Chi-restraints excluded: chain k residue 89 LYS Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain m residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 237 optimal weight: 0.9990 chunk 275 optimal weight: 10.0000 chunk 79 optimal weight: 30.0000 chunk 113 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 67 ASN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN I 195 ASN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN m 50 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.244141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.217895 restraints weight = 35353.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.210085 restraints weight = 56388.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.208691 restraints weight = 60866.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.207971 restraints weight = 59437.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.206372 restraints weight = 51631.671| |-----------------------------------------------------------------------------| r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26613 Z= 0.184 Angle : 0.729 15.032 36423 Z= 0.334 Chirality : 0.046 0.293 4410 Planarity : 0.004 0.040 4380 Dihedral : 9.734 99.559 6152 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 7.54 % Allowed : 24.82 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.14 (0.15), residues: 3039 helix: 1.38 (0.30), residues: 342 sheet: -0.16 (0.18), residues: 849 loop : -1.53 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 617 TYR 0.019 0.002 TYR E 91 PHE 0.024 0.002 PHE G 376 TRP 0.015 0.001 TRP m 96 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.18 (26433) covalent geometry : angle 0.64776 / 0.32 (35928) SS BOND : bond 0.00567 / 0.29 ( 45) SS BOND : angle 1.73571 / 1.15 ( 90) hydrogen bonds : bond 0.03672 / 2.42 ( 701) hydrogen bonds : angle 5.51098 / 3.82 ( 1956) link_ALPHA1-2 : bond 0.00923 / 0.52 ( 6) link_ALPHA1-2 : angle 1.76074 / 1.15 ( 18) link_ALPHA1-3 : bond 0.01048 / 0.61 ( 12) link_ALPHA1-3 : angle 1.76399 / 1.15 ( 36) link_ALPHA1-6 : bond 0.00892 / 0.51 ( 9) link_ALPHA1-6 : angle 1.58677 / 1.02 ( 27) link_BETA1-4 : bond 0.00713 / 0.38 ( 48) link_BETA1-4 : angle 2.57578 / 2.06 ( 144) link_NAG-ASN : bond 0.00632 / 0.44 ( 60) link_NAG-ASN : angle 3.94495 / 2.77 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 269 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 454 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7401 (mt) REVERT: G 503 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.5906 (ptp-170) REVERT: B 603 ILE cc_start: 0.7204 (OUTLIER) cc_final: 0.6874 (tt) REVERT: h 80 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6300 (mp) REVERT: A 114 GLN cc_start: 0.8588 (tm-30) cc_final: 0.7989 (tm-30) REVERT: A 376 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7560 (p90) REVERT: C 544 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7487 (tp) REVERT: d 100 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: I 114 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8331 (tt0) REVERT: I 283 ASN cc_start: 0.7613 (OUTLIER) cc_final: 0.7247 (m-40) REVERT: I 454 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7447 (mt) REVERT: J 577 GLN cc_start: 0.7545 (mt0) cc_final: 0.7231 (mm-40) REVERT: k 2 MET cc_start: 0.4582 (tpp) cc_final: 0.4264 (tpp) outliers start: 202 outliers final: 163 residues processed: 439 average time/residue: 0.1335 time to fit residues: 98.9200 Evaluate side-chains 435 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 263 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 283 ASN Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain G residue 385 CYS Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 454 LEU Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain G residue 476 ARG Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain G residue 503 ARG Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain h residue 11 LEU Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 50 ASN Chi-restraints excluded: chain l residue 69 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 95 LYS Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 577 GLN Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 95 THR Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain e residue 50 ASN Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 195 ASN Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 258 GLN Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 283 ASN Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain I residue 345 VAL Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 385 CYS Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 423 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 454 LEU Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 584 GLU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 598 CYS Chi-restraints excluded: chain J residue 601 LYS Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 629 LEU Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 646 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 36 TRP Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain k residue 21 THR Chi-restraints excluded: chain k residue 80 LEU Chi-restraints excluded: chain k residue 89 LYS Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 50 ASN Chi-restraints excluded: chain m residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 50 optimal weight: 1.9990 chunk 158 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 186 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 278 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 281 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 67 ASN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN A 352 HIS E 37 GLN I 195 ASN I 302 ASN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.254152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.217302 restraints weight = 36392.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.196000 restraints weight = 56512.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.193929 restraints weight = 62004.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.192240 restraints weight = 50818.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.193243 restraints weight = 42212.153| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 26613 Z= 0.251 Angle : 0.803 16.253 36423 Z= 0.372 Chirality : 0.048 0.290 4410 Planarity : 0.004 0.042 4380 Dihedral : 10.068 99.706 6152 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.77 % Favored : 92.20 % Rotamer: Outliers : 7.76 % Allowed : 24.67 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.31 (0.15), residues: 3039 helix: 1.10 (0.29), residues: 342 sheet: -0.34 (0.18), residues: 864 loop : -1.58 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 617 TYR 0.025 0.002 TYR E 91 PHE 0.030 0.003 PHE G 376 TRP 0.017 0.002 TRP m 96 HIS 0.006 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.25 (26433) covalent geometry : angle 0.71972 / 0.35 (35928) SS BOND : bond 0.00706 / 0.39 ( 45) SS BOND : angle 1.86790 / 1.25 ( 90) hydrogen bonds : bond 0.04090 / 2.68 ( 701) hydrogen bonds : angle 5.68969 / 3.96 ( 1956) link_ALPHA1-2 : bond 0.00776 / 0.43 ( 6) link_ALPHA1-2 : angle 1.71068 / 1.14 ( 18) link_ALPHA1-3 : bond 0.01030 / 0.59 ( 12) link_ALPHA1-3 : angle 1.81636 / 1.19 ( 36) link_ALPHA1-6 : bond 0.00845 / 0.49 ( 9) link_ALPHA1-6 : angle 1.59995 / 1.03 ( 27) link_BETA1-4 : bond 0.00682 / 0.38 ( 48) link_BETA1-4 : angle 2.72206 / 2.15 ( 144) link_NAG-ASN : bond 0.00708 / 0.48 ( 60) link_NAG-ASN : angle 4.25497 / 2.96 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 267 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.7985 (mm) REVERT: G 454 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7475 (mt) REVERT: G 503 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.5697 (ptp-170) REVERT: B 603 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.7088 (tt) REVERT: h 80 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.5768 (mp) REVERT: A 376 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7693 (p90) REVERT: A 454 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7772 (mt) REVERT: C 640 GLN cc_start: 0.6589 (tm-30) cc_final: 0.6370 (tm-30) REVERT: I 283 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7508 (m-40) REVERT: I 454 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7656 (mt) outliers start: 208 outliers final: 176 residues processed: 442 average time/residue: 0.1378 time to fit residues: 102.8885 Evaluate side-chains 443 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 258 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 283 ASN Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain G residue 385 CYS Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 454 LEU Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 476 ARG Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain G residue 503 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain h residue 11 LEU Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 50 ASN Chi-restraints excluded: chain l residue 69 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 598 CYS Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 29 ILE Chi-restraints excluded: chain d residue 95 THR Chi-restraints excluded: chain e residue 50 ASN Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 195 ASN Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 258 GLN Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 283 ASN Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain I residue 345 VAL Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 385 CYS Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 423 ILE Chi-restraints excluded: chain I residue 425 ASN Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 454 LEU Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 583 VAL Chi-restraints excluded: chain J residue 584 GLU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 598 CYS Chi-restraints excluded: chain J residue 601 LYS Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 629 LEU Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 646 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 36 TRP Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain k residue 21 THR Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 50 ASN Chi-restraints excluded: chain m residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 50 optimal weight: 0.7980 chunk 252 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 177 optimal weight: 20.0000 chunk 212 optimal weight: 0.9980 chunk 163 optimal weight: 7.9990 chunk 87 optimal weight: 0.0670 chunk 160 optimal weight: 0.9990 chunk 230 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 103 GLN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 ASN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.249348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.225689 restraints weight = 35165.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.218951 restraints weight = 54595.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.216688 restraints weight = 57553.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.215953 restraints weight = 58764.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.214198 restraints weight = 49342.477| |-----------------------------------------------------------------------------| r_work (final): 0.4487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26613 Z= 0.126 Angle : 0.702 14.147 36423 Z= 0.321 Chirality : 0.045 0.291 4410 Planarity : 0.004 0.040 4380 Dihedral : 9.677 98.121 6152 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 5.86 % Allowed : 26.88 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.13 (0.15), residues: 3039 helix: 1.43 (0.30), residues: 342 sheet: -0.15 (0.19), residues: 816 loop : -1.52 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 617 TYR 0.013 0.001 TYR A 435 PHE 0.023 0.001 PHE I 223 TRP 0.017 0.001 TRP l 96 HIS 0.002 0.001 HIS I 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (26433) covalent geometry : angle 0.62272 / 0.30 (35928) SS BOND : bond 0.00438 / 0.21 ( 45) SS BOND : angle 1.37869 / 0.93 ( 90) hydrogen bonds : bond 0.03332 / 2.19 ( 701) hydrogen bonds : angle 5.29411 / 3.66 ( 1956) link_ALPHA1-2 : bond 0.00700 / 0.38 ( 6) link_ALPHA1-2 : angle 1.61897 / 1.05 ( 18) link_ALPHA1-3 : bond 0.01140 / 0.66 ( 12) link_ALPHA1-3 : angle 1.69424 / 1.10 ( 36) link_ALPHA1-6 : bond 0.00827 / 0.47 ( 9) link_ALPHA1-6 : angle 1.50271 / 0.97 ( 27) link_BETA1-4 : bond 0.00751 / 0.40 ( 48) link_BETA1-4 : angle 2.52523 / 2.04 ( 144) link_NAG-ASN : bond 0.00628 / 0.44 ( 60) link_NAG-ASN : angle 3.86758 / 2.78 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 270 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 103 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7788 (tm-30) REVERT: G 454 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7379 (mt) REVERT: G 503 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.5897 (ptp-170) REVERT: B 603 ILE cc_start: 0.7172 (OUTLIER) cc_final: 0.6868 (tt) REVERT: h 80 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6354 (mp) REVERT: A 114 GLN cc_start: 0.8545 (tm-30) cc_final: 0.7912 (tm-30) REVERT: A 223 PHE cc_start: 0.8285 (m-80) cc_final: 0.7898 (m-10) REVERT: A 376 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7462 (p90) REVERT: C 544 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7291 (tp) REVERT: C 640 GLN cc_start: 0.6543 (tm-30) cc_final: 0.6317 (tm-30) REVERT: d 100 TYR cc_start: 0.6978 (p90) cc_final: 0.6767 (p90) REVERT: I 114 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8227 (tt0) outliers start: 157 outliers final: 132 residues processed: 403 average time/residue: 0.1415 time to fit residues: 96.4351 Evaluate side-chains 402 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 263 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 283 ASN Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain G residue 385 CYS Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 454 LEU Chi-restraints excluded: chain G residue 476 ARG Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain G residue 503 ARG Chi-restraints excluded: chain B residue 575 GLN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain h residue 11 LEU Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 50 ASN Chi-restraints excluded: chain l residue 69 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 95 THR Chi-restraints excluded: chain e residue 50 ASN Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 195 ASN Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain I residue 258 GLN Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 345 VAL Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 385 CYS Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 425 ASN Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 584 GLU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 598 CYS Chi-restraints excluded: chain J residue 601 LYS Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 629 LEU Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 646 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 36 TRP Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain k residue 21 THR Chi-restraints excluded: chain m residue 50 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 187 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 180 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 160 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 67 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN A 195 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN I 195 ASN ** J 540 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 = 0.4800 r_free = 0.4800 target = 0.259397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.223187 restraints weight = 36285.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.201553 restraints weight = 55678.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.196218 restraints weight = 54712.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.196199 restraints weight = 43534.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.196952 restraints weight = 39311.224| |-----------------------------------------------------------------------------| r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26613 Z= 0.160 Angle : 0.727 14.637 36423 Z= 0.332 Chirality : 0.046 0.288 4410 Planarity : 0.004 0.052 4380 Dihedral : 9.633 97.543 6149 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 5.71 % Allowed : 26.91 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.14 (0.15), residues: 3039 helix: 1.42 (0.30), residues: 342 sheet: -0.16 (0.19), residues: 816 loop : -1.53 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 192 TYR 0.015 0.001 TYR E 91 PHE 0.022 0.002 PHE I 376 TRP 0.017 0.001 TRP l 96 HIS 0.003 0.001 HIS I 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (26433) covalent geometry : angle 0.64272 / 0.31 (35928) SS BOND : bond 0.00490 / 0.26 ( 45) SS BOND : angle 1.45089 / 0.99 ( 90) hydrogen bonds : bond 0.03444 / 2.26 ( 701) hydrogen bonds : angle 5.28935 / 3.66 ( 1956) link_ALPHA1-2 : bond 0.00658 / 0.36 ( 6) link_ALPHA1-2 : angle 1.62569 / 1.07 ( 18) link_ALPHA1-3 : bond 0.01102 / 0.64 ( 12) link_ALPHA1-3 : angle 1.73201 / 1.13 ( 36) link_ALPHA1-6 : bond 0.00797 / 0.45 ( 9) link_ALPHA1-6 : angle 1.53984 / 1.00 ( 27) link_BETA1-4 : bond 0.00708 / 0.38 ( 48) link_BETA1-4 : angle 2.54850 / 2.05 ( 144) link_NAG-ASN : bond 0.00630 / 0.44 ( 60) link_NAG-ASN : angle 4.13565 / 2.87 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 257 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 454 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7482 (mt) REVERT: G 503 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.5574 (ptp-170) REVERT: B 603 ILE cc_start: 0.7130 (OUTLIER) cc_final: 0.6835 (tt) REVERT: h 80 LEU cc_start: 0.6479 (OUTLIER) cc_final: 0.5613 (mp) REVERT: A 114 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8002 (tm-30) REVERT: A 130 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7478 (mt0) REVERT: A 376 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7542 (p90) REVERT: C 544 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7415 (tp) REVERT: C 621 GLU cc_start: 0.7117 (pm20) cc_final: 0.6865 (pm20) REVERT: C 640 GLN cc_start: 0.6707 (tm-30) cc_final: 0.6420 (tm-30) REVERT: d 100 TYR cc_start: 0.7359 (p90) cc_final: 0.7131 (p90) REVERT: I 114 GLN cc_start: 0.8619 (tm-30) cc_final: 0.8335 (tt0) REVERT: J 577 GLN cc_start: 0.7532 (mt0) cc_final: 0.7259 (mm-40) REVERT: J 601 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7321 (tptp) outliers start: 153 outliers final: 139 residues processed: 387 average time/residue: 0.1352 time to fit residues: 88.9321 Evaluate side-chains 403 residues out of total 2679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 256 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 283 ASN Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain G residue 385 CYS Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 454 LEU Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 476 ARG Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain G residue 503 ARG Chi-restraints excluded: chain B residue 575 GLN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain h residue 11 LEU Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 50 ASN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 29 ILE Chi-restraints excluded: chain d residue 95 THR Chi-restraints excluded: chain e residue 50 ASN Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 195 ASN Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 258 GLN Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 345 VAL Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 385 CYS Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 584 GLU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 598 CYS Chi-restraints excluded: chain J residue 601 LYS Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 629 LEU Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 646 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 36 TRP Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain k residue 21 THR Chi-restraints excluded: chain m residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 62 optimal weight: 6.9990 chunk 226 optimal weight: 1.9990 chunk 255 optimal weight: 0.3980 chunk 271 optimal weight: 0.3980 chunk 261 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 40 optimal weight: 0.2980 chunk 168 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 101 optimal weight: 0.0980 chunk 39 optimal weight: 0.9980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.248213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.225732 restraints weight = 35011.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.218278 restraints weight = 50528.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.215179 restraints weight = 65434.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.213865 restraints weight = 61710.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.212102 restraints weight = 53900.013| |-----------------------------------------------------------------------------| r_work (final): 0.4469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.187 26613 Z= 0.187 Angle : 0.965 59.199 36423 Z= 0.504 Chirality : 0.048 0.788 4410 Planarity : 0.005 0.129 4380 Dihedral : 9.637 97.519 6149 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 5.86 % Allowed : 26.80 % Favored : 67.34 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.14 (0.15), residues: 3039 helix: 1.44 (0.30), residues: 342 sheet: -0.16 (0.19), residues: 816 loop : -1.53 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 192 TYR 0.015 0.001 TYR I 191 PHE 0.021 0.002 PHE I 376 TRP 0.015 0.001 TRP l 96 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 (26433) covalent geometry : angle 0.90589 / 0.49 (35928) SS BOND : bond 0.00429 / 0.23 ( 45) SS BOND : angle 1.41544 / 0.97 ( 90) hydrogen bonds : bond 0.03519 / 2.36 ( 701) hydrogen bonds : angle 5.31902 / 3.69 ( 1956) link_ALPHA1-2 : bond 0.00625 / 0.33 ( 6) link_ALPHA1-2 : angle 1.62796 / 1.07 ( 18) link_ALPHA1-3 : bond 0.01123 / 0.66 ( 12) link_ALPHA1-3 : angle 1.74348 / 1.14 ( 36) link_ALPHA1-6 : bond 0.00761 / 0.43 ( 9) link_ALPHA1-6 : angle 1.54349 / 1.00 ( 27) link_BETA1-4 : bond 0.00662 / 0.37 ( 48) link_BETA1-4 : angle 2.54552 / 2.05 ( 144) link_NAG-ASN : bond 0.00629 / 0.44 ( 60) link_NAG-ASN : angle 4.13305 / 2.87 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4124.25 seconds wall clock time: 72 minutes 10.07 seconds (4330.07 seconds total)