Starting phenix.real_space_refine on Fri Sep 19 09:38:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v8x_21111/09_2025/6v8x_21111_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v8x_21111/09_2025/6v8x_21111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6v8x_21111/09_2025/6v8x_21111_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v8x_21111/09_2025/6v8x_21111_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v8x_21111/09_2025/6v8x_21111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v8x_21111/09_2025/6v8x_21111.map" } resolution = 3.0 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= 0.009 sd= 0.142 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 147 5.16 5 C 15531 2.51 5 N 4170 2.21 5 O 4977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24825 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3453 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 4 Chain: "B" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1025 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "C" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1710 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 206} Chain: "D" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1615 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 195} Chain: "E" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3453 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 4 Chain: "F" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1025 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "G" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1710 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 206} Chain: "H" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1615 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 195} Chain: "I" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3453 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 4 Chain: "J" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1025 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "K" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1710 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 206} Chain: "L" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1615 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 195} Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: "P" 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: "Q" 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" 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: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 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: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 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: "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: 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: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 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: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 5.66, per 1000 atoms: 0.23 Number of scatterers: 24825 At special positions: 0 Unit cell: (184.13, 202.543, 125.642, 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 147 16.00 O 4977 8.00 N 4170 7.00 C 15531 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.07 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.01 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.07 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.12 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.11 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.09 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.24 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.31 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.00 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=1.91 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 98 " distance=1.98 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 216 " - pdb=" SG CYS D 216 " distance=2.00 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.19 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.07 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.01 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.07 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.12 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.10 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.09 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.24 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.31 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.00 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=1.91 Simple disulfide: pdb=" SG CYS G 32 " - pdb=" SG CYS G 98 " distance=1.98 Simple disulfide: pdb=" SG CYS G 140 " - pdb=" SG CYS G 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 216 " - pdb=" SG CYS H 216 " distance=2.00 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.19 Simple disulfide: pdb=" SG CYS H 136 " - pdb=" SG CYS H 196 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.07 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.01 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.06 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.12 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=2.11 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.09 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.24 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.31 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.00 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=1.91 Simple disulfide: pdb=" SG CYS K 32 " - pdb=" SG CYS K 98 " distance=1.98 Simple disulfide: pdb=" SG CYS K 140 " - pdb=" SG CYS K 196 " distance=2.04 Simple disulfide: pdb=" SG CYS K 216 " - pdb=" SG CYS L 216 " distance=2.00 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.19 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 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 ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA Y 3 " - " MAN Y 4 " " BMA k 3 " - " MAN k 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " 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 r 2 " - " BMA r 3 " " 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-ASN " NAG A 613 " - " ASN A 448 " " NAG A 617 " - " ASN A 355 " " NAG A 627 " - " ASN A 133 " " NAG A 632 " - " ASN A 339 " " NAG B 701 " - " ASN B 611 " " NAG E 613 " - " ASN E 448 " " NAG E 617 " - " ASN E 355 " " NAG E 627 " - " ASN E 133 " " NAG E 632 " - " ASN E 339 " " NAG F 701 " - " ASN F 611 " " NAG I 613 " - " ASN I 448 " " NAG I 617 " - " ASN I 355 " " NAG I 627 " - " ASN I 133 " " NAG I 632 " - " ASN I 339 " " NAG J 701 " - " ASN J 611 " " NAG M 1 " - " ASN A 363 " " NAG N 1 " - " ASN A 392 " " NAG O 1 " - " ASN A 386 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 276 " " NAG R 1 " - " ASN A 295 " " NAG S 1 " - " ASN A 160 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN A 197 " " NAG V 1 " - " ASN A 88 " " NAG W 1 " - " ASN A 332 " " NAG X 1 " - " ASN A 301 " " NAG Y 1 " - " ASN E 363 " " NAG Z 1 " - " ASN E 392 " " NAG a 1 " - " ASN E 386 " " NAG b 1 " - " ASN E 262 " " NAG c 1 " - " ASN E 276 " " NAG d 1 " - " ASN E 295 " " NAG e 1 " - " ASN E 160 " " NAG f 1 " - " ASN E 156 " " NAG g 1 " - " ASN E 197 " " NAG h 1 " - " ASN E 88 " " NAG i 1 " - " ASN E 332 " " NAG j 1 " - " ASN E 301 " " NAG k 1 " - " ASN I 363 " " NAG l 1 " - " ASN I 392 " " NAG m 1 " - " ASN I 386 " " NAG n 1 " - " ASN I 262 " " NAG o 1 " - " ASN I 276 " " NAG p 1 " - " ASN I 295 " " NAG q 1 " - " ASN I 160 " " NAG r 1 " - " ASN I 156 " " NAG s 1 " - " ASN I 197 " " NAG t 1 " - " ASN I 88 " " NAG u 1 " - " ASN I 332 " " NAG v 1 " - " ASN I 301 " Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 997.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5562 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 66 sheets defined 16.2% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.553A pdb=" N LEU A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP A 113 " --> pdb=" O ILE A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 4.050A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 354 removed outlier: 3.534A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 478 removed outlier: 3.945A pdb=" N ASP A 477 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 478 " --> pdb=" O MET A 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 474 through 478' Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.872A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 596 removed outlier: 3.807A pdb=" N GLY B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 removed outlier: 3.675A pdb=" N SER B 615 " --> pdb=" O SER B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 4.036A pdb=" N TRP B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 removed outlier: 4.091A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 646 removed outlier: 3.657A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 664 removed outlier: 5.107A pdb=" N GLN B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 660 " --> pdb=" O ASN B 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 4.030A pdb=" N CYS C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.722A pdb=" N GLN C 64 " --> pdb=" O ARG C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.651A pdb=" N THR C 87 " --> pdb=" O VAL C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 204 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 187 through 192 removed outlier: 4.140A pdb=" N LYS D 192 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 115 removed outlier: 3.554A pdb=" N LEU E 111 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 4.050A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 354 removed outlier: 3.534A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 474 through 478 removed outlier: 3.945A pdb=" N ASP E 477 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN E 478 " --> pdb=" O MET E 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 474 through 478' Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.872A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 566 through 596 removed outlier: 3.807A pdb=" N GLY F 572 " --> pdb=" O LEU F 568 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU F 581 " --> pdb=" O GLN F 577 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 removed outlier: 3.674A pdb=" N SER F 615 " --> pdb=" O SER F 612 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 removed outlier: 4.036A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 removed outlier: 4.091A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 646 removed outlier: 3.657A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 664 removed outlier: 5.108A pdb=" N GLN F 652 " --> pdb=" O GLU F 648 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLN F 653 " --> pdb=" O SER F 649 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP F 659 " --> pdb=" O LYS F 655 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU F 660 " --> pdb=" O ASN F 656 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 4.030A pdb=" N CYS G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 removed outlier: 3.722A pdb=" N GLN G 64 " --> pdb=" O ARG G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.651A pdb=" N THR G 87 " --> pdb=" O VAL G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 204 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'H' and resid 187 through 192 removed outlier: 4.139A pdb=" N LYS H 192 " --> pdb=" O GLU H 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 115 removed outlier: 3.553A pdb=" N LEU I 111 " --> pdb=" O ASP I 107 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP I 113 " --> pdb=" O ILE I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 removed outlier: 4.050A pdb=" N CYS I 126 " --> pdb=" O THR I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 341 through 354 removed outlier: 3.534A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 474 through 478 removed outlier: 3.945A pdb=" N ASP I 477 " --> pdb=" O ASP I 474 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN I 478 " --> pdb=" O MET I 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 474 through 478' Processing helix chain 'J' and resid 536 through 542 removed outlier: 3.872A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 566 through 596 removed outlier: 3.807A pdb=" N GLY J 572 " --> pdb=" O LEU J 568 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN J 575 " --> pdb=" O TRP J 571 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA J 578 " --> pdb=" O LYS J 574 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU J 581 " --> pdb=" O GLN J 577 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL J 583 " --> pdb=" O ARG J 579 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP J 589 " --> pdb=" O ARG J 585 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU J 592 " --> pdb=" O ARG J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 611 through 615 removed outlier: 3.674A pdb=" N SER J 615 " --> pdb=" O SER J 612 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 624 removed outlier: 4.036A pdb=" N TRP J 623 " --> pdb=" O LEU J 619 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 635 removed outlier: 4.091A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE J 635 " --> pdb=" O TRP J 631 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 646 removed outlier: 3.657A pdb=" N ILE J 642 " --> pdb=" O TYR J 638 " (cutoff:3.500A) Processing helix chain 'J' and resid 646 through 664 removed outlier: 5.108A pdb=" N GLN J 652 " --> pdb=" O GLU J 648 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLN J 653 " --> pdb=" O SER J 649 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP J 659 " --> pdb=" O LYS J 655 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU J 660 " --> pdb=" O ASN J 656 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 4.030A pdb=" N CYS K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 removed outlier: 3.722A pdb=" N GLN K 64 " --> pdb=" O ARG 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: 3.652A pdb=" N THR K 87 " --> pdb=" O VAL K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 204 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 187 through 192 removed outlier: 4.140A pdb=" N LYS L 192 " --> pdb=" O GLU L 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.535A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.704A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 227 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.817A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 172 Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 172 removed outlier: 4.671A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.406A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.243A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.203A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.236A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.935A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.933A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 297 current: chain 'A' and resid 358 through 361 removed outlier: 3.541A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 10.933A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.935A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.236A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.203A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 444 through 456 current: chain 'A' and resid 413 through 415 Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AB2, first strand: chain 'A' and resid 383 through 385 Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AB4, first strand: chain 'C' and resid 19 through 23 Processing sheet with id=AB5, first strand: chain 'C' and resid 57 through 59 removed outlier: 3.996A pdb=" N ASN C 58 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU C 46 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N TRP C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 121 through 123 Processing sheet with id=AB7, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB8, first strand: chain 'C' and resid 153 through 154 removed outlier: 3.801A pdb=" N VAL C 198 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL C 207 " --> pdb=" O VAL C 198 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AC1, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.696A pdb=" N TRP D 35 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 19 through 24 removed outlier: 3.694A pdb=" N TYR D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER D 65 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER D 63 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 117 through 118 removed outlier: 5.389A pdb=" N ASN D 139 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU D 177 " --> pdb=" O ASN D 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 150 through 152 Processing sheet with id=AC5, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.535A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.705A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS E 227 " --> pdb=" O SER E 243 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 55 through 56 Processing sheet with id=AC8, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.817A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 169 through 172 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 172 removed outlier: 4.671A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.405A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.242A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.202A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.235A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.933A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 297 current: chain 'E' and resid 358 through 361 removed outlier: 3.541A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 271 through 273 removed outlier: 10.933A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.235A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 12.202A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 444 through 456 current: chain 'E' and resid 413 through 415 Processing sheet with id=AD5, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AD6, first strand: chain 'E' and resid 383 through 385 Processing sheet with id=AD7, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AD8, first strand: chain 'G' and resid 19 through 23 Processing sheet with id=AD9, first strand: chain 'G' and resid 57 through 59 removed outlier: 3.995A pdb=" N ASN G 58 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU G 46 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 121 through 123 Processing sheet with id=AE2, first strand: chain 'G' and resid 136 through 137 Processing sheet with id=AE3, first strand: chain 'G' and resid 153 through 154 removed outlier: 3.800A pdb=" N VAL G 198 " --> pdb=" O VAL G 207 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL G 207 " --> pdb=" O VAL G 198 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.696A pdb=" N TRP H 35 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 19 through 24 removed outlier: 3.694A pdb=" N TYR H 71 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER H 65 " --> pdb=" O ASN H 72 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER H 63 " --> pdb=" O THR H 74 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 117 through 118 removed outlier: 5.390A pdb=" N ASN H 139 " --> pdb=" O LEU H 177 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU H 177 " --> pdb=" O ASN H 139 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 150 through 152 Processing sheet with id=AE9, first strand: chain 'I' and resid 494 through 499 removed outlier: 5.535A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.705A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS I 227 " --> pdb=" O SER I 243 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 55 through 56 Processing sheet with id=AF3, first strand: chain 'I' and resid 91 through 92 removed outlier: 3.817A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 169 through 172 Processing sheet with id=AF5, first strand: chain 'I' and resid 169 through 172 removed outlier: 4.671A pdb=" N LYS I 189 " --> pdb=" O CYS I 131 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 200 through 203 removed outlier: 6.405A pdb=" N ALA I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N TYR I 435 " --> pdb=" O ALA I 200 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.243A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 12.203A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 12.236A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 10.933A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 284 through 297 current: chain 'I' and resid 358 through 361 removed outlier: 3.541A pdb=" N SER I 393 " --> pdb=" O PHE I 361 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 271 through 273 removed outlier: 10.933A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 12.236A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 12.203A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 444 through 456 current: chain 'I' and resid 413 through 415 Processing sheet with id=AF9, first strand: chain 'I' and resid 304 through 308 Processing sheet with id=AG1, first strand: chain 'I' and resid 383 through 385 Processing sheet with id=AG2, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=AG3, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AG4, first strand: chain 'K' and resid 57 through 59 removed outlier: 3.997A pdb=" N ASN K 58 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU K 46 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N TRP K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 121 through 123 Processing sheet with id=AG6, first strand: chain 'K' and resid 136 through 137 Processing sheet with id=AG7, first strand: chain 'K' and resid 153 through 154 removed outlier: 3.800A pdb=" N VAL K 198 " --> pdb=" O VAL K 207 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL K 207 " --> pdb=" O VAL K 198 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 169 through 170 Processing sheet with id=AG9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.696A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.694A pdb=" N TYR L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER L 65 " --> pdb=" O ASN L 72 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 117 through 118 removed outlier: 5.389A pdb=" N ASN L 139 " --> pdb=" O LEU L 177 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU L 177 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 150 through 152 594 hydrogen bonds defined for protein. 1530 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: 4.85 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5411 1.32 - 1.46: 8151 1.46 - 1.59: 11581 1.59 - 1.72: 3 1.72 - 1.86: 192 Bond restraints: 25338 Sorted by residual: bond pdb=" N PRO I 299 " pdb=" CD PRO I 299 " ideal model delta sigma weight residual 1.473 1.577 -0.104 1.40e-02 5.10e+03 5.53e+01 bond pdb=" N PRO A 299 " pdb=" CD PRO A 299 " ideal model delta sigma weight residual 1.473 1.576 -0.103 1.40e-02 5.10e+03 5.44e+01 bond pdb=" N PRO E 299 " pdb=" CD PRO E 299 " ideal model delta sigma weight residual 1.473 1.576 -0.103 1.40e-02 5.10e+03 5.43e+01 bond pdb=" CB TRP G 50 " pdb=" CG TRP G 50 " ideal model delta sigma weight residual 1.498 1.300 0.198 3.10e-02 1.04e+03 4.09e+01 bond pdb=" CB TRP K 50 " pdb=" CG TRP K 50 " ideal model delta sigma weight residual 1.498 1.300 0.198 3.10e-02 1.04e+03 4.09e+01 ... (remaining 25333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 32440 2.90 - 5.79: 1682 5.79 - 8.69: 222 8.69 - 11.59: 63 11.59 - 14.48: 9 Bond angle restraints: 34416 Sorted by residual: angle pdb=" C SER D 65 " pdb=" N ARG D 66 " pdb=" CA ARG D 66 " ideal model delta sigma weight residual 121.70 134.19 -12.49 1.80e+00 3.09e-01 4.81e+01 angle pdb=" C SER L 65 " pdb=" N ARG L 66 " pdb=" CA ARG L 66 " ideal model delta sigma weight residual 121.70 134.16 -12.46 1.80e+00 3.09e-01 4.79e+01 angle pdb=" C SER H 65 " pdb=" N ARG H 66 " pdb=" CA ARG H 66 " ideal model delta sigma weight residual 121.70 134.12 -12.42 1.80e+00 3.09e-01 4.76e+01 angle pdb=" C TRP C 50 " pdb=" CA TRP C 50 " pdb=" CB TRP C 50 " ideal model delta sigma weight residual 112.63 98.15 14.48 2.16e+00 2.14e-01 4.50e+01 angle pdb=" C TRP K 50 " pdb=" CA TRP K 50 " pdb=" CB TRP K 50 " ideal model delta sigma weight residual 112.63 98.16 14.47 2.16e+00 2.14e-01 4.49e+01 ... (remaining 34411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.64: 15802 22.64 - 45.28: 522 45.28 - 67.92: 140 67.92 - 90.56: 96 90.56 - 113.21: 57 Dihedral angle restraints: 16617 sinusoidal: 7986 harmonic: 8631 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual 93.00 175.94 -82.94 1 1.00e+01 1.00e-02 8.42e+01 dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 92 " pdb=" CB CYS G 92 " ideal model delta sinusoidal sigma weight residual 93.00 175.92 -82.92 1 1.00e+01 1.00e-02 8.42e+01 dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 92 " pdb=" CB CYS K 92 " ideal model delta sinusoidal sigma weight residual 93.00 175.92 -82.92 1 1.00e+01 1.00e-02 8.42e+01 ... (remaining 16614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 3635 0.117 - 0.234: 466 0.234 - 0.351: 39 0.351 - 0.468: 12 0.468 - 0.585: 9 Chirality restraints: 4161 Sorted by residual: chirality pdb=" CB ILE E 309 " pdb=" CA ILE E 309 " pdb=" CG1 ILE E 309 " pdb=" CG2 ILE E 309 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.57e+00 chirality pdb=" CB ILE A 309 " pdb=" CA ILE A 309 " pdb=" CG1 ILE A 309 " pdb=" CG2 ILE A 309 " both_signs ideal model delta sigma weight residual False 2.64 2.07 0.58 2.00e-01 2.50e+01 8.39e+00 chirality pdb=" CB ILE I 309 " pdb=" CA ILE I 309 " pdb=" CG1 ILE I 309 " pdb=" CG2 ILE I 309 " both_signs ideal model delta sigma weight residual False 2.64 2.07 0.58 2.00e-01 2.50e+01 8.38e+00 ... (remaining 4158 not shown) Planarity restraints: 4311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 1 " -0.152 2.00e-02 2.50e+03 1.29e-01 2.07e+02 pdb=" C7 NAG X 1 " 0.029 2.00e-02 2.50e+03 pdb=" C8 NAG X 1 " 0.036 2.00e-02 2.50e+03 pdb=" N2 NAG X 1 " 0.208 2.00e-02 2.50e+03 pdb=" O7 NAG X 1 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 1 " -0.152 2.00e-02 2.50e+03 1.29e-01 2.07e+02 pdb=" C7 NAG j 1 " 0.030 2.00e-02 2.50e+03 pdb=" C8 NAG j 1 " 0.036 2.00e-02 2.50e+03 pdb=" N2 NAG j 1 " 0.207 2.00e-02 2.50e+03 pdb=" O7 NAG j 1 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG v 1 " 0.152 2.00e-02 2.50e+03 1.29e-01 2.07e+02 pdb=" C7 NAG v 1 " -0.029 2.00e-02 2.50e+03 pdb=" C8 NAG v 1 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG v 1 " -0.208 2.00e-02 2.50e+03 pdb=" O7 NAG v 1 " 0.120 2.00e-02 2.50e+03 ... (remaining 4308 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2726 2.72 - 3.27: 21824 3.27 - 3.81: 37757 3.81 - 4.36: 45871 4.36 - 4.90: 78416 Nonbonded interactions: 186594 Sorted by model distance: nonbonded pdb=" OE1 GLN G 6 " pdb=" OG1 THR G 107 " model vdw 2.180 3.040 nonbonded pdb=" OE1 GLN K 6 " pdb=" OG1 THR K 107 " model vdw 2.180 3.040 nonbonded pdb=" OE1 GLN C 6 " pdb=" OG1 THR C 107 " model vdw 2.180 3.040 nonbonded pdb=" OG1 THR A 303 " pdb=" N ASP A 322 " model vdw 2.257 3.120 nonbonded pdb=" OG1 THR E 303 " pdb=" N ASP E 322 " model vdw 2.257 3.120 ... (remaining 186589 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Y' selection = chain 'k' } ncs_group { reference = chain 'N' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'f' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.790 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: 0.030 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 22.890 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 : 0.018 0.280 25494 Z= 0.813 Angle : 1.592 24.380 34833 Z= 0.813 Chirality : 0.084 0.585 4161 Planarity : 0.009 0.129 4260 Dihedral : 15.174 113.205 10902 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.92 % Allowed : 8.49 % Favored : 90.59 % Rotamer: Outliers : 0.23 % Allowed : 1.83 % Favored : 97.95 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.90 (0.13), residues: 2943 helix: -4.12 (0.13), residues: 429 sheet: -2.05 (0.16), residues: 843 loop : -2.48 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.002 ARG I 298 TYR 0.033 0.005 TYR H 87 PHE 0.065 0.006 PHE D 98 TRP 0.056 0.006 TRP G 50 HIS 0.011 0.003 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.01746 (25338) covalent geometry : angle 1.48123 (34416) SS BOND : bond 0.10420 ( 51) SS BOND : angle 6.75426 ( 102) hydrogen bonds : bond 0.29475 ( 564) hydrogen bonds : angle 9.86511 ( 1530) link_ALPHA1-3 : bond 0.00193 ( 3) link_ALPHA1-3 : angle 1.45894 ( 9) link_BETA1-4 : bond 0.01186 ( 51) link_BETA1-4 : angle 4.75685 ( 153) link_NAG-ASN : bond 0.01531 ( 51) link_NAG-ASN : angle 5.50610 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 652 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7422 (m-10) cc_final: 0.7099 (m-10) REVERT: A 217 TYR cc_start: 0.7708 (m-80) cc_final: 0.6673 (m-80) REVERT: A 474 ASP cc_start: 0.7215 (t0) cc_final: 0.7006 (t0) REVERT: B 536 THR cc_start: 0.7429 (p) cc_final: 0.7108 (t) REVERT: B 566 LEU cc_start: 0.9086 (pp) cc_final: 0.8186 (tm) REVERT: D 175 TYR cc_start: 0.8105 (m-80) cc_final: 0.7493 (m-10) REVERT: E 474 ASP cc_start: 0.7246 (t0) cc_final: 0.6971 (t0) REVERT: H 77 ASN cc_start: 0.8131 (t0) cc_final: 0.7868 (t0) REVERT: H 175 TYR cc_start: 0.8092 (m-80) cc_final: 0.7564 (m-10) REVERT: I 53 PHE cc_start: 0.7258 (m-10) cc_final: 0.6926 (m-10) REVERT: I 107 ASP cc_start: 0.7813 (m-30) cc_final: 0.7589 (m-30) REVERT: I 217 TYR cc_start: 0.7233 (m-80) cc_final: 0.6981 (m-80) REVERT: I 232 LYS cc_start: 0.7488 (mptt) cc_final: 0.7268 (mmtt) REVERT: I 318 TYR cc_start: 0.7934 (m-80) cc_final: 0.7663 (m-10) REVERT: J 536 THR cc_start: 0.7502 (p) cc_final: 0.7069 (t) REVERT: K 100 ASP cc_start: 0.6601 (t0) cc_final: 0.5649 (p0) REVERT: L 58 ILE cc_start: 0.7573 (mm) cc_final: 0.7313 (mp) REVERT: L 175 TYR cc_start: 0.8071 (m-80) cc_final: 0.7470 (m-10) outliers start: 6 outliers final: 1 residues processed: 655 average time/residue: 0.7375 time to fit residues: 544.7590 Evaluate side-chains 343 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 342 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 573 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 0.0570 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN B 616 ASN C 102 HIS C 197 ASN E 130 GLN ** F 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN F 651 ASN G 197 ASN I 130 GLN J 607 ASN J 651 ASN K 102 HIS K 197 ASN L 126 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.147195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.112644 restraints weight = 55579.904| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 4.71 r_work: 0.3510 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25494 Z= 0.170 Angle : 0.909 15.029 34833 Z= 0.438 Chirality : 0.050 0.285 4161 Planarity : 0.006 0.046 4260 Dihedral : 13.675 83.957 5384 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.80 % Favored : 92.80 % Rotamer: Outliers : 3.50 % Allowed : 12.86 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.14), residues: 2943 helix: -2.53 (0.21), residues: 396 sheet: -1.70 (0.17), residues: 843 loop : -2.14 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 476 TYR 0.018 0.002 TYR H 49 PHE 0.026 0.002 PHE C 146 TRP 0.020 0.002 TRP C 154 HIS 0.006 0.001 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00377 (25338) covalent geometry : angle 0.85699 (34416) SS BOND : bond 0.00406 ( 51) SS BOND : angle 1.64452 ( 102) hydrogen bonds : bond 0.06077 ( 564) hydrogen bonds : angle 6.75478 ( 1530) link_ALPHA1-3 : bond 0.00737 ( 3) link_ALPHA1-3 : angle 2.60609 ( 9) link_BETA1-4 : bond 0.00551 ( 51) link_BETA1-4 : angle 3.31070 ( 153) link_NAG-ASN : bond 0.00384 ( 51) link_NAG-ASN : angle 3.15206 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 435 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7820 (m-10) cc_final: 0.7465 (m-10) REVERT: A 72 HIS cc_start: 0.5106 (OUTLIER) cc_final: 0.4357 (m-70) REVERT: A 99 ASN cc_start: 0.8315 (t0) cc_final: 0.7765 (t0) REVERT: A 217 TYR cc_start: 0.7927 (m-80) cc_final: 0.7184 (m-80) REVERT: A 232 LYS cc_start: 0.7907 (mmtt) cc_final: 0.7472 (tmtt) REVERT: A 318 TYR cc_start: 0.8356 (m-80) cc_final: 0.8139 (m-80) REVERT: B 566 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8472 (pp) REVERT: B 573 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.8962 (tp) REVERT: C 16 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7368 (pm20) REVERT: C 96 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7413 (mtmt) REVERT: D 39 ARG cc_start: 0.6708 (ttm110) cc_final: 0.6360 (ttm110) REVERT: D 103 LYS cc_start: 0.8111 (tptp) cc_final: 0.7593 (tptt) REVERT: E 308 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8515 (mtm-85) REVERT: E 315 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8112 (mp10) REVERT: E 318 TYR cc_start: 0.8154 (m-80) cc_final: 0.7949 (m-10) REVERT: F 571 TRP cc_start: 0.8600 (m100) cc_final: 0.8352 (m100) REVERT: G 105 ARG cc_start: 0.7347 (ptm-80) cc_final: 0.7057 (ptt90) REVERT: H 11 LEU cc_start: 0.7564 (mm) cc_final: 0.7219 (mt) REVERT: H 39 ARG cc_start: 0.6505 (ttm110) cc_final: 0.6296 (ttm110) REVERT: H 77 ASN cc_start: 0.8471 (t0) cc_final: 0.8112 (t0) REVERT: H 103 LYS cc_start: 0.8199 (tptp) cc_final: 0.7731 (tptt) REVERT: I 46 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.6396 (mmmt) REVERT: I 53 PHE cc_start: 0.7882 (m-10) cc_final: 0.7609 (m-10) REVERT: I 72 HIS cc_start: 0.5097 (OUTLIER) cc_final: 0.3668 (m-70) REVERT: I 99 ASN cc_start: 0.8601 (t0) cc_final: 0.7298 (t0) REVERT: I 107 ASP cc_start: 0.8431 (m-30) cc_final: 0.8214 (m-30) REVERT: I 114 GLN cc_start: 0.7798 (mt0) cc_final: 0.7234 (mt0) REVERT: I 217 TYR cc_start: 0.7938 (m-80) cc_final: 0.7561 (m-80) REVERT: I 308 ARG cc_start: 0.8586 (mtt90) cc_final: 0.8307 (mtm-85) REVERT: I 315 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8066 (mp10) REVERT: I 318 TYR cc_start: 0.8417 (m-80) cc_final: 0.8180 (m-10) REVERT: I 434 MET cc_start: 0.8390 (ptp) cc_final: 0.8124 (ptp) REVERT: K 50 TRP cc_start: 0.8074 (OUTLIER) cc_final: 0.7051 (m-10) REVERT: L 39 ARG cc_start: 0.6835 (ttm110) cc_final: 0.6409 (ttm110) REVERT: L 103 LYS cc_start: 0.8115 (tptp) cc_final: 0.7558 (tptt) outliers start: 92 outliers final: 17 residues processed: 493 average time/residue: 0.6876 time to fit residues: 384.3463 Evaluate side-chains 365 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 339 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain G residue 50 TRP Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 72 HIS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain J residue 565 LEU Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 615 SER Chi-restraints excluded: chain J residue 630 GLN Chi-restraints excluded: chain K residue 50 TRP Chi-restraints excluded: chain K residue 82 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 175 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 163 optimal weight: 0.4980 chunk 81 optimal weight: 0.0670 chunk 83 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 171 optimal weight: 20.0000 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN E 432 GLN F 616 ASN F 640 GLN F 651 ASN H 89 GLN H 126 GLN I 234 ASN J 564 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.145527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.111564 restraints weight = 56091.556| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 4.90 r_work: 0.3471 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25494 Z= 0.155 Angle : 0.828 12.727 34833 Z= 0.397 Chirality : 0.050 0.323 4161 Planarity : 0.005 0.041 4260 Dihedral : 11.058 70.164 5382 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.20 % Favored : 92.46 % Rotamer: Outliers : 3.73 % Allowed : 15.53 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.62 (0.14), residues: 2943 helix: -1.98 (0.23), residues: 414 sheet: -1.37 (0.18), residues: 750 loop : -1.88 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 23 TYR 0.019 0.002 TYR I 173 PHE 0.021 0.001 PHE K 146 TRP 0.017 0.001 TRP I 479 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00349 (25338) covalent geometry : angle 0.78255 (34416) SS BOND : bond 0.00493 ( 51) SS BOND : angle 1.56893 ( 102) hydrogen bonds : bond 0.05313 ( 564) hydrogen bonds : angle 6.30336 ( 1530) link_ALPHA1-3 : bond 0.00950 ( 3) link_ALPHA1-3 : angle 2.16415 ( 9) link_BETA1-4 : bond 0.00572 ( 51) link_BETA1-4 : angle 2.91127 ( 153) link_NAG-ASN : bond 0.00371 ( 51) link_NAG-ASN : angle 2.82281 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 384 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.5291 (OUTLIER) cc_final: 0.4553 (m-70) REVERT: A 99 ASN cc_start: 0.8193 (t0) cc_final: 0.7326 (t0) REVERT: A 121 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8253 (mptt) REVERT: A 217 TYR cc_start: 0.8046 (m-80) cc_final: 0.7298 (m-80) REVERT: A 232 LYS cc_start: 0.7991 (mmtt) cc_final: 0.7592 (tmtt) REVERT: A 318 TYR cc_start: 0.8438 (m-80) cc_final: 0.8224 (m-80) REVERT: B 536 THR cc_start: 0.7370 (p) cc_final: 0.7088 (t) REVERT: B 575 GLN cc_start: 0.8257 (mp10) cc_final: 0.8036 (mp10) REVERT: C 16 GLU cc_start: 0.7672 (pt0) cc_final: 0.7448 (pm20) REVERT: C 96 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7538 (mtmt) REVERT: D 103 LYS cc_start: 0.8138 (tptp) cc_final: 0.7845 (tptp) REVERT: E 232 LYS cc_start: 0.7946 (mmtt) cc_final: 0.7463 (tmtt) REVERT: E 315 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8186 (mp-120) REVERT: F 571 TRP cc_start: 0.8649 (m100) cc_final: 0.8357 (m100) REVERT: H 11 LEU cc_start: 0.7627 (mm) cc_final: 0.7215 (tp) REVERT: H 39 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.6241 (ttm110) REVERT: H 77 ASN cc_start: 0.8505 (t0) cc_final: 0.8084 (t0) REVERT: H 103 LYS cc_start: 0.8233 (tptp) cc_final: 0.7785 (tptt) REVERT: I 99 ASN cc_start: 0.8422 (t0) cc_final: 0.8207 (t0) REVERT: I 173 TYR cc_start: 0.8770 (p90) cc_final: 0.8539 (p90) REVERT: I 217 TYR cc_start: 0.8072 (m-80) cc_final: 0.7625 (m-80) REVERT: I 234 ASN cc_start: 0.7082 (OUTLIER) cc_final: 0.6685 (p0) REVERT: I 315 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8128 (mp10) REVERT: I 368 ASP cc_start: 0.8017 (t70) cc_final: 0.7230 (t0) REVERT: K 16 GLU cc_start: 0.7377 (pp20) cc_final: 0.6682 (pp20) REVERT: K 50 TRP cc_start: 0.8150 (OUTLIER) cc_final: 0.6962 (m-10) REVERT: L 103 LYS cc_start: 0.8184 (tptp) cc_final: 0.7569 (tptt) outliers start: 98 outliers final: 39 residues processed: 457 average time/residue: 0.6539 time to fit residues: 341.5825 Evaluate side-chains 369 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 324 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain G residue 50 TRP Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 331 CYS Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 565 LEU Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 615 SER Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 50 TRP Chi-restraints excluded: chain K residue 82 ARG Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 96 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 205 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 284 optimal weight: 20.0000 chunk 155 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 225 optimal weight: 0.0870 chunk 128 optimal weight: 0.5980 chunk 235 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN F 564 HIS F 616 ASN G 102 HIS H 89 GLN ** I 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.144331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.109990 restraints weight = 55359.364| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 4.90 r_work: 0.3460 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25494 Z= 0.159 Angle : 0.793 11.018 34833 Z= 0.382 Chirality : 0.048 0.285 4161 Planarity : 0.005 0.041 4260 Dihedral : 9.764 59.160 5382 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.44 % Favored : 92.25 % Rotamer: Outliers : 3.61 % Allowed : 16.44 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.28 (0.15), residues: 2943 helix: -1.53 (0.25), residues: 396 sheet: -1.15 (0.18), residues: 753 loop : -1.71 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 585 TYR 0.028 0.002 TYR C 176 PHE 0.017 0.001 PHE C 146 TRP 0.013 0.001 TRP A 479 HIS 0.005 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00367 (25338) covalent geometry : angle 0.75177 (34416) SS BOND : bond 0.00530 ( 51) SS BOND : angle 1.81221 ( 102) hydrogen bonds : bond 0.04790 ( 564) hydrogen bonds : angle 6.12431 ( 1530) link_ALPHA1-3 : bond 0.00991 ( 3) link_ALPHA1-3 : angle 2.30730 ( 9) link_BETA1-4 : bond 0.00487 ( 51) link_BETA1-4 : angle 2.61431 ( 153) link_NAG-ASN : bond 0.00306 ( 51) link_NAG-ASN : angle 2.60342 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 361 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.5469 (OUTLIER) cc_final: 0.4825 (m-70) REVERT: A 217 TYR cc_start: 0.8050 (m-80) cc_final: 0.7233 (m-80) REVERT: A 232 LYS cc_start: 0.8036 (mmtt) cc_final: 0.7622 (tmtt) REVERT: A 315 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8287 (mp-120) REVERT: B 536 THR cc_start: 0.7454 (p) cc_final: 0.7176 (t) REVERT: B 566 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8551 (pp) REVERT: B 575 GLN cc_start: 0.8352 (mp10) cc_final: 0.8080 (mp10) REVERT: C 16 GLU cc_start: 0.7743 (pt0) cc_final: 0.7456 (pm20) REVERT: D 103 LYS cc_start: 0.8127 (tptp) cc_final: 0.7611 (tptt) REVERT: E 46 LYS cc_start: 0.8633 (tppp) cc_final: 0.8409 (tppp) REVERT: E 95 MET cc_start: 0.9013 (ptm) cc_final: 0.8733 (ptm) REVERT: E 121 LYS cc_start: 0.8287 (mtmm) cc_final: 0.7942 (mptt) REVERT: E 232 LYS cc_start: 0.8064 (mmtt) cc_final: 0.7644 (tmtt) REVERT: E 315 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8202 (mp-120) REVERT: E 384 TYR cc_start: 0.9005 (m-80) cc_final: 0.8779 (m-80) REVERT: F 575 GLN cc_start: 0.8259 (mp10) cc_final: 0.7947 (mp10) REVERT: H 11 LEU cc_start: 0.7634 (mm) cc_final: 0.7255 (tp) REVERT: H 77 ASN cc_start: 0.8483 (t0) cc_final: 0.8095 (t0) REVERT: H 103 LYS cc_start: 0.8189 (tptp) cc_final: 0.7768 (tptt) REVERT: I 99 ASN cc_start: 0.8562 (t0) cc_final: 0.7780 (t0) REVERT: I 173 TYR cc_start: 0.8782 (p90) cc_final: 0.8525 (p90) REVERT: I 217 TYR cc_start: 0.8207 (m-80) cc_final: 0.7625 (m-80) REVERT: I 315 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8147 (mp-120) REVERT: I 318 TYR cc_start: 0.8571 (m-80) cc_final: 0.8199 (m-10) REVERT: I 370 GLU cc_start: 0.8110 (mp0) cc_final: 0.7861 (mp0) REVERT: I 434 MET cc_start: 0.8668 (ptt) cc_final: 0.8459 (ptt) REVERT: K 16 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6814 (pp20) REVERT: K 50 TRP cc_start: 0.8236 (OUTLIER) cc_final: 0.6959 (m-10) REVERT: L 39 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.6018 (mtm180) REVERT: L 103 LYS cc_start: 0.8128 (tptp) cc_final: 0.7529 (tptt) outliers start: 95 outliers final: 35 residues processed: 425 average time/residue: 0.7190 time to fit residues: 348.3592 Evaluate side-chains 363 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 323 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 328 GLN Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain G residue 50 TRP Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 615 SER Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 50 TRP Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 96 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 248 optimal weight: 0.9990 chunk 289 optimal weight: 6.9990 chunk 281 optimal weight: 8.9990 chunk 137 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 278 optimal weight: 5.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN E 170 GLN E 440 GLN F 616 ASN F 651 ASN H 89 GLN I 234 ASN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.139839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.103470 restraints weight = 54308.545| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 4.69 r_work: 0.3375 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 25494 Z= 0.290 Angle : 0.907 12.203 34833 Z= 0.442 Chirality : 0.053 0.397 4161 Planarity : 0.006 0.095 4260 Dihedral : 9.703 59.988 5382 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.83 % Favored : 90.86 % Rotamer: Outliers : 4.60 % Allowed : 17.01 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.43 (0.15), residues: 2943 helix: -1.67 (0.25), residues: 396 sheet: -1.42 (0.18), residues: 837 loop : -1.70 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 24 TYR 0.020 0.002 TYR A 173 PHE 0.026 0.003 PHE G 146 TRP 0.022 0.002 TRP E 479 HIS 0.007 0.002 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00682 (25338) covalent geometry : angle 0.85985 (34416) SS BOND : bond 0.00682 ( 51) SS BOND : angle 2.46231 ( 102) hydrogen bonds : bond 0.05564 ( 564) hydrogen bonds : angle 6.42641 ( 1530) link_ALPHA1-3 : bond 0.00883 ( 3) link_ALPHA1-3 : angle 2.32025 ( 9) link_BETA1-4 : bond 0.00521 ( 51) link_BETA1-4 : angle 2.67374 ( 153) link_NAG-ASN : bond 0.00820 ( 51) link_NAG-ASN : angle 3.07819 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 338 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8090 (m-10) cc_final: 0.7791 (m-10) REVERT: A 217 TYR cc_start: 0.8234 (m-80) cc_final: 0.7123 (m-80) REVERT: A 232 LYS cc_start: 0.8191 (mmtt) cc_final: 0.7766 (tmtt) REVERT: B 575 GLN cc_start: 0.8420 (mp10) cc_final: 0.8172 (mp10) REVERT: B 624 ASP cc_start: 0.8130 (m-30) cc_final: 0.7456 (p0) REVERT: C 16 GLU cc_start: 0.8098 (pt0) cc_final: 0.7632 (pm20) REVERT: D 103 LYS cc_start: 0.8016 (tptp) cc_final: 0.7525 (tptt) REVERT: E 95 MET cc_start: 0.9176 (ptm) cc_final: 0.8972 (ptm) REVERT: E 121 LYS cc_start: 0.8407 (mtmm) cc_final: 0.8122 (mptt) REVERT: E 129 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8845 (tt) REVERT: E 232 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7732 (tmtt) REVERT: E 290 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7771 (p) REVERT: E 478 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8257 (m-40) REVERT: F 571 TRP cc_start: 0.8697 (m100) cc_final: 0.8353 (m100) REVERT: G 20 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8275 (tt) REVERT: H 77 ASN cc_start: 0.8510 (t0) cc_final: 0.8049 (t0) REVERT: I 122 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8900 (mt) REVERT: I 166 ARG cc_start: 0.8067 (ppt-90) cc_final: 0.7756 (ptt-90) REVERT: I 173 TYR cc_start: 0.8959 (p90) cc_final: 0.8301 (p90) REVERT: I 217 TYR cc_start: 0.8417 (m-80) cc_final: 0.7540 (m-80) REVERT: I 290 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7832 (p) REVERT: K 16 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.6847 (pp20) REVERT: L 103 LYS cc_start: 0.8096 (tptp) cc_final: 0.7540 (tptt) outliers start: 121 outliers final: 60 residues processed: 421 average time/residue: 0.6692 time to fit residues: 322.2581 Evaluate side-chains 376 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 309 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 478 ASN Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 50 TRP Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 502 LYS Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 565 LEU Chi-restraints excluded: chain J residue 589 ASP Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 615 SER Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 50 TRP Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 96 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 280 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 165 optimal weight: 20.0000 chunk 153 optimal weight: 0.0050 chunk 1 optimal weight: 0.5980 chunk 262 optimal weight: 30.0000 chunk 269 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 227 optimal weight: 0.8980 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN F 651 ASN H 89 GLN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 440 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.141486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.106643 restraints weight = 54989.614| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 4.92 r_work: 0.3408 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 25494 Z= 0.186 Angle : 0.828 10.226 34833 Z= 0.402 Chirality : 0.049 0.303 4161 Planarity : 0.005 0.099 4260 Dihedral : 9.059 59.736 5382 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.12 % Favored : 91.57 % Rotamer: Outliers : 4.03 % Allowed : 18.23 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.15), residues: 2943 helix: -1.36 (0.26), residues: 396 sheet: -1.37 (0.18), residues: 828 loop : -1.61 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 23 TYR 0.025 0.002 TYR K 176 PHE 0.025 0.002 PHE G 146 TRP 0.024 0.002 TRP E 479 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00442 (25338) covalent geometry : angle 0.79058 (34416) SS BOND : bond 0.00527 ( 51) SS BOND : angle 1.84307 ( 102) hydrogen bonds : bond 0.04859 ( 564) hydrogen bonds : angle 6.16021 ( 1530) link_ALPHA1-3 : bond 0.00852 ( 3) link_ALPHA1-3 : angle 2.38960 ( 9) link_BETA1-4 : bond 0.00448 ( 51) link_BETA1-4 : angle 2.34168 ( 153) link_NAG-ASN : bond 0.00456 ( 51) link_NAG-ASN : angle 2.75614 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 332 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.8136 (m-80) cc_final: 0.7082 (m-80) REVERT: A 232 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7723 (tmtt) REVERT: A 290 THR cc_start: 0.7800 (OUTLIER) cc_final: 0.7429 (p) REVERT: A 424 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8518 (tp) REVERT: B 575 GLN cc_start: 0.8403 (mp10) cc_final: 0.8090 (mp10) REVERT: B 624 ASP cc_start: 0.8157 (m-30) cc_final: 0.7421 (p0) REVERT: C 16 GLU cc_start: 0.8022 (pt0) cc_final: 0.7688 (pm20) REVERT: C 31 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8129 (p0) REVERT: C 100 ASP cc_start: 0.7719 (m-30) cc_final: 0.7515 (m-30) REVERT: D 103 LYS cc_start: 0.7966 (tptp) cc_final: 0.7539 (tptt) REVERT: E 95 MET cc_start: 0.9161 (ptm) cc_final: 0.8945 (ptm) REVERT: E 121 LYS cc_start: 0.8411 (mtmm) cc_final: 0.8147 (mptt) REVERT: E 129 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8780 (tt) REVERT: E 166 ARG cc_start: 0.8082 (ppt-90) cc_final: 0.7857 (ptt180) REVERT: E 232 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7686 (tmtt) REVERT: E 290 THR cc_start: 0.8146 (OUTLIER) cc_final: 0.7864 (p) REVERT: H 77 ASN cc_start: 0.8464 (t0) cc_final: 0.7942 (t0) REVERT: I 46 LYS cc_start: 0.8496 (mmmt) cc_final: 0.8090 (mmmt) REVERT: I 161 MET cc_start: 0.8639 (tpp) cc_final: 0.8424 (mmm) REVERT: I 173 TYR cc_start: 0.8915 (p90) cc_final: 0.8258 (p90) REVERT: I 217 TYR cc_start: 0.8440 (m-80) cc_final: 0.7450 (m-80) REVERT: I 290 THR cc_start: 0.8079 (OUTLIER) cc_final: 0.7812 (p) REVERT: I 476 ARG cc_start: 0.8748 (mtm-85) cc_final: 0.8267 (mtm-85) REVERT: K 16 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.6983 (pp20) REVERT: K 20 ILE cc_start: 0.8448 (pt) cc_final: 0.8201 (mt) REVERT: K 50 TRP cc_start: 0.8524 (OUTLIER) cc_final: 0.7314 (m-10) REVERT: L 103 LYS cc_start: 0.8047 (tptp) cc_final: 0.7492 (tptt) outliers start: 106 outliers final: 46 residues processed: 408 average time/residue: 0.6619 time to fit residues: 310.5543 Evaluate side-chains 365 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 311 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 50 TRP Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 502 LYS Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 565 LEU Chi-restraints excluded: chain J residue 589 ASP Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 615 SER Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 50 TRP Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 82 ARG Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 96 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 280 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 261 optimal weight: 20.0000 chunk 128 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 HIS B 650 GLN B 651 ASN D 72 ASN E 170 GLN F 616 ASN F 651 ASN H 72 ASN H 89 GLN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 630 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.141132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.102425 restraints weight = 54125.153| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 4.77 r_work: 0.3375 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 25494 Z= 0.185 Angle : 0.812 10.594 34833 Z= 0.395 Chirality : 0.049 0.441 4161 Planarity : 0.005 0.054 4260 Dihedral : 8.738 59.677 5382 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.15 % Favored : 91.54 % Rotamer: Outliers : 4.07 % Allowed : 18.61 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.15), residues: 2943 helix: -1.29 (0.26), residues: 396 sheet: -1.33 (0.18), residues: 813 loop : -1.61 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 23 TYR 0.023 0.002 TYR A 173 PHE 0.028 0.002 PHE G 146 TRP 0.025 0.002 TRP E 479 HIS 0.004 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00438 (25338) covalent geometry : angle 0.77710 (34416) SS BOND : bond 0.00613 ( 51) SS BOND : angle 1.74629 ( 102) hydrogen bonds : bond 0.04725 ( 564) hydrogen bonds : angle 6.07191 ( 1530) link_ALPHA1-3 : bond 0.00878 ( 3) link_ALPHA1-3 : angle 2.28684 ( 9) link_BETA1-4 : bond 0.00430 ( 51) link_BETA1-4 : angle 2.17373 ( 153) link_NAG-ASN : bond 0.00421 ( 51) link_NAG-ASN : angle 2.65840 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 338 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ASP cc_start: 0.2047 (OUTLIER) cc_final: 0.1397 (m-30) REVERT: A 217 TYR cc_start: 0.8167 (m-80) cc_final: 0.7020 (m-80) REVERT: A 232 LYS cc_start: 0.8197 (mmtt) cc_final: 0.7819 (tmtt) REVERT: A 290 THR cc_start: 0.7841 (OUTLIER) cc_final: 0.7514 (p) REVERT: B 575 GLN cc_start: 0.8413 (mp10) cc_final: 0.8094 (mp10) REVERT: B 624 ASP cc_start: 0.7984 (m-30) cc_final: 0.7359 (p0) REVERT: C 16 GLU cc_start: 0.8061 (pt0) cc_final: 0.7802 (pm20) REVERT: C 31 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.8028 (p0) REVERT: C 146 PHE cc_start: 0.7286 (m-80) cc_final: 0.6821 (m-80) REVERT: E 121 LYS cc_start: 0.8466 (mtmm) cc_final: 0.8231 (mptt) REVERT: E 129 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8806 (tt) REVERT: E 151 ASP cc_start: 0.2842 (OUTLIER) cc_final: 0.2602 (t0) REVERT: E 232 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7740 (tmtt) REVERT: E 290 THR cc_start: 0.8193 (OUTLIER) cc_final: 0.7937 (p) REVERT: E 315 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8390 (mp-120) REVERT: E 492 GLU cc_start: 0.7818 (pm20) cc_final: 0.7615 (pm20) REVERT: H 77 ASN cc_start: 0.8362 (t0) cc_final: 0.7804 (t0) REVERT: I 173 TYR cc_start: 0.8893 (p90) cc_final: 0.8268 (p90) REVERT: I 213 ILE cc_start: 0.8670 (tp) cc_final: 0.7976 (pt) REVERT: I 217 TYR cc_start: 0.8456 (m-80) cc_final: 0.7479 (m-80) REVERT: I 290 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.7930 (p) REVERT: I 476 ARG cc_start: 0.8770 (mtm-85) cc_final: 0.8314 (mtm-85) REVERT: J 577 GLN cc_start: 0.8443 (mt0) cc_final: 0.8147 (mt0) REVERT: K 16 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7053 (pp20) REVERT: K 50 TRP cc_start: 0.8491 (OUTLIER) cc_final: 0.7325 (m-10) REVERT: L 103 LYS cc_start: 0.8085 (tptp) cc_final: 0.7505 (tptt) outliers start: 107 outliers final: 54 residues processed: 417 average time/residue: 0.6291 time to fit residues: 301.7358 Evaluate side-chains 366 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 303 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 50 TRP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 439 ILE Chi-restraints excluded: chain I residue 502 LYS Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 565 LEU Chi-restraints excluded: chain J residue 589 ASP Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 615 SER Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 50 TRP Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 82 ARG Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 96 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 191 optimal weight: 20.0000 chunk 97 optimal weight: 2.9990 chunk 290 optimal weight: 4.9990 chunk 172 optimal weight: 20.0000 chunk 185 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 33 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 224 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN F 651 ASN H 72 ASN H 89 GLN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.140530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.105444 restraints weight = 55083.378| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 4.92 r_work: 0.3388 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 25494 Z= 0.218 Angle : 0.844 10.974 34833 Z= 0.411 Chirality : 0.050 0.404 4161 Planarity : 0.005 0.052 4260 Dihedral : 8.718 59.696 5382 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.09 % Favored : 91.61 % Rotamer: Outliers : 3.88 % Allowed : 19.29 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.15), residues: 2943 helix: -1.32 (0.26), residues: 396 sheet: -1.32 (0.18), residues: 786 loop : -1.65 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 23 TYR 0.020 0.002 TYR K 194 PHE 0.030 0.002 PHE G 146 TRP 0.033 0.002 TRP C 154 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00515 (25338) covalent geometry : angle 0.80925 (34416) SS BOND : bond 0.00473 ( 51) SS BOND : angle 1.92741 ( 102) hydrogen bonds : bond 0.04846 ( 564) hydrogen bonds : angle 6.10062 ( 1530) link_ALPHA1-3 : bond 0.00746 ( 3) link_ALPHA1-3 : angle 2.08819 ( 9) link_BETA1-4 : bond 0.00410 ( 51) link_BETA1-4 : angle 2.10973 ( 153) link_NAG-ASN : bond 0.00520 ( 51) link_NAG-ASN : angle 2.74664 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 327 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ASP cc_start: 0.2152 (OUTLIER) cc_final: 0.1569 (m-30) REVERT: A 217 TYR cc_start: 0.8118 (m-80) cc_final: 0.6941 (m-80) REVERT: A 232 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7791 (tmtt) REVERT: A 290 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7567 (p) REVERT: A 424 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8506 (tp) REVERT: B 575 GLN cc_start: 0.8411 (mp10) cc_final: 0.8075 (mp10) REVERT: B 624 ASP cc_start: 0.8057 (m-30) cc_final: 0.7376 (p0) REVERT: C 16 GLU cc_start: 0.8105 (pt0) cc_final: 0.7797 (pm20) REVERT: D 24 ARG cc_start: 0.6947 (tpt170) cc_final: 0.6660 (tpm170) REVERT: E 121 LYS cc_start: 0.8470 (mtmm) cc_final: 0.8261 (mptt) REVERT: E 129 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8762 (tt) REVERT: E 232 LYS cc_start: 0.8171 (mmtt) cc_final: 0.7728 (tmtt) REVERT: E 290 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.8012 (p) REVERT: E 448 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8518 (p0) REVERT: F 577 GLN cc_start: 0.8483 (mt0) cc_final: 0.8214 (mt0) REVERT: H 77 ASN cc_start: 0.8411 (t0) cc_final: 0.7849 (t0) REVERT: I 46 LYS cc_start: 0.8511 (mmmt) cc_final: 0.8004 (mmmt) REVERT: I 166 ARG cc_start: 0.7865 (ppt-90) cc_final: 0.7621 (ptt180) REVERT: I 173 TYR cc_start: 0.8880 (p90) cc_final: 0.8277 (p90) REVERT: I 213 ILE cc_start: 0.8738 (tp) cc_final: 0.8097 (pt) REVERT: I 290 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7955 (p) REVERT: I 476 ARG cc_start: 0.8746 (mtm-85) cc_final: 0.8222 (mtm-85) REVERT: J 577 GLN cc_start: 0.8425 (mt0) cc_final: 0.8103 (mt0) REVERT: K 16 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7004 (pp20) REVERT: K 50 TRP cc_start: 0.8623 (OUTLIER) cc_final: 0.7375 (m-10) REVERT: L 103 LYS cc_start: 0.7980 (tptp) cc_final: 0.7667 (tptp) outliers start: 102 outliers final: 59 residues processed: 408 average time/residue: 0.6267 time to fit residues: 294.6431 Evaluate side-chains 380 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 312 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 50 TRP Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain H residue 72 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 439 ILE Chi-restraints excluded: chain I residue 502 LYS Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 565 LEU Chi-restraints excluded: chain J residue 589 ASP Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 615 SER Chi-restraints excluded: chain J residue 622 ILE Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 50 TRP Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 82 ARG Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 47 optimal weight: 0.6980 chunk 173 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 168 optimal weight: 0.0030 chunk 199 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 195 optimal weight: 0.0370 chunk 241 optimal weight: 0.5980 chunk 152 optimal weight: 4.9990 overall best weight: 0.4268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN F 651 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 ASN H 89 GLN ** I 374 HIS ** 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 = 0.4183 r_free = 0.4183 target = 0.142696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.104350 restraints weight = 54422.192| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 4.90 r_work: 0.3394 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.5423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 25494 Z= 0.133 Angle : 0.784 12.316 34833 Z= 0.380 Chirality : 0.048 0.381 4161 Planarity : 0.005 0.053 4260 Dihedral : 8.202 59.857 5382 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.41 % Favored : 92.29 % Rotamer: Outliers : 2.36 % Allowed : 21.16 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.15), residues: 2943 helix: -1.12 (0.27), residues: 396 sheet: -1.26 (0.18), residues: 792 loop : -1.62 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 23 TYR 0.027 0.001 TYR A 173 PHE 0.028 0.001 PHE G 146 TRP 0.031 0.001 TRP E 479 HIS 0.004 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00311 (25338) covalent geometry : angle 0.75747 (34416) SS BOND : bond 0.00391 ( 51) SS BOND : angle 1.52428 ( 102) hydrogen bonds : bond 0.04222 ( 564) hydrogen bonds : angle 5.83302 ( 1530) link_ALPHA1-3 : bond 0.00726 ( 3) link_ALPHA1-3 : angle 1.85653 ( 9) link_BETA1-4 : bond 0.00467 ( 51) link_BETA1-4 : angle 1.85325 ( 153) link_NAG-ASN : bond 0.00311 ( 51) link_NAG-ASN : angle 2.38011 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 348 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 TYR cc_start: 0.8744 (p90) cc_final: 0.7946 (p90) REVERT: A 199 SER cc_start: 0.9126 (t) cc_final: 0.8858 (m) REVERT: A 213 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8081 (pt) REVERT: A 232 LYS cc_start: 0.8107 (mmtt) cc_final: 0.7778 (tmtt) REVERT: A 290 THR cc_start: 0.7898 (OUTLIER) cc_final: 0.7544 (p) REVERT: A 368 ASP cc_start: 0.7985 (t70) cc_final: 0.7229 (t0) REVERT: B 571 TRP cc_start: 0.8480 (m100) cc_final: 0.8258 (m100) REVERT: B 575 GLN cc_start: 0.8387 (mp10) cc_final: 0.8059 (mp10) REVERT: B 588 ARG cc_start: 0.8120 (tpt170) cc_final: 0.7774 (mmt180) REVERT: C 16 GLU cc_start: 0.8076 (pt0) cc_final: 0.7741 (pm20) REVERT: C 99 ASP cc_start: 0.8366 (p0) cc_final: 0.8007 (p0) REVERT: E 129 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8855 (tt) REVERT: E 232 LYS cc_start: 0.8175 (mmtt) cc_final: 0.7718 (tmtt) REVERT: E 448 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8411 (p0) REVERT: F 529 THR cc_start: 0.8612 (p) cc_final: 0.8375 (t) REVERT: F 577 GLN cc_start: 0.8478 (mt0) cc_final: 0.8224 (mt0) REVERT: G 16 GLU cc_start: 0.7766 (pt0) cc_final: 0.7468 (pp20) REVERT: G 20 ILE cc_start: 0.8623 (pt) cc_final: 0.8273 (mp) REVERT: G 146 PHE cc_start: 0.7855 (m-80) cc_final: 0.7570 (m-80) REVERT: I 121 LYS cc_start: 0.8462 (ttmm) cc_final: 0.8242 (mtmm) REVERT: I 166 ARG cc_start: 0.7710 (ppt-90) cc_final: 0.7467 (ptt180) REVERT: I 173 TYR cc_start: 0.8890 (p90) cc_final: 0.8240 (p90) REVERT: I 213 ILE cc_start: 0.8781 (tp) cc_final: 0.8129 (pt) REVERT: I 217 TYR cc_start: 0.8503 (m-80) cc_final: 0.7335 (m-80) REVERT: I 290 THR cc_start: 0.8292 (OUTLIER) cc_final: 0.8026 (p) REVERT: I 315 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8229 (mp-120) REVERT: I 476 ARG cc_start: 0.8738 (mtm-85) cc_final: 0.8301 (mtm-85) REVERT: J 529 THR cc_start: 0.8386 (p) cc_final: 0.8149 (t) REVERT: J 577 GLN cc_start: 0.8435 (mt0) cc_final: 0.8124 (mt0) REVERT: K 16 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7243 (pp20) REVERT: K 50 TRP cc_start: 0.8194 (OUTLIER) cc_final: 0.7060 (m-10) REVERT: L 58 ILE cc_start: 0.7537 (mp) cc_final: 0.7314 (mm) REVERT: L 70 ASP cc_start: 0.7678 (m-30) cc_final: 0.7197 (m-30) outliers start: 62 outliers final: 36 residues processed: 396 average time/residue: 0.6603 time to fit residues: 300.0578 Evaluate side-chains 366 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 323 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 50 TRP Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 439 ILE Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 589 ASP Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 615 SER Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 50 TRP Chi-restraints excluded: chain K residue 82 ARG Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain L residue 79 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 275 optimal weight: 3.9990 chunk 250 optimal weight: 0.9980 chunk 262 optimal weight: 9.9990 chunk 251 optimal weight: 2.9990 chunk 272 optimal weight: 0.0030 chunk 137 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 189 optimal weight: 30.0000 chunk 249 optimal weight: 0.9980 chunk 162 optimal weight: 0.2980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN H 139 ASN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.142471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.103924 restraints weight = 54530.507| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 4.75 r_work: 0.3401 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25494 Z= 0.146 Angle : 0.807 13.182 34833 Z= 0.390 Chirality : 0.048 0.525 4161 Planarity : 0.005 0.061 4260 Dihedral : 8.082 59.890 5382 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.41 % Favored : 92.29 % Rotamer: Outliers : 2.05 % Allowed : 22.37 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.15), residues: 2943 helix: -0.98 (0.28), residues: 378 sheet: -1.20 (0.18), residues: 807 loop : -1.55 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 166 TYR 0.025 0.001 TYR A 173 PHE 0.030 0.001 PHE G 146 TRP 0.032 0.001 TRP E 479 HIS 0.003 0.001 HIS K 102 Details of bonding type rmsd covalent geometry : bond 0.00351 (25338) covalent geometry : angle 0.78336 (34416) SS BOND : bond 0.00398 ( 51) SS BOND : angle 1.51183 ( 102) hydrogen bonds : bond 0.04149 ( 564) hydrogen bonds : angle 5.80751 ( 1530) link_ALPHA1-3 : bond 0.00663 ( 3) link_ALPHA1-3 : angle 1.67533 ( 9) link_BETA1-4 : bond 0.00436 ( 51) link_BETA1-4 : angle 1.78706 ( 153) link_NAG-ASN : bond 0.00286 ( 51) link_NAG-ASN : angle 2.33868 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 340 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8099 (m-10) cc_final: 0.7832 (m-10) REVERT: A 166 ARG cc_start: 0.7906 (ppt-90) cc_final: 0.7593 (ptt180) REVERT: A 199 SER cc_start: 0.9130 (t) cc_final: 0.8846 (m) REVERT: A 213 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8070 (pt) REVERT: A 217 TYR cc_start: 0.8256 (m-80) cc_final: 0.7034 (m-80) REVERT: A 232 LYS cc_start: 0.8084 (mmtt) cc_final: 0.7735 (tmtt) REVERT: A 290 THR cc_start: 0.7907 (OUTLIER) cc_final: 0.7559 (p) REVERT: A 424 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8487 (tp) REVERT: B 575 GLN cc_start: 0.8409 (mp10) cc_final: 0.8018 (mp10) REVERT: C 16 GLU cc_start: 0.8061 (pt0) cc_final: 0.7714 (pm20) REVERT: C 99 ASP cc_start: 0.8337 (p0) cc_final: 0.8009 (p0) REVERT: E 129 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8831 (tt) REVERT: E 232 LYS cc_start: 0.8199 (mmtt) cc_final: 0.7706 (tmtt) REVERT: E 352 HIS cc_start: 0.7212 (m-70) cc_final: 0.6975 (m90) REVERT: E 448 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8360 (p0) REVERT: F 529 THR cc_start: 0.8589 (p) cc_final: 0.8356 (t) REVERT: F 577 GLN cc_start: 0.8515 (mt0) cc_final: 0.8231 (mt0) REVERT: G 16 GLU cc_start: 0.7812 (pt0) cc_final: 0.7453 (pp20) REVERT: G 146 PHE cc_start: 0.7868 (m-80) cc_final: 0.7374 (m-80) REVERT: H 103 LYS cc_start: 0.8066 (tptp) cc_final: 0.7575 (tptt) REVERT: I 121 LYS cc_start: 0.8498 (ttmm) cc_final: 0.8265 (mtmm) REVERT: I 151 ASP cc_start: 0.2320 (OUTLIER) cc_final: 0.1977 (t0) REVERT: I 173 TYR cc_start: 0.8898 (p90) cc_final: 0.8272 (p90) REVERT: I 213 ILE cc_start: 0.8773 (tp) cc_final: 0.8110 (pt) REVERT: I 290 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.8006 (p) REVERT: I 315 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8211 (mp-120) REVERT: I 476 ARG cc_start: 0.8760 (mtm-85) cc_final: 0.8301 (mtm-85) REVERT: J 529 THR cc_start: 0.8306 (p) cc_final: 0.8066 (t) REVERT: J 571 TRP cc_start: 0.8644 (m100) cc_final: 0.8263 (m100) REVERT: J 577 GLN cc_start: 0.8438 (mt0) cc_final: 0.8121 (mt0) REVERT: K 16 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7109 (pp20) REVERT: K 50 TRP cc_start: 0.8252 (OUTLIER) cc_final: 0.6817 (m-10) REVERT: L 58 ILE cc_start: 0.7545 (mp) cc_final: 0.7324 (mm) REVERT: L 103 LYS cc_start: 0.8095 (tptp) cc_final: 0.7552 (tptt) outliers start: 54 outliers final: 35 residues processed: 384 average time/residue: 0.6265 time to fit residues: 277.3779 Evaluate side-chains 367 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 323 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 50 TRP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 615 SER Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 50 TRP Chi-restraints excluded: chain K residue 82 ARG Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain L residue 79 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 76 optimal weight: 6.9990 chunk 251 optimal weight: 0.9980 chunk 67 optimal weight: 0.0470 chunk 235 optimal weight: 2.9990 chunk 212 optimal weight: 0.6980 chunk 230 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 chunk 195 optimal weight: 3.9990 chunk 231 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN I 114 GLN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 618 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.142472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.104304 restraints weight = 54403.158| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 4.78 r_work: 0.3394 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25494 Z= 0.146 Angle : 0.806 13.028 34833 Z= 0.388 Chirality : 0.048 0.502 4161 Planarity : 0.005 0.069 4260 Dihedral : 7.990 59.880 5382 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.85 % Favored : 91.91 % Rotamer: Outliers : 2.36 % Allowed : 22.18 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.15), residues: 2943 helix: -0.96 (0.28), residues: 378 sheet: -1.13 (0.18), residues: 807 loop : -1.51 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 298 TYR 0.019 0.001 TYR E 435 PHE 0.027 0.001 PHE G 146 TRP 0.030 0.001 TRP E 479 HIS 0.005 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00349 (25338) covalent geometry : angle 0.78365 (34416) SS BOND : bond 0.00413 ( 51) SS BOND : angle 1.50758 ( 102) hydrogen bonds : bond 0.04147 ( 564) hydrogen bonds : angle 5.78450 ( 1530) link_ALPHA1-3 : bond 0.00649 ( 3) link_ALPHA1-3 : angle 1.64126 ( 9) link_BETA1-4 : bond 0.00431 ( 51) link_BETA1-4 : angle 1.69204 ( 153) link_NAG-ASN : bond 0.00278 ( 51) link_NAG-ASN : angle 2.28995 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10375.70 seconds wall clock time: 177 minutes 17.28 seconds (10637.28 seconds total)