Starting phenix.real_space_refine on Mon Aug 10 07:28:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9om5_70607/08_2026/9om5_70607_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9om5_70607/08_2026/9om5_70607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9om5_70607/08_2026/9om5_70607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9om5_70607/08_2026/9om5_70607.map" model { file = "/net/cci-nas-00/data/ceres_data/9om5_70607/08_2026/9om5_70607_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9om5_70607/08_2026/9om5_70607_neut.cif" } resolution = 3.4 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= 0.012 sd= 1.376 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 168 5.16 5 C 26832 2.51 5 N 7251 2.21 5 O 8586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42837 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2537 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 20, 'TRANS': 304} Chain: "B" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1393 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "C" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2537 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 20, 'TRANS': 304} Chain: "D" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1393 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "E" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2537 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 20, 'TRANS': 304} Chain: "F" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1393 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "G" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1680 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1574 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 195} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1680 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1574 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 195} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1680 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1574 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 195} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "a" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1682 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 206} Chain: "b" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1689 Classifications: {'peptide': 219} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Chain: "c" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1682 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 206} Chain: "d" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1689 Classifications: {'peptide': 219} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Chain: "e" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1682 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 206} Chain: "f" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1689 Classifications: {'peptide': 219} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Chain: "g" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1682 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 206} Chain: "h" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1689 Classifications: {'peptide': 219} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Chain: "i" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1682 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 206} Chain: "j" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1689 Classifications: {'peptide': 219} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Chain: "k" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1682 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 206} Chain: "l" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1689 Classifications: {'peptide': 219} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 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: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 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: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: "D" 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: "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: "e" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 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: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 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: 9.64, per 1000 atoms: 0.23 Number of scatterers: 42837 At special positions: 0 Unit cell: (202.52, 200.03, 216.63, 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 168 16.00 O 8586 8.00 N 7251 7.00 C 26832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.07 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.04 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.01 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.04 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 99 " distance=2.03 Simple disulfide: pdb=" SG CYS G 155 " - pdb=" SG CYS G 211 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 130 " - pdb=" SG CYS H 190 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 99 " distance=2.03 Simple disulfide: pdb=" SG CYS I 155 " - pdb=" SG CYS I 211 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 130 " - pdb=" SG CYS J 190 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 99 " distance=2.03 Simple disulfide: pdb=" SG CYS K 155 " - pdb=" SG CYS K 211 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 130 " - pdb=" SG CYS L 190 " distance=2.03 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS a 93 " distance=2.04 Simple disulfide: pdb=" SG CYS a 144 " - pdb=" SG CYS a 200 " distance=2.05 Simple disulfide: pdb=" SG CYS a 220 " - pdb=" SG CYS b 219 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 93 " distance=2.03 Simple disulfide: pdb=" SG CYS b 139 " - pdb=" SG CYS b 199 " distance=2.04 Simple disulfide: pdb=" SG CYS c 22 " - pdb=" SG CYS c 93 " distance=2.03 Simple disulfide: pdb=" SG CYS c 144 " - pdb=" SG CYS c 200 " distance=2.03 Simple disulfide: pdb=" SG CYS d 23 " - pdb=" SG CYS d 93 " distance=2.04 Simple disulfide: pdb=" SG CYS d 139 " - pdb=" SG CYS d 199 " distance=2.04 Simple disulfide: pdb=" SG CYS e 22 " - pdb=" SG CYS e 93 " distance=2.04 Simple disulfide: pdb=" SG CYS e 144 " - pdb=" SG CYS e 200 " distance=2.04 Simple disulfide: pdb=" SG CYS e 220 " - pdb=" SG CYS f 219 " distance=2.04 Simple disulfide: pdb=" SG CYS f 23 " - pdb=" SG CYS f 93 " distance=2.04 Simple disulfide: pdb=" SG CYS f 139 " - pdb=" SG CYS f 199 " distance=2.04 Simple disulfide: pdb=" SG CYS g 22 " - pdb=" SG CYS g 93 " distance=2.03 Simple disulfide: pdb=" SG CYS g 144 " - pdb=" SG CYS g 200 " distance=2.03 Simple disulfide: pdb=" SG CYS h 23 " - pdb=" SG CYS h 93 " distance=2.04 Simple disulfide: pdb=" SG CYS h 139 " - pdb=" SG CYS h 199 " distance=2.04 Simple disulfide: pdb=" SG CYS i 22 " - pdb=" SG CYS i 93 " distance=2.04 Simple disulfide: pdb=" SG CYS i 144 " - pdb=" SG CYS i 200 " distance=2.04 Simple disulfide: pdb=" SG CYS i 220 " - pdb=" SG CYS j 219 " distance=2.03 Simple disulfide: pdb=" SG CYS j 23 " - pdb=" SG CYS j 93 " distance=2.04 Simple disulfide: pdb=" SG CYS j 139 " - pdb=" SG CYS j 199 " distance=2.04 Simple disulfide: pdb=" SG CYS k 22 " - pdb=" SG CYS k 93 " distance=2.03 Simple disulfide: pdb=" SG CYS k 144 " - pdb=" SG CYS k 200 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 93 " distance=2.03 Simple disulfide: pdb=" SG CYS l 139 " - pdb=" SG CYS l 199 " 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 O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " BMA Z 3 " - " MAN Z 4 " " BMA o 3 " - " MAN o 4 " " BMA q 3 " - " MAN q 4 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA Q 3 " - " MAN Q 5 " " BMA S 3 " - " MAN S 5 " " BMA X 3 " - " MAN X 5 " " BMA Z 3 " - " MAN Z 5 " " BMA q 3 " - " MAN q 5 " " BMA s 3 " - " MAN s 5 " BETA1-4 " 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG 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 p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " NAG-ASN " NAG B 301 " - " ASN B 154 " " NAG D 301 " - " ASN D 154 " " NAG F 301 " - " ASN F 154 " " NAG M 1 " - " ASN A 133 " " NAG N 1 " - " ASN A 246 " " NAG O 1 " - " ASN A 165 " " NAG P 1 " - " ASN A 63 " " NAG Q 1 " - " ASN A 38 " " NAG S 1 " - " ASN A 126 " " NAG T 1 " - " ASN C 133 " " NAG U 1 " - " ASN C 246 " " NAG V 1 " - " ASN C 165 " " NAG W 1 " - " ASN C 63 " " NAG X 1 " - " ASN C 38 " " NAG Z 1 " - " ASN C 126 " " NAG m 1 " - " ASN E 133 " " NAG n 1 " - " ASN E 246 " " NAG o 1 " - " ASN E 165 " " NAG p 1 " - " ASN E 63 " " NAG q 1 " - " ASN E 38 " " NAG s 1 " - " ASN E 126 " Time building additional restraints: 4.01 Conformation dependent library (CDL) restraints added in 1.7 seconds 10740 Ramachandran restraints generated. 5370 Oldfield, 0 Emsley, 5370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10044 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 115 sheets defined 11.1% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.544A pdb=" N ALA A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 222 through 226 Processing helix chain 'B' and resid 38 through 56 Processing helix chain 'B' and resid 75 through 127 removed outlier: 3.589A pdb=" N ASP B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 155 Processing helix chain 'B' and resid 163 through 171 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'D' and resid 38 through 56 Processing helix chain 'D' and resid 75 through 127 removed outlier: 3.717A pdb=" N ASP D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 155 Processing helix chain 'D' and resid 163 through 171 Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.577A pdb=" N ALA E 69 " --> pdb=" O THR E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 77 removed outlier: 3.586A pdb=" N ASP E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 116 Processing helix chain 'E' and resid 222 through 226 Processing helix chain 'F' and resid 38 through 56 Processing helix chain 'F' and resid 75 through 127 removed outlier: 3.677A pdb=" N ASP F 79 " --> pdb=" O GLY F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 155 Processing helix chain 'F' and resid 163 through 171 Processing helix chain 'G' and resid 90 through 94 Processing helix chain 'G' and resid 202 through 204 No H-bonds generated for 'chain 'G' and resid 202 through 204' Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.216A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 124 removed outlier: 3.516A pdb=" N GLY H 124 " --> pdb=" O GLN H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 184 removed outlier: 3.555A pdb=" N LYS H 184 " --> pdb=" O ALA H 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 94 Processing helix chain 'I' and resid 202 through 204 No H-bonds generated for 'chain 'I' and resid 202 through 204' Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.228A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 124 removed outlier: 3.514A pdb=" N GLY J 124 " --> pdb=" O GLN J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 184 removed outlier: 3.549A pdb=" N LYS J 184 " --> pdb=" O ALA J 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 94 Processing helix chain 'K' and resid 202 through 204 No H-bonds generated for 'chain 'K' and resid 202 through 204' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.227A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 124 removed outlier: 3.512A pdb=" N GLY L 124 " --> pdb=" O GLN L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 184 removed outlier: 3.538A pdb=" N LYS L 184 " --> pdb=" O ALA L 180 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 88 Processing helix chain 'a' and resid 160 through 162 No H-bonds generated for 'chain 'a' and resid 160 through 162' Processing helix chain 'a' and resid 191 through 195 removed outlier: 3.774A pdb=" N GLY a 194 " --> pdb=" O SER a 191 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 88 Processing helix chain 'b' and resid 126 through 132 Processing helix chain 'b' and resid 188 through 194 removed outlier: 3.878A pdb=" N HIS b 194 " --> pdb=" O ASP b 190 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 88 Processing helix chain 'c' and resid 135 through 137 No H-bonds generated for 'chain 'c' and resid 135 through 137' Processing helix chain 'c' and resid 191 through 193 No H-bonds generated for 'chain 'c' and resid 191 through 193' Processing helix chain 'd' and resid 84 through 88 removed outlier: 3.540A pdb=" N ALA d 88 " --> pdb=" O PRO d 85 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 193 Processing helix chain 'e' and resid 84 through 88 Processing helix chain 'e' and resid 160 through 162 No H-bonds generated for 'chain 'e' and resid 160 through 162' Processing helix chain 'e' and resid 191 through 195 removed outlier: 3.915A pdb=" N GLY e 194 " --> pdb=" O SER e 191 " (cutoff:3.500A) Processing helix chain 'f' and resid 84 through 88 Processing helix chain 'f' and resid 126 through 132 Processing helix chain 'f' and resid 188 through 193 Processing helix chain 'g' and resid 84 through 88 Processing helix chain 'g' and resid 191 through 193 No H-bonds generated for 'chain 'g' and resid 191 through 193' Processing helix chain 'h' and resid 84 through 88 Processing helix chain 'h' and resid 129 through 132 Processing helix chain 'h' and resid 188 through 194 removed outlier: 3.670A pdb=" N HIS h 194 " --> pdb=" O ASP h 190 " (cutoff:3.500A) Processing helix chain 'i' and resid 84 through 88 Processing helix chain 'i' and resid 160 through 162 No H-bonds generated for 'chain 'i' and resid 160 through 162' Processing helix chain 'i' and resid 191 through 195 removed outlier: 3.912A pdb=" N GLY i 194 " --> pdb=" O SER i 191 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 88 Processing helix chain 'j' and resid 126 through 132 Processing helix chain 'j' and resid 188 through 193 Processing helix chain 'k' and resid 84 through 88 Processing helix chain 'k' and resid 191 through 193 No H-bonds generated for 'chain 'k' and resid 191 through 193' Processing helix chain 'l' and resid 84 through 88 removed outlier: 3.521A pdb=" N ALA l 88 " --> pdb=" O PRO l 85 " (cutoff:3.500A) Processing helix chain 'l' and resid 126 through 132 removed outlier: 3.544A pdb=" N SER l 132 " --> pdb=" O GLU l 128 " (cutoff:3.500A) Processing helix chain 'l' and resid 188 through 193 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 17 removed outlier: 3.627A pdb=" N GLY A 16 " --> pdb=" O GLY B 23 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY B 23 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR B 22 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 removed outlier: 4.285A pdb=" N GLN A 44 " --> pdb=" O PHE A 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 59 removed outlier: 6.912A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.608A pdb=" N PHE A 258 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 136 through 140 Processing sheet with id=AA8, first strand: chain 'A' and resid 179 through 183 Processing sheet with id=AA9, first strand: chain 'D' and resid 31 through 37 removed outlier: 4.655A pdb=" N TYR D 22 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY D 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY C 16 " --> pdb=" O GLY D 23 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 13 " --> pdb=" O PHE D 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 41 removed outlier: 3.551A pdb=" N LEU C 316 " --> pdb=" O THR C 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB4, first strand: chain 'C' and resid 58 through 59 removed outlier: 6.031A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 100 through 101 removed outlier: 3.625A pdb=" N ILE C 232 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 136 through 140 Processing sheet with id=AB7, first strand: chain 'C' and resid 164 through 168 removed outlier: 3.662A pdb=" N VAL C 166 " --> pdb=" O ILE C 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 236 through 237 Processing sheet with id=AB9, first strand: chain 'E' and resid 12 through 17 removed outlier: 3.542A pdb=" N GLY E 16 " --> pdb=" O GLY F 23 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY F 23 " --> pdb=" O GLY E 16 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AC2, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AC3, first strand: chain 'E' and resid 58 through 59 removed outlier: 6.821A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 120 through 122 removed outlier: 3.718A pdb=" N ASN E 121 " --> pdb=" O TYR E 257 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE E 258 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 136 through 140 Processing sheet with id=AC6, first strand: chain 'E' and resid 151 through 153 Processing sheet with id=AC7, first strand: chain 'E' and resid 166 through 167 removed outlier: 3.733A pdb=" N VAL E 166 " --> pdb=" O ILE E 245 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE E 245 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER E 205 " --> pdb=" O LEU E 244 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 294 through 295 Processing sheet with id=AC9, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD1, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.709A pdb=" N VAL G 124 " --> pdb=" O ALA G 95 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA G 95 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP G 36 " --> pdb=" O ARG G 52 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ARG G 52 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP G 38 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER G 42 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 135 through 139 removed outlier: 5.125A pdb=" N ALA G 152 " --> pdb=" O VAL G 199 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL G 199 " --> pdb=" O ALA G 152 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY G 154 " --> pdb=" O VAL G 197 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL G 197 " --> pdb=" O GLY G 154 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LEU G 156 " --> pdb=" O SER G 195 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N SER G 195 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LYS G 158 " --> pdb=" O LEU G 193 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU G 193 " --> pdb=" O LYS G 158 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 135 through 139 removed outlier: 5.125A pdb=" N ALA G 152 " --> pdb=" O VAL G 199 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL G 199 " --> pdb=" O ALA G 152 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY G 154 " --> pdb=" O VAL G 197 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL G 197 " --> pdb=" O GLY G 154 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LEU G 156 " --> pdb=" O SER G 195 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N SER G 195 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LYS G 158 " --> pdb=" O LEU G 193 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU G 193 " --> pdb=" O LYS G 158 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 166 through 169 removed outlier: 3.767A pdb=" N CYS G 211 " --> pdb=" O LYS G 224 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS G 224 " --> pdb=" O CYS G 211 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AD6, first strand: chain 'H' and resid 10 through 14 removed outlier: 6.950A pdb=" N LEU H 11 " --> pdb=" O GLU H 101 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LYS H 103 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ALA H 13 " --> pdb=" O LYS H 103 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA H 84 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 110 through 114 removed outlier: 5.672A pdb=" N TYR H 169 " --> pdb=" O ASN H 134 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 150 through 151 removed outlier: 4.661A pdb=" N TRP H 144 " --> pdb=" O GLN H 151 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR H 188 " --> pdb=" O PHE H 205 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.733A pdb=" N VAL I 124 " --> pdb=" O ALA I 95 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA I 95 " --> pdb=" O VAL I 124 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP I 36 " --> pdb=" O ARG I 52 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG I 52 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP I 38 " --> pdb=" O LEU I 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 135 through 139 removed outlier: 5.123A pdb=" N ALA I 152 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL I 199 " --> pdb=" O ALA I 152 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY I 154 " --> pdb=" O VAL I 197 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL I 197 " --> pdb=" O GLY I 154 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU I 156 " --> pdb=" O SER I 195 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N SER I 195 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LYS I 158 " --> pdb=" O LEU I 193 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU I 193 " --> pdb=" O LYS I 158 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 135 through 139 removed outlier: 5.123A pdb=" N ALA I 152 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL I 199 " --> pdb=" O ALA I 152 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY I 154 " --> pdb=" O VAL I 197 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL I 197 " --> pdb=" O GLY I 154 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU I 156 " --> pdb=" O SER I 195 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N SER I 195 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LYS I 158 " --> pdb=" O LEU I 193 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU I 193 " --> pdb=" O LYS I 158 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 165 through 169 removed outlier: 4.192A pdb=" N TYR I 209 " --> pdb=" O VAL I 226 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS I 211 " --> pdb=" O LYS I 224 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS I 224 " --> pdb=" O CYS I 211 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AE6, first strand: chain 'J' and resid 10 through 14 removed outlier: 6.945A pdb=" N LEU J 11 " --> pdb=" O GLU J 101 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LYS J 103 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA J 13 " --> pdb=" O LYS J 103 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA J 84 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 110 through 114 removed outlier: 5.652A pdb=" N TYR J 169 " --> pdb=" O ASN J 134 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 150 through 151 removed outlier: 4.656A pdb=" N TRP J 144 " --> pdb=" O GLN J 151 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR J 188 " --> pdb=" O PHE J 205 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.573A pdb=" N VAL K 124 " --> pdb=" O ALA K 95 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA K 95 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP K 36 " --> pdb=" O ARG K 52 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG K 52 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TRP K 38 " --> pdb=" O LEU K 50 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER K 42 " --> pdb=" O GLY K 46 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 135 through 139 removed outlier: 5.129A pdb=" N ALA K 152 " --> pdb=" O VAL K 199 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL K 199 " --> pdb=" O ALA K 152 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLY K 154 " --> pdb=" O VAL K 197 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL K 197 " --> pdb=" O GLY K 154 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU K 156 " --> pdb=" O SER K 195 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER K 195 " --> pdb=" O LEU K 156 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS K 158 " --> pdb=" O LEU K 193 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU K 193 " --> pdb=" O LYS K 158 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 135 through 139 removed outlier: 5.129A pdb=" N ALA K 152 " --> pdb=" O VAL K 199 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL K 199 " --> pdb=" O ALA K 152 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLY K 154 " --> pdb=" O VAL K 197 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL K 197 " --> pdb=" O GLY K 154 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU K 156 " --> pdb=" O SER K 195 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER K 195 " --> pdb=" O LEU K 156 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS K 158 " --> pdb=" O LEU K 193 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU K 193 " --> pdb=" O LYS K 158 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 166 through 169 removed outlier: 4.199A pdb=" N TYR K 209 " --> pdb=" O VAL K 226 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS K 211 " --> pdb=" O LYS K 224 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS K 224 " --> pdb=" O CYS K 211 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.941A pdb=" N LEU L 11 " --> pdb=" O GLU L 101 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LYS L 103 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA L 13 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA L 84 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 110 through 114 removed outlier: 5.655A pdb=" N TYR L 169 " --> pdb=" O ASN L 134 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 150 through 151 removed outlier: 4.663A pdb=" N TRP L 144 " --> pdb=" O GLN L 151 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR L 188 " --> pdb=" O PHE L 205 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 5 through 8 Processing sheet with id=AG1, first strand: chain 'a' and resid 11 through 12 removed outlier: 6.677A pdb=" N TRP a 34 " --> pdb=" O GLU a 50 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU a 50 " --> pdb=" O TRP a 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP a 36 " --> pdb=" O VAL a 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 124 through 128 Processing sheet with id=AG3, first strand: chain 'a' and resid 124 through 128 removed outlier: 6.137A pdb=" N TYR a 180 " --> pdb=" O ASP a 148 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'a' and resid 155 through 158 removed outlier: 4.228A pdb=" N TYR a 198 " --> pdb=" O VAL a 215 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'b' and resid 4 through 6 Processing sheet with id=AG6, first strand: chain 'b' and resid 13 through 14 removed outlier: 5.587A pdb=" N VAL b 13 " --> pdb=" O LYS b 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'b' and resid 58 through 59 removed outlier: 6.451A pdb=" N TRP b 40 " --> pdb=" O LEU b 52 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR b 54 " --> pdb=" O LEU b 38 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU b 38 " --> pdb=" O TYR b 54 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'b' and resid 121 through 123 removed outlier: 5.141A pdb=" N SER b 136 " --> pdb=" O LEU b 186 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU b 186 " --> pdb=" O SER b 136 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL b 138 " --> pdb=" O LEU b 184 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU b 184 " --> pdb=" O VAL b 138 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU b 140 " --> pdb=" O SER b 182 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N SER b 182 " --> pdb=" O LEU b 140 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASN b 142 " --> pdb=" O LEU b 180 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU b 180 " --> pdb=" O ASN b 142 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 149 through 155 Processing sheet with id=AH1, first strand: chain 'c' and resid 11 through 12 removed outlier: 6.960A pdb=" N TRP c 34 " --> pdb=" O GLU c 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLU c 50 " --> pdb=" O TRP c 34 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TRP c 36 " --> pdb=" O VAL c 48 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'c' and resid 18 through 23 Processing sheet with id=AH3, first strand: chain 'c' and resid 124 through 127 removed outlier: 3.572A pdb=" N ASP c 148 " --> pdb=" O TYR c 180 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR c 180 " --> pdb=" O ASP c 148 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'c' and resid 124 through 127 removed outlier: 3.572A pdb=" N ASP c 148 " --> pdb=" O TYR c 180 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR c 180 " --> pdb=" O ASP c 148 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'c' and resid 155 through 158 removed outlier: 4.261A pdb=" N TYR c 198 " --> pdb=" O VAL c 215 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'd' and resid 4 through 6 removed outlier: 3.598A pdb=" N ARG d 70 " --> pdb=" O THR d 77 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'd' and resid 13 through 14 removed outlier: 5.654A pdb=" N VAL d 13 " --> pdb=" O LYS d 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'd' and resid 49 through 54 removed outlier: 6.473A pdb=" N TRP d 40 " --> pdb=" O LEU d 52 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR d 54 " --> pdb=" O LEU d 38 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU d 38 " --> pdb=" O TYR d 54 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN d 95 " --> pdb=" O THR d 102 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR d 102 " --> pdb=" O GLN d 95 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'd' and resid 49 through 54 removed outlier: 6.473A pdb=" N TRP d 40 " --> pdb=" O LEU d 52 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR d 54 " --> pdb=" O LEU d 38 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU d 38 " --> pdb=" O TYR d 54 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'd' and resid 134 through 144 removed outlier: 5.924A pdb=" N TYR d 178 " --> pdb=" O ASN d 143 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'd' and resid 159 through 160 removed outlier: 4.647A pdb=" N TRP d 153 " --> pdb=" O GLN d 160 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'e' and resid 5 through 8 Processing sheet with id=AI4, first strand: chain 'e' and resid 11 through 12 removed outlier: 6.567A pdb=" N TRP e 34 " --> pdb=" O GLU e 50 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU e 50 " --> pdb=" O TRP e 34 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TRP e 36 " --> pdb=" O VAL e 48 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'e' and resid 11 through 12 removed outlier: 3.713A pdb=" N MET e 106 " --> pdb=" O ARG e 95 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'e' and resid 124 through 128 Processing sheet with id=AI7, first strand: chain 'e' and resid 124 through 128 removed outlier: 6.224A pdb=" N TYR e 180 " --> pdb=" O ASP e 148 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL e 185 " --> pdb=" O HIS e 168 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'e' and resid 154 through 158 removed outlier: 4.304A pdb=" N TYR e 198 " --> pdb=" O VAL e 215 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'f' and resid 4 through 6 Processing sheet with id=AJ1, first strand: chain 'f' and resid 13 through 14 removed outlier: 5.663A pdb=" N VAL f 13 " --> pdb=" O LYS f 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ1 Processing sheet with id=AJ2, first strand: chain 'f' and resid 50 through 54 removed outlier: 6.548A pdb=" N TRP f 40 " --> pdb=" O LEU f 52 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR f 54 " --> pdb=" O LEU f 38 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU f 38 " --> pdb=" O TYR f 54 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'f' and resid 121 through 123 removed outlier: 5.162A pdb=" N SER f 136 " --> pdb=" O LEU f 186 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LEU f 186 " --> pdb=" O SER f 136 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL f 138 " --> pdb=" O LEU f 184 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU f 184 " --> pdb=" O VAL f 138 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU f 140 " --> pdb=" O SER f 182 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N SER f 182 " --> pdb=" O LEU f 140 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ASN f 142 " --> pdb=" O LEU f 180 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU f 180 " --> pdb=" O ASN f 142 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'f' and resid 158 through 159 Processing sheet with id=AJ5, first strand: chain 'g' and resid 11 through 12 removed outlier: 3.548A pdb=" N VAL g 12 " --> pdb=" O THR g 114 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N TRP g 34 " --> pdb=" O GLU g 50 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLU g 50 " --> pdb=" O TRP g 34 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N TRP g 36 " --> pdb=" O VAL g 48 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'g' and resid 18 through 23 removed outlier: 3.511A pdb=" N LYS g 79 " --> pdb=" O THR g 66 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'g' and resid 124 through 127 removed outlier: 3.665A pdb=" N ASP g 148 " --> pdb=" O TYR g 180 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR g 180 " --> pdb=" O ASP g 148 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'g' and resid 124 through 127 removed outlier: 3.665A pdb=" N ASP g 148 " --> pdb=" O TYR g 180 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR g 180 " --> pdb=" O ASP g 148 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'g' and resid 155 through 158 removed outlier: 4.241A pdb=" N TYR g 198 " --> pdb=" O VAL g 215 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'h' and resid 4 through 6 removed outlier: 3.764A pdb=" N ARG h 70 " --> pdb=" O THR h 77 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'h' and resid 13 through 14 removed outlier: 5.582A pdb=" N VAL h 13 " --> pdb=" O LYS h 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK2 Processing sheet with id=AK3, first strand: chain 'h' and resid 49 through 53 removed outlier: 6.475A pdb=" N TRP h 40 " --> pdb=" O LEU h 52 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'h' and resid 119 through 121 removed outlier: 5.816A pdb=" N TYR h 178 " --> pdb=" O ASN h 143 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'h' and resid 159 through 160 removed outlier: 4.333A pdb=" N TRP h 153 " --> pdb=" O GLN h 160 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'i' and resid 5 through 8 Processing sheet with id=AK7, first strand: chain 'i' and resid 11 through 12 removed outlier: 6.553A pdb=" N TRP i 34 " --> pdb=" O GLU i 50 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU i 50 " --> pdb=" O TRP i 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP i 36 " --> pdb=" O VAL i 48 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'i' and resid 11 through 12 removed outlier: 3.885A pdb=" N MET i 106 " --> pdb=" O ARG i 95 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'i' and resid 124 through 128 Processing sheet with id=AL1, first strand: chain 'i' and resid 124 through 128 removed outlier: 5.946A pdb=" N TYR i 180 " --> pdb=" O ASP i 148 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL i 185 " --> pdb=" O HIS i 168 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'i' and resid 155 through 158 removed outlier: 4.473A pdb=" N TYR i 198 " --> pdb=" O VAL i 215 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'j' and resid 4 through 6 removed outlier: 3.578A pdb=" N THR j 77 " --> pdb=" O ARG j 70 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'j' and resid 13 through 14 removed outlier: 5.841A pdb=" N VAL j 13 " --> pdb=" O LYS j 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL4 Processing sheet with id=AL5, first strand: chain 'j' and resid 58 through 59 removed outlier: 6.501A pdb=" N TRP j 40 " --> pdb=" O LEU j 52 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N TYR j 54 " --> pdb=" O LEU j 38 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU j 38 " --> pdb=" O TYR j 54 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'j' and resid 121 through 123 removed outlier: 5.166A pdb=" N SER j 136 " --> pdb=" O LEU j 186 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU j 186 " --> pdb=" O SER j 136 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL j 138 " --> pdb=" O LEU j 184 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU j 184 " --> pdb=" O VAL j 138 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU j 140 " --> pdb=" O SER j 182 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N SER j 182 " --> pdb=" O LEU j 140 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASN j 142 " --> pdb=" O LEU j 180 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU j 180 " --> pdb=" O ASN j 142 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'j' and resid 150 through 155 Processing sheet with id=AL8, first strand: chain 'k' and resid 11 through 12 removed outlier: 7.144A pdb=" N TRP k 34 " --> pdb=" O GLU k 50 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLU k 50 " --> pdb=" O TRP k 34 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TRP k 36 " --> pdb=" O VAL k 48 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'k' and resid 18 through 23 removed outlier: 3.549A pdb=" N LYS k 79 " --> pdb=" O THR k 66 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'k' and resid 124 through 127 removed outlier: 4.942A pdb=" N ALA k 141 " --> pdb=" O VAL k 188 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL k 188 " --> pdb=" O ALA k 141 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLY k 143 " --> pdb=" O VAL k 186 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL k 186 " --> pdb=" O GLY k 143 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU k 145 " --> pdb=" O SER k 184 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N SER k 184 " --> pdb=" O LEU k 145 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LYS k 147 " --> pdb=" O LEU k 182 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU k 182 " --> pdb=" O LYS k 147 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'k' and resid 155 through 158 removed outlier: 4.269A pdb=" N TYR k 198 " --> pdb=" O VAL k 215 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'l' and resid 4 through 6 removed outlier: 3.749A pdb=" N ARG l 70 " --> pdb=" O THR l 77 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'l' and resid 13 through 14 removed outlier: 5.586A pdb=" N VAL l 13 " --> pdb=" O LYS l 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM4 Processing sheet with id=AM5, first strand: chain 'l' and resid 49 through 53 removed outlier: 6.523A pdb=" N TRP l 40 " --> pdb=" O LEU l 52 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'l' and resid 134 through 144 removed outlier: 5.878A pdb=" N TYR l 178 " --> pdb=" O ASN l 143 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'l' and resid 159 through 160 removed outlier: 4.328A pdb=" N TRP l 153 " --> pdb=" O GLN l 160 " (cutoff:3.500A) 1513 hydrogen bonds defined for protein. 3801 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: 13.99 Time building geometry restraints manager: 5.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.02: 1 1.02 - 1.23: 277 1.23 - 1.44: 18844 1.44 - 1.65: 24461 1.65 - 1.85: 211 Bond restraints: 43794 Sorted by residual: bond pdb=" CG PRO h 209 " pdb=" CD PRO h 209 " ideal model delta sigma weight residual 1.503 0.814 0.689 3.40e-02 8.65e+02 4.10e+02 bond pdb=" CG PRO e 41 " pdb=" CD PRO e 41 " ideal model delta sigma weight residual 1.503 1.148 0.355 3.40e-02 8.65e+02 1.09e+02 bond pdb=" N PRO h 209 " pdb=" CD PRO h 209 " ideal model delta sigma weight residual 1.473 1.618 -0.145 1.40e-02 5.10e+03 1.08e+02 bond pdb=" N PRO e 41 " pdb=" CD PRO e 41 " ideal model delta sigma weight residual 1.473 1.567 -0.094 1.40e-02 5.10e+03 4.54e+01 bond pdb=" CA PRO d 124 " pdb=" C PRO d 124 " ideal model delta sigma weight residual 1.517 1.475 0.043 9.30e-03 1.16e+04 2.10e+01 ... (remaining 43789 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.39: 59482 6.39 - 12.77: 61 12.77 - 19.16: 7 19.16 - 25.55: 2 25.55 - 31.93: 1 Bond angle restraints: 59553 Sorted by residual: angle pdb=" N PRO h 209 " pdb=" CD PRO h 209 " pdb=" CG PRO h 209 " ideal model delta sigma weight residual 103.20 71.27 31.93 1.50e+00 4.44e-01 4.53e+02 angle pdb=" CA PRO l 209 " pdb=" N PRO l 209 " pdb=" CD PRO l 209 " ideal model delta sigma weight residual 112.00 93.65 18.35 1.40e+00 5.10e-01 1.72e+02 angle pdb=" N PRO e 41 " pdb=" CD PRO e 41 " pdb=" CG PRO e 41 " ideal model delta sigma weight residual 103.20 85.00 18.20 1.50e+00 4.44e-01 1.47e+02 angle pdb=" CA PRO h 209 " pdb=" CB PRO h 209 " pdb=" CG PRO h 209 " ideal model delta sigma weight residual 104.50 82.82 21.68 1.90e+00 2.77e-01 1.30e+02 angle pdb=" CA PRO e 41 " pdb=" N PRO e 41 " pdb=" CD PRO e 41 " ideal model delta sigma weight residual 112.00 96.16 15.84 1.40e+00 5.10e-01 1.28e+02 ... (remaining 59548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.74: 24922 25.74 - 51.49: 1651 51.49 - 77.23: 306 77.23 - 102.97: 305 102.97 - 128.72: 182 Dihedral angle restraints: 27366 sinusoidal: 11715 harmonic: 15651 Sorted by residual: dihedral pdb=" CB CYS e 144 " pdb=" SG CYS e 144 " pdb=" SG CYS e 200 " pdb=" CB CYS e 200 " ideal model delta sinusoidal sigma weight residual 93.00 175.55 -82.55 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS a 144 " pdb=" SG CYS a 144 " pdb=" SG CYS a 200 " pdb=" CB CYS a 200 " ideal model delta sinusoidal sigma weight residual -86.00 -167.79 81.79 1 1.00e+01 1.00e-02 8.23e+01 dihedral pdb=" CB CYS i 144 " pdb=" SG CYS i 144 " pdb=" SG CYS i 200 " pdb=" CB CYS i 200 " ideal model delta sinusoidal sigma weight residual 93.00 174.11 -81.11 1 1.00e+01 1.00e-02 8.12e+01 ... (remaining 27363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 6834 0.145 - 0.290: 92 0.290 - 0.435: 5 0.435 - 0.580: 0 0.580 - 0.725: 3 Chirality restraints: 6934 Sorted by residual: chirality pdb=" C1 NAG q 1 " pdb=" ND2 ASN E 38 " pdb=" C2 NAG q 1 " pdb=" O5 NAG q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN A 38 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C 38 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.07e+01 ... (remaining 6931 not shown) Planarity restraints: 7566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER l 208 " -0.127 5.00e-02 4.00e+02 1.74e-01 4.82e+01 pdb=" N PRO l 209 " 0.299 5.00e-02 4.00e+02 pdb=" CA PRO l 209 " -0.087 5.00e-02 4.00e+02 pdb=" CD PRO l 209 " -0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 305 " 0.109 5.00e-02 4.00e+02 1.62e-01 4.22e+01 pdb=" N PRO C 306 " -0.281 5.00e-02 4.00e+02 pdb=" CA PRO C 306 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO C 306 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA e 40 " 0.095 5.00e-02 4.00e+02 1.29e-01 2.66e+01 pdb=" N PRO e 41 " -0.222 5.00e-02 4.00e+02 pdb=" CA PRO e 41 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO e 41 " 0.067 5.00e-02 4.00e+02 ... (remaining 7563 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 302 2.49 - 3.09: 30956 3.09 - 3.69: 68705 3.69 - 4.30: 98587 4.30 - 4.90: 162470 Nonbonded interactions: 361020 Sorted by model distance: nonbonded pdb=" CE1 PHE h 123 " pdb=" O SER h 136 " model vdw 1.884 3.340 nonbonded pdb=" OE1 GLU f 200 " pdb=" OG1 THR f 211 " model vdw 2.055 3.040 nonbonded pdb=" OD2 ASP d 33 " pdb=" OH TYR d 37 " model vdw 2.069 3.040 nonbonded pdb=" OG SER G 135 " pdb=" OD1 ASP G 159 " model vdw 2.082 3.040 nonbonded pdb=" OD2 ASP h 33 " pdb=" OH TYR h 37 " model vdw 2.084 3.040 ... (remaining 361015 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'm' selection = chain 'n' selection = chain 'p' selection = chain 'r' } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'X' selection = chain 'Z' selection = chain 'q' selection = chain 's' } ncs_group { reference = chain 'V' selection = chain 'o' } ncs_group { reference = chain 'a' selection = chain 'c' selection = (chain 'e' and resid 1 through 222) selection = chain 'g' selection = (chain 'i' and resid 1 through 222) selection = chain 'k' } ncs_group { reference = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'l' } 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: 6.170 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: 0.050 Extract box with map and model: 1.000 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 44.650 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6115 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 : 0.007 0.689 43927 Z= 0.292 Angle : 0.971 31.931 59898 Z= 0.488 Chirality : 0.056 0.725 6934 Planarity : 0.006 0.174 7545 Dihedral : 23.103 128.717 17160 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.18 % Favored : 93.54 % Rotamer: Outliers : 0.79 % Allowed : 17.86 % Favored : 81.35 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.12), residues: 5370 helix: 1.90 (0.25), residues: 430 sheet: -0.34 (0.12), residues: 1944 loop : -1.22 (0.12), residues: 2996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG e 5 TYR 0.023 0.001 TYR E 302 PHE 0.032 0.002 PHE C 258 TRP 0.037 0.002 TRP C 180 HIS 0.007 0.001 HIS E 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00671 / 0.29 (43794) covalent geometry : angle 0.93716 / 0.48 (59553) SS BOND : bond 0.00802 / 0.45 ( 54) SS BOND : angle 1.58373 / 0.90 ( 108) hydrogen bonds : bond 0.15309 / 10.54 ( 1428) hydrogen bonds : angle 7.52119 / 5.32 ( 3801) link_ALPHA1-3 : bond 0.01188 / 0.55 ( 9) link_ALPHA1-3 : angle 2.86367 / 1.80 ( 27) link_ALPHA1-6 : bond 0.00564 / 0.30 ( 7) link_ALPHA1-6 : angle 1.73624 / 1.02 ( 21) link_BETA1-4 : bond 0.01629 / 0.92 ( 42) link_BETA1-4 : angle 4.50218 / 2.88 ( 126) link_NAG-ASN : bond 0.00866 / 0.45 ( 21) link_NAG-ASN : angle 4.02188 / 2.80 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10740 Ramachandran restraints generated. 5370 Oldfield, 0 Emsley, 5370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10740 Ramachandran restraints generated. 5370 Oldfield, 0 Emsley, 5370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 4704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 391 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASN cc_start: 0.7295 (OUTLIER) cc_final: 0.7083 (t0) REVERT: A 62 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8203 (tp30) REVERT: A 63 ASN cc_start: 0.6318 (OUTLIER) cc_final: 0.5559 (p0) REVERT: A 202 ILE cc_start: 0.9408 (mp) cc_final: 0.9138 (mm) REVERT: A 259 LYS cc_start: 0.5850 (OUTLIER) cc_final: 0.4026 (tptm) REVERT: B 167 LEU cc_start: 0.9295 (mt) cc_final: 0.9056 (pp) REVERT: E 38 ASN cc_start: 0.7185 (OUTLIER) cc_final: 0.6613 (t0) REVERT: E 63 ASN cc_start: 0.5129 (OUTLIER) cc_final: 0.4870 (p0) REVERT: E 100 TYR cc_start: 0.8212 (p90) cc_final: 0.7880 (p90) REVERT: E 259 LYS cc_start: 0.5995 (OUTLIER) cc_final: 0.4583 (tttt) REVERT: G 132 LYS cc_start: 0.9636 (mptt) cc_final: 0.9433 (ptmt) REVERT: G 191 TYR cc_start: 0.9448 (t80) cc_final: 0.9024 (t80) REVERT: H 70 ASP cc_start: 0.9510 (m-30) cc_final: 0.9031 (p0) REVERT: I 137 PHE cc_start: 0.9423 (m-80) cc_final: 0.8926 (m-80) REVERT: I 191 TYR cc_start: 0.9672 (m-80) cc_final: 0.9291 (t80) REVERT: J 185 HIS cc_start: 0.8655 (m90) cc_final: 0.7968 (m90) REVERT: K 191 TYR cc_start: 0.9585 (m-80) cc_final: 0.9171 (m-80) REVERT: L 185 HIS cc_start: 0.8526 (m90) cc_final: 0.8057 (m90) REVERT: a 46 GLN cc_start: 0.7944 (tp-100) cc_final: 0.7551 (tm-30) REVERT: a 199 ILE cc_start: 0.8269 (mm) cc_final: 0.7938 (mm) REVERT: a 203 ASN cc_start: 0.7874 (t0) cc_final: 0.7564 (t0) REVERT: c 18 LEU cc_start: 0.8083 (tt) cc_final: 0.7709 (tt) REVERT: c 65 MET cc_start: 0.7268 (ppp) cc_final: 0.6798 (ppp) REVERT: c 149 TYR cc_start: 0.8554 (p90) cc_final: 0.8220 (p90) REVERT: d 2 ILE cc_start: 0.7021 (mp) cc_final: 0.6517 (tp) REVERT: e 203 ASN cc_start: 0.7540 (t0) cc_final: 0.7136 (t0) REVERT: f 103 PHE cc_start: 0.6999 (m-80) cc_final: 0.6750 (m-80) REVERT: g 65 MET cc_start: 0.5792 (ptp) cc_final: 0.5487 (ptp) REVERT: h 174 LYS cc_start: 0.7712 (mttt) cc_final: 0.7330 (tmtt) REVERT: k 180 TYR cc_start: 0.7196 (OUTLIER) cc_final: 0.6935 (t80) outliers start: 37 outliers final: 20 residues processed: 423 average time/residue: 0.2536 time to fit residues: 173.7947 Evaluate side-chains 330 residues out of total 4704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 303 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain g residue 67 ILE Chi-restraints excluded: chain h residue 59 ARG Chi-restraints excluded: chain h residue 94 MET Chi-restraints excluded: chain i residue 201 ASN Chi-restraints excluded: chain k residue 67 ILE Chi-restraints excluded: chain k residue 180 TYR Chi-restraints excluded: chain l residue 45 ARG Chi-restraints excluded: chain l residue 122 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 531 random chunks: chunk 394 optimal weight: 10.0000 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 chunk 523 optimal weight: 30.0000 chunk 497 optimal weight: 0.8980 chunk 414 optimal weight: 0.0000 chunk 310 optimal weight: 0.9990 chunk 488 optimal weight: 9.9990 chunk 366 optimal weight: 4.9990 chunk 223 optimal weight: 40.0000 overall best weight: 2.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN D 65 GLN E 210 GLN G 104 HIS H 194 HIS ** J 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 HIS ** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 143 ASN j 143 ASN l 194 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.095401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.079950 restraints weight = 315365.066| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 10.27 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 43927 Z= 0.176 Angle : 0.807 17.002 59898 Z= 0.380 Chirality : 0.051 0.354 6934 Planarity : 0.006 0.170 7545 Dihedral : 19.008 119.539 7579 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.66 % Favored : 94.17 % Rotamer: Outliers : 2.96 % Allowed : 17.07 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.12), residues: 5370 helix: 1.83 (0.24), residues: 435 sheet: -0.18 (0.12), residues: 1970 loop : -1.10 (0.12), residues: 2965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG a 95 TYR 0.031 0.002 TYR d 145 PHE 0.020 0.002 PHE f 76 TRP 0.025 0.002 TRP a 7 HIS 0.009 0.002 HIS L 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (43794) covalent geometry : angle 0.77548 / 0.37 (59553) SS BOND : bond 0.00599 / 0.33 ( 54) SS BOND : angle 1.30495 / 0.78 ( 108) hydrogen bonds : bond 0.03705 / 2.52 ( 1428) hydrogen bonds : angle 6.12739 / 4.29 ( 3801) link_ALPHA1-3 : bond 0.01704 / 0.80 ( 9) link_ALPHA1-3 : angle 2.30368 / 1.39 ( 27) link_ALPHA1-6 : bond 0.00838 / 0.47 ( 7) link_ALPHA1-6 : angle 2.97697 / 1.81 ( 21) link_BETA1-4 : bond 0.00925 / 0.58 ( 42) link_BETA1-4 : angle 3.68284 / 2.51 ( 126) link_NAG-ASN : bond 0.00745 / 0.36 ( 21) link_NAG-ASN : angle 3.96387 / 2.84 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10740 Ramachandran restraints generated. 5370 Oldfield, 0 Emsley, 5370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10740 Ramachandran restraints generated. 5370 Oldfield, 0 Emsley, 5370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 4704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 327 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7532 (t0) REVERT: A 62 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8441 (tm-30) REVERT: B 56 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8867 (tp) REVERT: C 168 MET cc_start: 0.8574 (mmt) cc_final: 0.8029 (mmt) REVERT: C 208 ARG cc_start: 0.7982 (tmm-80) cc_final: 0.6906 (ptt90) REVERT: E 38 ASN cc_start: 0.7928 (OUTLIER) cc_final: 0.7321 (t0) REVERT: E 63 ASN cc_start: 0.5004 (OUTLIER) cc_final: 0.4779 (p0) REVERT: F 56 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8821 (tp) REVERT: G 123 MET cc_start: 0.9119 (tpp) cc_final: 0.8718 (tpp) REVERT: G 191 TYR cc_start: 0.9529 (OUTLIER) cc_final: 0.9146 (t80) REVERT: H 70 ASP cc_start: 0.9523 (m-30) cc_final: 0.9071 (p0) REVERT: I 191 TYR cc_start: 0.9694 (m-80) cc_final: 0.9350 (t80) REVERT: J 70 ASP cc_start: 0.9644 (m-30) cc_final: 0.9193 (p0) REVERT: K 137 PHE cc_start: 0.9579 (m-80) cc_final: 0.9231 (m-80) REVERT: K 191 TYR cc_start: 0.9614 (m-80) cc_final: 0.9187 (m-80) REVERT: L 70 ASP cc_start: 0.9563 (m-30) cc_final: 0.9084 (p0) REVERT: L 185 HIS cc_start: 0.8336 (m90) cc_final: 0.8073 (m90) REVERT: a 46 GLN cc_start: 0.8076 (tp-100) cc_final: 0.7507 (tm-30) REVERT: a 133 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6842 (pptt) REVERT: a 199 ILE cc_start: 0.8685 (mm) cc_final: 0.8439 (mm) REVERT: a 203 ASN cc_start: 0.7711 (t0) cc_final: 0.7473 (t0) REVERT: c 18 LEU cc_start: 0.8109 (tt) cc_final: 0.7841 (tt) REVERT: d 2 ILE cc_start: 0.6791 (mp) cc_final: 0.6405 (tp) REVERT: d 42 HIS cc_start: 0.8429 (OUTLIER) cc_final: 0.8170 (t-170) REVERT: e 7 TRP cc_start: 0.8711 (p-90) cc_final: 0.8022 (p-90) REVERT: e 107 TRP cc_start: 0.5235 (m100) cc_final: 0.5028 (m100) REVERT: e 203 ASN cc_start: 0.7590 (t0) cc_final: 0.7246 (t0) REVERT: f 171 GLN cc_start: 0.6380 (mm-40) cc_final: 0.5856 (mm110) REVERT: g 106 MET cc_start: 0.6637 (tmm) cc_final: 0.6162 (tmm) REVERT: h 61 PHE cc_start: 0.6405 (OUTLIER) cc_final: 0.6134 (t80) REVERT: h 174 LYS cc_start: 0.7819 (mttt) cc_final: 0.7522 (tmtt) REVERT: i 7 TRP cc_start: 0.8570 (p-90) cc_final: 0.8135 (p-90) REVERT: k 65 MET cc_start: 0.5965 (ptp) cc_final: 0.5620 (ptp) REVERT: k 106 MET cc_start: 0.6952 (tmt) cc_final: 0.6422 (tmm) outliers start: 139 outliers final: 63 residues processed: 441 average time/residue: 0.2261 time to fit residues: 167.8938 Evaluate side-chains 358 residues out of total 4704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 285 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain E residue 127 TRP Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain G residue 191 TYR Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain I residue 132 LYS Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain K residue 210 ILE Chi-restraints excluded: chain a residue 67 ILE Chi-restraints excluded: chain a residue 133 LYS Chi-restraints excluded: chain a residue 144 CYS Chi-restraints excluded: chain a residue 145 LEU Chi-restraints excluded: chain b residue 79 ASP Chi-restraints excluded: chain b residue 173 SER Chi-restraints excluded: chain b residue 193 LYS Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 193 LEU Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 144 CYS Chi-restraints excluded: chain e residue 182 LEU Chi-restraints excluded: chain e residue 199 ILE Chi-restraints excluded: chain f residue 20 SER Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 173 SER Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain g residue 67 ILE Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 45 ARG Chi-restraints excluded: chain h residue 61 PHE Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 137 VAL Chi-restraints excluded: chain h residue 140 LEU Chi-restraints excluded: chain h residue 194 HIS Chi-restraints excluded: chain i residue 37 VAL Chi-restraints excluded: chain i residue 144 CYS Chi-restraints excluded: chain j residue 68 SER Chi-restraints excluded: chain j residue 94 MET Chi-restraints excluded: chain j residue 214 PHE Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 67 ILE Chi-restraints excluded: chain k residue 103 GLU Chi-restraints excluded: chain k residue 180 TYR Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 94 MET Chi-restraints excluded: chain l residue 114 THR Chi-restraints excluded: chain l residue 122 ILE Chi-restraints excluded: chain l residue 137 VAL Chi-restraints excluded: chain l residue 140 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 531 random chunks: chunk 530 optimal weight: 6.9990 chunk 248 optimal weight: 40.0000 chunk 71 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 chunk 250 optimal weight: 8.9990 chunk 242 optimal weight: 5.9990 chunk 289 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 158 optimal weight: 9.9990 chunk 464 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 HIS ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN C 18 HIS C 132 GLN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN C 210 GLN E 18 HIS E 144 ASN E 173 GLN E 184 HIS F 159 HIS G 85 GLN I 85 GLN I 120 GLN K 85 GLN K 120 GLN ** a 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 17 GLN b 47 GLN b 55 HIS b 171 GLN ** b 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 56 ASN e 3 GLN e 6 GLN ** e 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 47 GLN ** h 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 203 ASN j 129 GLN l 47 GLN ** l 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 194 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.087102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.072119 restraints weight = 358721.939| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 10.45 r_work: 0.3753 rms_B_bonded: 10.41 restraints_weight: 2.0000 r_work: 0.3856 rms_B_bonded: 7.78 restraints_weight: 4.0000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 43927 Z= 0.334 Angle : 0.945 19.020 59898 Z= 0.469 Chirality : 0.052 0.403 6934 Planarity : 0.007 0.176 7545 Dihedral : 15.955 120.301 7546 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 25.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.42 % Favored : 91.40 % Rotamer: Outliers : 4.68 % Allowed : 18.16 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.11), residues: 5370 helix: 1.34 (0.24), residues: 459 sheet: -0.50 (0.12), residues: 1985 loop : -1.34 (0.12), residues: 2926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG a 95 TYR 0.048 0.003 TYR c 180 PHE 0.044 0.003 PHE a 32 TRP 0.034 0.003 TRP E 153 HIS 0.013 0.002 HIS b 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00703 / 0.33 (43794) covalent geometry : angle 0.92101 / 0.46 (59553) SS BOND : bond 0.01091 / 0.69 ( 54) SS BOND : angle 1.84574 / 1.13 ( 108) hydrogen bonds : bond 0.05094 / 3.43 ( 1428) hydrogen bonds : angle 7.11134 / 4.95 ( 3801) link_ALPHA1-3 : bond 0.02046 / 0.96 ( 9) link_ALPHA1-3 : angle 2.88879 / 1.89 ( 27) link_ALPHA1-6 : bond 0.01213 / 0.65 ( 7) link_ALPHA1-6 : angle 2.39720 / 1.47 ( 21) link_BETA1-4 : bond 0.00884 / 0.56 ( 42) link_BETA1-4 : angle 3.42354 / 2.30 ( 126) link_NAG-ASN : bond 0.00840 / 0.42 ( 21) link_NAG-ASN : angle 3.47470 / 2.46 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10740 Ramachandran restraints generated. 5370 Oldfield, 0 Emsley, 5370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10740 Ramachandran restraints generated. 5370 Oldfield, 0 Emsley, 5370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 4704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 312 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8404 (tm-30) REVERT: A 101 ASP cc_start: 0.8855 (t0) cc_final: 0.8654 (p0) REVERT: B 56 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8794 (tp) REVERT: B 78 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8681 (pt0) REVERT: C 100 TYR cc_start: 0.9458 (p90) cc_final: 0.9146 (p90) REVERT: C 244 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8552 (tt) REVERT: C 251 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9012 (pt) REVERT: C 268 MET cc_start: 0.6215 (OUTLIER) cc_final: 0.5201 (tmm) REVERT: D 78 GLN cc_start: 0.8930 (tt0) cc_final: 0.8596 (pt0) REVERT: E 63 ASN cc_start: 0.6307 (OUTLIER) cc_final: 0.5995 (p0) REVERT: E 302 TYR cc_start: 0.4963 (OUTLIER) cc_final: 0.3530 (m-80) REVERT: F 56 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8819 (tp) REVERT: G 191 TYR cc_start: 0.9631 (OUTLIER) cc_final: 0.9363 (t80) REVERT: I 120 GLN cc_start: 0.9723 (OUTLIER) cc_final: 0.9221 (pm20) REVERT: I 191 TYR cc_start: 0.9805 (m-80) cc_final: 0.9575 (t80) REVERT: J 70 ASP cc_start: 0.9629 (m-30) cc_final: 0.9225 (p0) REVERT: K 120 GLN cc_start: 0.9786 (OUTLIER) cc_final: 0.9220 (pm20) REVERT: K 159 ASP cc_start: 0.9843 (m-30) cc_final: 0.9638 (p0) REVERT: K 191 TYR cc_start: 0.9649 (m-80) cc_final: 0.9325 (m-80) REVERT: L 70 ASP cc_start: 0.9578 (m-30) cc_final: 0.9051 (p0) REVERT: a 7 TRP cc_start: 0.8805 (p-90) cc_final: 0.8176 (p-90) REVERT: a 46 GLN cc_start: 0.8236 (tp-100) cc_final: 0.7743 (tm-30) REVERT: a 186 VAL cc_start: 0.6892 (OUTLIER) cc_final: 0.6548 (p) REVERT: a 220 CYS cc_start: 0.0502 (OUTLIER) cc_final: -0.1346 (t) REVERT: c 18 LEU cc_start: 0.8233 (tt) cc_final: 0.7975 (tt) REVERT: c 75 GLN cc_start: 0.8940 (mt0) cc_final: 0.8532 (mt0) REVERT: c 106 MET cc_start: 0.7157 (tmm) cc_final: 0.6611 (tmm) REVERT: d 2 ILE cc_start: 0.7132 (mp) cc_final: 0.6737 (tp) REVERT: d 142 ASN cc_start: 0.4173 (t0) cc_final: 0.3832 (t0) REVERT: d 181 SER cc_start: 0.3478 (OUTLIER) cc_final: 0.3272 (m) REVERT: e 7 TRP cc_start: 0.9086 (p-90) cc_final: 0.8283 (p-90) REVERT: e 203 ASN cc_start: 0.7891 (t0) cc_final: 0.7590 (t0) REVERT: f 171 GLN cc_start: 0.7436 (mm110) cc_final: 0.6619 (mm110) REVERT: g 65 MET cc_start: 0.6260 (ptp) cc_final: 0.6028 (ptp) REVERT: g 76 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.7235 (p90) REVERT: g 180 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.8246 (t80) REVERT: i 174 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9076 (mt) REVERT: k 65 MET cc_start: 0.6248 (ptp) cc_final: 0.5466 (ptt) outliers start: 220 outliers final: 119 residues processed: 494 average time/residue: 0.2331 time to fit residues: 195.3435 Evaluate side-chains 414 residues out of total 4704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 277 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLN Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain C residue 1 GLN Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain E residue 1 GLN Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain E residue 127 TRP Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 302 TYR Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 191 TYR Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain I residue 132 LYS Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain K residue 210 ILE Chi-restraints excluded: chain a residue 37 VAL Chi-restraints excluded: chain a residue 67 ILE Chi-restraints excluded: chain a residue 144 CYS Chi-restraints excluded: chain a residue 182 LEU Chi-restraints excluded: chain a residue 186 VAL Chi-restraints excluded: chain a residue 213 LYS Chi-restraints excluded: chain a residue 220 CYS Chi-restraints excluded: chain b residue 4 LEU Chi-restraints excluded: chain b residue 17 GLN Chi-restraints excluded: chain b residue 68 SER Chi-restraints excluded: chain b residue 80 ILE Chi-restraints excluded: chain b residue 94 MET Chi-restraints excluded: chain b residue 115 VAL Chi-restraints excluded: chain b residue 140 LEU Chi-restraints excluded: chain b residue 193 LYS Chi-restraints excluded: chain c residue 34 TRP Chi-restraints excluded: chain c residue 51 ILE Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 193 LEU Chi-restraints excluded: chain d residue 94 MET Chi-restraints excluded: chain d residue 97 THR Chi-restraints excluded: chain d residue 151 VAL Chi-restraints excluded: chain d residue 181 SER Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain e residue 6 GLN Chi-restraints excluded: chain e residue 23 GLU Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 67 ILE Chi-restraints excluded: chain e residue 120 THR Chi-restraints excluded: chain e residue 144 CYS Chi-restraints excluded: chain e residue 174 LEU Chi-restraints excluded: chain e residue 182 LEU Chi-restraints excluded: chain e residue 186 VAL Chi-restraints excluded: chain e residue 199 ILE Chi-restraints excluded: chain f residue 20 SER Chi-restraints excluded: chain f residue 41 LEU Chi-restraints excluded: chain f residue 115 VAL Chi-restraints excluded: chain g residue 18 LEU Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain g residue 63 VAL Chi-restraints excluded: chain g residue 67 ILE Chi-restraints excluded: chain g residue 76 PHE Chi-restraints excluded: chain g residue 93 CYS Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 116 SER Chi-restraints excluded: chain g residue 180 TYR Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 65 ASP Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 137 VAL Chi-restraints excluded: chain h residue 186 LEU Chi-restraints excluded: chain h residue 194 HIS Chi-restraints excluded: chain i residue 4 LEU Chi-restraints excluded: chain i residue 37 VAL Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain i residue 103 GLU Chi-restraints excluded: chain i residue 144 CYS Chi-restraints excluded: chain i residue 174 LEU Chi-restraints excluded: chain i residue 182 LEU Chi-restraints excluded: chain i residue 186 VAL Chi-restraints excluded: chain i residue 199 ILE Chi-restraints excluded: chain i residue 201 ASN Chi-restraints excluded: chain i residue 213 LYS Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 31 HIS Chi-restraints excluded: chain j residue 55 HIS Chi-restraints excluded: chain j residue 70 ARG Chi-restraints excluded: chain j residue 80 ILE Chi-restraints excluded: chain j residue 114 THR Chi-restraints excluded: chain j residue 115 VAL Chi-restraints excluded: chain j residue 176 SER Chi-restraints excluded: chain j residue 214 PHE Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 67 ILE Chi-restraints excluded: chain k residue 93 CYS Chi-restraints excluded: chain k residue 100 VAL Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain k residue 145 LEU Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain k residue 164 THR Chi-restraints excluded: chain k residue 180 TYR Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 114 THR Chi-restraints excluded: chain l residue 122 ILE Chi-restraints excluded: chain l residue 137 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 531 random chunks: chunk 407 optimal weight: 5.9990 chunk 238 optimal weight: 9.9990 chunk 403 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 228 optimal weight: 0.0670 chunk 25 optimal weight: 7.9990 chunk 250 optimal weight: 40.0000 chunk 463 optimal weight: 6.9990 chunk 405 optimal weight: 6.9990 chunk 445 optimal weight: 5.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 121 ASN C 191 GLN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 HIS ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN a 203 ASN ** b 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 75 ASN h 55 HIS ** i 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 171 GLN l 55 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.089523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.074598 restraints weight = 350761.226| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 10.07 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 43927 Z= 0.177 Angle : 0.766 17.909 59898 Z= 0.369 Chirality : 0.048 0.287 6934 Planarity : 0.006 0.173 7545 Dihedral : 14.242 116.650 7538 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.96 % Favored : 92.85 % Rotamer: Outliers : 3.79 % Allowed : 19.31 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.12), residues: 5370 helix: 1.50 (0.24), residues: 458 sheet: -0.31 (0.12), residues: 1925 loop : -1.28 (0.11), residues: 2987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG h 59 TYR 0.024 0.002 TYR l 54 PHE 0.028 0.002 PHE I 137 TRP 0.024 0.002 TRP E 127 HIS 0.009 0.001 HIS j 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (43794) covalent geometry : angle 0.73832 / 0.36 (59553) SS BOND : bond 0.00593 / 0.38 ( 54) SS BOND : angle 1.33920 / 0.79 ( 108) hydrogen bonds : bond 0.03523 / 2.40 ( 1428) hydrogen bonds : angle 6.55170 / 4.57 ( 3801) link_ALPHA1-3 : bond 0.01874 / 0.89 ( 9) link_ALPHA1-3 : angle 2.77666 / 1.70 ( 27) link_ALPHA1-6 : bond 0.00918 / 0.53 ( 7) link_ALPHA1-6 : angle 2.35360 / 1.41 ( 21) link_BETA1-4 : bond 0.00862 / 0.49 ( 42) link_BETA1-4 : angle 3.37095 / 2.28 ( 126) link_NAG-ASN : bond 0.00677 / 0.34 ( 21) link_NAG-ASN : angle 3.34010 / 2.39 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10740 Ramachandran restraints generated. 5370 Oldfield, 0 Emsley, 5370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10740 Ramachandran restraints generated. 5370 Oldfield, 0 Emsley, 5370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 4704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 314 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.9031 (tp) REVERT: B 78 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8083 (pt0) REVERT: C 13 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9122 (pt) REVERT: C 62 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8237 (tp30) REVERT: C 100 TYR cc_start: 0.9400 (p90) cc_final: 0.9129 (p90) REVERT: C 244 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8679 (tt) REVERT: C 268 MET cc_start: 0.5811 (mmm) cc_final: 0.5418 (mmm) REVERT: D 78 GLN cc_start: 0.8774 (tt0) cc_final: 0.8398 (pt0) REVERT: E 13 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8994 (pt) REVERT: E 38 ASN cc_start: 0.7994 (OUTLIER) cc_final: 0.7094 (t0) REVERT: E 63 ASN cc_start: 0.5815 (OUTLIER) cc_final: 0.5562 (p0) REVERT: E 177 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8145 (tt) REVERT: F 56 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.9004 (tp) REVERT: G 123 MET cc_start: 0.9244 (tpp) cc_final: 0.8868 (tpp) REVERT: G 191 TYR cc_start: 0.9690 (OUTLIER) cc_final: 0.9417 (t80) REVERT: H 70 ASP cc_start: 0.9421 (m-30) cc_final: 0.9075 (p0) REVERT: I 191 TYR cc_start: 0.9808 (m-80) cc_final: 0.9585 (t80) REVERT: J 70 ASP cc_start: 0.9575 (m-30) cc_final: 0.9176 (p0) REVERT: K 159 ASP cc_start: 0.9815 (m-30) cc_final: 0.9613 (p0) REVERT: K 191 TYR cc_start: 0.9658 (m-80) cc_final: 0.9342 (m-80) REVERT: L 70 ASP cc_start: 0.9489 (m-30) cc_final: 0.8979 (p0) REVERT: a 7 TRP cc_start: 0.8273 (p-90) cc_final: 0.7852 (p-90) REVERT: a 23 GLU cc_start: 0.6438 (tt0) cc_final: 0.6026 (pp20) REVERT: a 46 GLN cc_start: 0.8076 (tp-100) cc_final: 0.7557 (tm-30) REVERT: a 199 ILE cc_start: 0.8409 (mm) cc_final: 0.8134 (mm) REVERT: a 220 CYS cc_start: 0.0335 (OUTLIER) cc_final: -0.0870 (t) REVERT: c 106 MET cc_start: 0.6567 (tmm) cc_final: 0.6037 (tmm) REVERT: d 2 ILE cc_start: 0.7012 (mp) cc_final: 0.6715 (tp) REVERT: d 142 ASN cc_start: 0.4604 (t0) cc_final: 0.4251 (t0) REVERT: e 7 TRP cc_start: 0.8567 (p-90) cc_final: 0.8005 (p-90) REVERT: e 87 ASP cc_start: 0.1021 (OUTLIER) cc_final: 0.0550 (t0) REVERT: e 203 ASN cc_start: 0.8004 (t0) cc_final: 0.7665 (t0) REVERT: g 76 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7807 (p90) REVERT: g 106 MET cc_start: 0.6680 (tmm) cc_final: 0.6412 (tmm) REVERT: g 142 LEU cc_start: 0.5747 (OUTLIER) cc_final: 0.5282 (mp) REVERT: i 7 TRP cc_start: 0.8567 (p-90) cc_final: 0.8003 (p-90) REVERT: i 87 ASP cc_start: 0.1993 (OUTLIER) cc_final: 0.1730 (t0) REVERT: j 41 LEU cc_start: 0.7968 (tp) cc_final: 0.7744 (tp) REVERT: k 25 TYR cc_start: 0.8412 (m-80) cc_final: 0.8162 (m-80) REVERT: k 76 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8134 (p90) REVERT: l 215 ASN cc_start: 0.8542 (m-40) cc_final: 0.7805 (t0) outliers start: 178 outliers final: 93 residues processed: 457 average time/residue: 0.2291 time to fit residues: 180.1365 Evaluate side-chains 394 residues out of total 4704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 284 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain E residue 127 TRP Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 193 PHE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 302 TYR Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 191 TYR Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain I residue 37 ASN Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain K residue 37 ASN Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 67 ILE Chi-restraints excluded: chain a residue 93 CYS Chi-restraints excluded: chain a residue 144 CYS Chi-restraints excluded: chain a residue 220 CYS Chi-restraints excluded: chain b residue 68 SER Chi-restraints excluded: chain b residue 75 ASN Chi-restraints excluded: chain b residue 80 ILE Chi-restraints excluded: chain b residue 115 VAL Chi-restraints excluded: chain b residue 193 LYS Chi-restraints excluded: chain c residue 34 TRP Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 90 THR Chi-restraints excluded: chain c residue 112 LEU Chi-restraints excluded: chain c residue 154 VAL Chi-restraints excluded: chain c residue 180 TYR Chi-restraints excluded: chain d residue 32 SER Chi-restraints excluded: chain d residue 94 MET Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 87 ASP Chi-restraints excluded: chain e residue 103 GLU Chi-restraints excluded: chain e residue 199 ILE Chi-restraints excluded: chain f residue 20 SER Chi-restraints excluded: chain f residue 26 SER Chi-restraints excluded: chain f residue 169 THR Chi-restraints excluded: chain g residue 18 LEU Chi-restraints excluded: chain g residue 34 TRP Chi-restraints excluded: chain g residue 63 VAL Chi-restraints excluded: chain g residue 67 ILE Chi-restraints excluded: chain g residue 76 PHE Chi-restraints excluded: chain g residue 81 PHE Chi-restraints excluded: chain g residue 93 CYS Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 142 LEU Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain g residue 164 THR Chi-restraints excluded: chain g residue 180 TYR Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 45 ARG Chi-restraints excluded: chain h residue 94 MET Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 137 VAL Chi-restraints excluded: chain h residue 186 LEU Chi-restraints excluded: chain i residue 53 VAL Chi-restraints excluded: chain i residue 87 ASP Chi-restraints excluded: chain i residue 144 CYS Chi-restraints excluded: chain i residue 199 ILE Chi-restraints excluded: chain i residue 201 ASN Chi-restraints excluded: chain i residue 213 LYS Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 70 ARG Chi-restraints excluded: chain j residue 114 THR Chi-restraints excluded: chain j residue 115 VAL Chi-restraints excluded: chain k residue 53 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 67 ILE Chi-restraints excluded: chain k residue 76 PHE Chi-restraints excluded: chain k residue 93 CYS Chi-restraints excluded: chain k residue 100 VAL Chi-restraints excluded: chain k residue 164 THR Chi-restraints excluded: chain k residue 180 TYR Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 94 MET Chi-restraints excluded: chain l residue 114 THR Chi-restraints excluded: chain l residue 122 ILE Chi-restraints excluded: chain l residue 137 VAL Chi-restraints excluded: chain l residue 140 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 531 random chunks: chunk 398 optimal weight: 20.0000 chunk 122 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 377 optimal weight: 3.9990 chunk 244 optimal weight: 0.0870 chunk 486 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 296 optimal weight: 5.9990 chunk 383 optimal weight: 9.9990 chunk 410 optimal weight: 3.9990 overall best weight: 2.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 HIS ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 GLN J 90 GLN L 90 GLN ** a 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 17 GLN b 171 GLN ** b 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 17 GLN ** e 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 201 ASN h 30 HIS ** i 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.093154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.081874 restraints weight = 405409.100| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 9.27 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 43927 Z= 0.172 Angle : 0.752 17.772 59898 Z= 0.361 Chirality : 0.047 0.289 6934 Planarity : 0.005 0.172 7545 Dihedral : 13.457 117.425 7536 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.80 % Favored : 92.01 % Rotamer: Outliers : 3.66 % Allowed : 20.05 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.12), residues: 5370 helix: 1.57 (0.24), residues: 459 sheet: -0.35 (0.12), residues: 1961 loop : -1.25 (0.12), residues: 2950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG h 59 TYR 0.022 0.002 TYR l 54 PHE 0.021 0.002 PHE F 9 TRP 0.024 0.002 TRP e 34 HIS 0.006 0.001 HIS h 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (43794) covalent geometry : angle 0.72496 / 0.36 (59553) SS BOND : bond 0.00541 / 0.35 ( 54) SS BOND : angle 1.38732 / 0.85 ( 108) hydrogen bonds : bond 0.03405 / 2.32 ( 1428) hydrogen bonds : angle 6.38334 / 4.46 ( 3801) link_ALPHA1-3 : bond 0.01991 / 0.95 ( 9) link_ALPHA1-3 : angle 2.94981 / 1.85 ( 27) link_ALPHA1-6 : bond 0.01008 / 0.55 ( 7) link_ALPHA1-6 : angle 2.20233 / 1.32 ( 21) link_BETA1-4 : bond 0.00869 / 0.50 ( 42) link_BETA1-4 : angle 3.25958 / 2.20 ( 126) link_NAG-ASN : bond 0.00618 / 0.32 ( 21) link_NAG-ASN : angle 3.32963 / 2.39 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10740 Ramachandran restraints generated. 5370 Oldfield, 0 Emsley, 5370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10740 Ramachandran restraints generated. 5370 Oldfield, 0 Emsley, 5370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 4704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 313 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8355 (tm-30) REVERT: A 208 ARG cc_start: 0.6723 (ptt180) cc_final: 0.5825 (ptp-170) REVERT: A 211 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8285 (pm20) REVERT: B 78 GLN cc_start: 0.8706 (pt0) cc_final: 0.8300 (pt0) REVERT: C 13 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9117 (pt) REVERT: C 62 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8266 (tp30) REVERT: C 244 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8603 (tt) REVERT: C 268 MET cc_start: 0.5867 (mmm) cc_final: 0.5319 (tmm) REVERT: D 17 MET cc_start: 0.8558 (ttp) cc_final: 0.8358 (ttp) REVERT: D 78 GLN cc_start: 0.8814 (tt0) cc_final: 0.8480 (pt0) REVERT: E 13 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8972 (pt) REVERT: E 63 ASN cc_start: 0.5994 (OUTLIER) cc_final: 0.5777 (p0) REVERT: E 211 GLN cc_start: 0.9050 (mt0) cc_final: 0.8504 (mt0) REVERT: F 56 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8923 (tp) REVERT: G 123 MET cc_start: 0.9260 (tpp) cc_final: 0.8902 (tpp) REVERT: G 159 ASP cc_start: 0.9793 (m-30) cc_final: 0.9564 (p0) REVERT: G 191 TYR cc_start: 0.9595 (OUTLIER) cc_final: 0.9256 (t80) REVERT: H 70 ASP cc_start: 0.9403 (m-30) cc_final: 0.9049 (p0) REVERT: I 191 TYR cc_start: 0.9749 (m-80) cc_final: 0.9387 (t80) REVERT: J 70 ASP cc_start: 0.9562 (m-30) cc_final: 0.9179 (p0) REVERT: K 191 TYR cc_start: 0.9636 (m-80) cc_final: 0.9238 (m-80) REVERT: L 70 ASP cc_start: 0.9466 (m-30) cc_final: 0.8965 (p0) REVERT: a 7 TRP cc_start: 0.8376 (p-90) cc_final: 0.7903 (p-90) REVERT: a 46 GLN cc_start: 0.8096 (tp-100) cc_final: 0.7564 (tm-30) REVERT: a 65 MET cc_start: 0.6612 (tmm) cc_final: 0.5727 (tmm) REVERT: a 199 ILE cc_start: 0.8249 (mm) cc_final: 0.7891 (mm) REVERT: a 220 CYS cc_start: 0.0792 (OUTLIER) cc_final: -0.0375 (t) REVERT: b 195 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.9032 (mmmt) REVERT: c 106 MET cc_start: 0.6771 (tmm) cc_final: 0.6267 (tmm) REVERT: d 2 ILE cc_start: 0.7455 (mp) cc_final: 0.7120 (tp) REVERT: d 142 ASN cc_start: 0.4663 (t0) cc_final: 0.4335 (t0) REVERT: e 7 TRP cc_start: 0.8664 (p-90) cc_final: 0.8044 (p-90) REVERT: e 65 MET cc_start: 0.7207 (tmm) cc_final: 0.6904 (tmm) REVERT: e 203 ASN cc_start: 0.8027 (t0) cc_final: 0.7696 (t0) REVERT: f 55 HIS cc_start: 0.8060 (OUTLIER) cc_final: 0.6567 (m90) REVERT: g 25 TYR cc_start: 0.8660 (m-10) cc_final: 0.8376 (m-80) REVERT: g 76 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7955 (p90) REVERT: g 106 MET cc_start: 0.6720 (tmm) cc_final: 0.6405 (tmm) REVERT: h 61 PHE cc_start: 0.6028 (OUTLIER) cc_final: 0.5803 (t80) REVERT: i 7 TRP cc_start: 0.8638 (p-90) cc_final: 0.8029 (p-90) REVERT: k 25 TYR cc_start: 0.8472 (m-80) cc_final: 0.8204 (m-80) REVERT: k 76 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8150 (p90) REVERT: k 106 MET cc_start: 0.6886 (tmt) cc_final: 0.6318 (tmm) REVERT: l 59 ARG cc_start: 0.6051 (mmt180) cc_final: 0.5216 (mmt180) REVERT: l 109 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7812 (tt) REVERT: l 215 ASN cc_start: 0.8590 (m-40) cc_final: 0.7628 (t0) outliers start: 172 outliers final: 112 residues processed: 455 average time/residue: 0.2379 time to fit residues: 184.6090 Evaluate side-chains 415 residues out of total 4704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 287 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain C residue 1 GLN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain E residue 1 GLN Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain E residue 127 TRP Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 193 PHE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 302 TYR Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain G residue 191 TYR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain I residue 37 ASN Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain K residue 37 ASN Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain a residue 67 ILE Chi-restraints excluded: chain a residue 93 CYS Chi-restraints excluded: chain a residue 144 CYS Chi-restraints excluded: chain a residue 170 PHE Chi-restraints excluded: chain a residue 220 CYS Chi-restraints excluded: chain b residue 4 LEU Chi-restraints excluded: chain b residue 68 SER Chi-restraints excluded: chain b residue 80 ILE Chi-restraints excluded: chain b residue 115 VAL Chi-restraints excluded: chain b residue 193 LYS Chi-restraints excluded: chain b residue 195 LYS Chi-restraints excluded: chain c residue 34 TRP Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 90 THR Chi-restraints excluded: chain c residue 112 LEU Chi-restraints excluded: chain c residue 180 TYR Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 94 MET Chi-restraints excluded: chain d residue 97 THR Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 103 GLU Chi-restraints excluded: chain e residue 144 CYS Chi-restraints excluded: chain e residue 182 LEU Chi-restraints excluded: chain e residue 199 ILE Chi-restraints excluded: chain e residue 201 ASN Chi-restraints excluded: chain f residue 20 SER Chi-restraints excluded: chain f residue 26 SER Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 67 ILE Chi-restraints excluded: chain f residue 80 ILE Chi-restraints excluded: chain f residue 141 LEU Chi-restraints excluded: chain g residue 29 LEU Chi-restraints excluded: chain g residue 34 TRP Chi-restraints excluded: chain g residue 63 VAL Chi-restraints excluded: chain g residue 67 ILE Chi-restraints excluded: chain g residue 76 PHE Chi-restraints excluded: chain g residue 81 PHE Chi-restraints excluded: chain g residue 82 TYR Chi-restraints excluded: chain g residue 93 CYS Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain g residue 154 VAL Chi-restraints excluded: chain g residue 164 THR Chi-restraints excluded: chain g residue 180 TYR Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 61 PHE Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 183 THR Chi-restraints excluded: chain h residue 186 LEU Chi-restraints excluded: chain i residue 53 VAL Chi-restraints excluded: chain i residue 144 CYS Chi-restraints excluded: chain i residue 199 ILE Chi-restraints excluded: chain i residue 201 ASN Chi-restraints excluded: chain i residue 213 LYS Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 70 ARG Chi-restraints excluded: chain j residue 107 THR Chi-restraints excluded: chain j residue 114 THR Chi-restraints excluded: chain j residue 115 VAL Chi-restraints excluded: chain j residue 141 LEU Chi-restraints excluded: chain j residue 176 SER Chi-restraints excluded: chain k residue 29 LEU Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 67 ILE Chi-restraints excluded: chain k residue 76 PHE Chi-restraints excluded: chain k residue 93 CYS Chi-restraints excluded: chain k residue 100 VAL Chi-restraints excluded: chain k residue 103 GLU Chi-restraints excluded: chain k residue 112 LEU Chi-restraints excluded: chain k residue 132 SER Chi-restraints excluded: chain k residue 154 VAL Chi-restraints excluded: chain k residue 164 THR Chi-restraints excluded: chain k residue 180 TYR Chi-restraints excluded: chain l residue 45 ARG Chi-restraints excluded: chain l residue 94 MET Chi-restraints excluded: chain l residue 109 LEU Chi-restraints excluded: chain l residue 114 THR Chi-restraints excluded: chain l residue 122 ILE Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 183 THR Chi-restraints excluded: chain l residue 186 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 531 random chunks: chunk 56 optimal weight: 2.9990 chunk 444 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 389 optimal weight: 8.9990 chunk 189 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 25 optimal weight: 0.0030 chunk 492 optimal weight: 2.9990 chunk 456 optimal weight: 4.9990 chunk 300 optimal weight: 0.9980 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN D 34 GLN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 HIS ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 250 ASN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN K 120 GLN ** a 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 17 GLN e 201 ASN ** h 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.094562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.083462 restraints weight = 405240.627| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 9.08 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 43927 Z= 0.138 Angle : 0.725 17.091 59898 Z= 0.346 Chirality : 0.047 0.287 6934 Planarity : 0.005 0.169 7545 Dihedral : 12.829 115.231 7536 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.76 % Favored : 93.05 % Rotamer: Outliers : 3.45 % Allowed : 20.82 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.12), residues: 5370 helix: 1.41 (0.24), residues: 477 sheet: -0.26 (0.12), residues: 1942 loop : -1.18 (0.12), residues: 2951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG h 45 TYR 0.019 0.001 TYR F 162 PHE 0.021 0.002 PHE B 9 TRP 0.022 0.001 TRP b 153 HIS 0.007 0.001 HIS f 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (43794) covalent geometry : angle 0.69741 / 0.34 (59553) SS BOND : bond 0.00420 / 0.26 ( 54) SS BOND : angle 1.24360 / 0.79 ( 108) hydrogen bonds : bond 0.03115 / 2.12 ( 1428) hydrogen bonds : angle 6.07697 / 4.25 ( 3801) link_ALPHA1-3 : bond 0.02226 / 1.05 ( 9) link_ALPHA1-3 : angle 3.29324 / 2.04 ( 27) link_ALPHA1-6 : bond 0.00959 / 0.53 ( 7) link_ALPHA1-6 : angle 2.11761 / 1.30 ( 21) link_BETA1-4 : bond 0.00866 / 0.49 ( 42) link_BETA1-4 : angle 3.18225 / 2.15 ( 126) link_NAG-ASN : bond 0.00613 / 0.32 ( 21) link_NAG-ASN : angle 3.30506 / 2.38 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10740 Ramachandran restraints generated. 5370 Oldfield, 0 Emsley, 5370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10740 Ramachandran restraints generated. 5370 Oldfield, 0 Emsley, 5370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 4704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 311 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8383 (tm-30) REVERT: A 208 ARG cc_start: 0.6777 (ptt180) cc_final: 0.6011 (ptp-170) REVERT: A 211 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8302 (pm20) REVERT: B 78 GLN cc_start: 0.8658 (pt0) cc_final: 0.8178 (pt0) REVERT: C 62 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8297 (tp30) REVERT: C 244 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8575 (tt) REVERT: C 268 MET cc_start: 0.5873 (mmm) cc_final: 0.5305 (tmm) REVERT: D 77 ILE cc_start: 0.9396 (mm) cc_final: 0.9176 (tp) REVERT: D 78 GLN cc_start: 0.8830 (tt0) cc_final: 0.8508 (pt0) REVERT: E 38 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7011 (t0) REVERT: E 63 ASN cc_start: 0.6160 (OUTLIER) cc_final: 0.5817 (p0) REVERT: E 211 GLN cc_start: 0.9042 (mt0) cc_final: 0.8539 (mt0) REVERT: E 268 MET cc_start: 0.4073 (OUTLIER) cc_final: 0.3770 (mmm) REVERT: F 56 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8905 (tp) REVERT: F 74 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7638 (tm-30) REVERT: G 123 MET cc_start: 0.9246 (tpp) cc_final: 0.8942 (tpp) REVERT: G 159 ASP cc_start: 0.9787 (m-30) cc_final: 0.9581 (p0) REVERT: G 191 TYR cc_start: 0.9607 (OUTLIER) cc_final: 0.9254 (t80) REVERT: H 70 ASP cc_start: 0.9388 (m-30) cc_final: 0.9033 (p0) REVERT: I 159 ASP cc_start: 0.9772 (m-30) cc_final: 0.9478 (p0) REVERT: I 191 TYR cc_start: 0.9753 (m-80) cc_final: 0.9372 (t80) REVERT: J 70 ASP cc_start: 0.9546 (m-30) cc_final: 0.9157 (p0) REVERT: K 191 TYR cc_start: 0.9641 (m-80) cc_final: 0.9253 (m-80) REVERT: L 70 ASP cc_start: 0.9461 (m-30) cc_final: 0.8974 (p0) REVERT: a 7 TRP cc_start: 0.8338 (p-90) cc_final: 0.7891 (p-90) REVERT: a 46 GLN cc_start: 0.8077 (tp-100) cc_final: 0.7479 (tm-30) REVERT: a 65 MET cc_start: 0.6740 (tmm) cc_final: 0.6223 (tmm) REVERT: a 199 ILE cc_start: 0.8129 (mm) cc_final: 0.7765 (mm) REVERT: a 220 CYS cc_start: 0.0542 (OUTLIER) cc_final: -0.0509 (t) REVERT: b 59 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7803 (ptt90) REVERT: d 2 ILE cc_start: 0.7472 (mp) cc_final: 0.7134 (tp) REVERT: d 142 ASN cc_start: 0.4517 (t0) cc_final: 0.4172 (t0) REVERT: d 153 TRP cc_start: 0.3519 (m100) cc_final: 0.2958 (m100) REVERT: e 7 TRP cc_start: 0.8578 (p-90) cc_final: 0.8031 (p-90) REVERT: e 203 ASN cc_start: 0.8031 (t0) cc_final: 0.7699 (t0) REVERT: f 109 LEU cc_start: 0.8550 (tt) cc_final: 0.8347 (tt) REVERT: g 25 TYR cc_start: 0.8583 (m-10) cc_final: 0.8318 (m-80) REVERT: g 76 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.8130 (p90) REVERT: g 106 MET cc_start: 0.6737 (tmm) cc_final: 0.6389 (tmm) REVERT: h 109 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7542 (tp) REVERT: i 7 TRP cc_start: 0.8550 (p-90) cc_final: 0.7983 (p-90) REVERT: k 25 TYR cc_start: 0.8412 (m-80) cc_final: 0.8159 (m-80) REVERT: k 76 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8264 (p90) REVERT: k 106 MET cc_start: 0.6866 (tmt) cc_final: 0.6298 (tmm) REVERT: l 59 ARG cc_start: 0.5849 (mmt180) cc_final: 0.5017 (mmt180) REVERT: l 109 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.7873 (tt) REVERT: l 215 ASN cc_start: 0.8656 (m-40) cc_final: 0.7711 (t0) outliers start: 162 outliers final: 104 residues processed: 448 average time/residue: 0.2434 time to fit residues: 185.0972 Evaluate side-chains 407 residues out of total 4704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 288 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain C residue 1 GLN Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain E residue 127 TRP Chi-restraints excluded: chain E residue 178 TYR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain G residue 191 TYR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain I residue 37 ASN Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain K residue 37 ASN Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 210 ILE Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain a residue 67 ILE Chi-restraints excluded: chain a residue 93 CYS Chi-restraints excluded: chain a residue 144 CYS Chi-restraints excluded: chain a residue 170 PHE Chi-restraints excluded: chain a residue 220 CYS Chi-restraints excluded: chain b residue 4 LEU Chi-restraints excluded: chain b residue 59 ARG Chi-restraints excluded: chain b residue 68 SER Chi-restraints excluded: chain b residue 75 ASN Chi-restraints excluded: chain b residue 115 VAL Chi-restraints excluded: chain b residue 193 LYS Chi-restraints excluded: chain c residue 34 TRP Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 90 THR Chi-restraints excluded: chain c residue 112 LEU Chi-restraints excluded: chain c residue 154 VAL Chi-restraints excluded: chain c residue 180 TYR Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 94 MET Chi-restraints excluded: chain d residue 97 THR Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 144 CYS Chi-restraints excluded: chain e residue 199 ILE Chi-restraints excluded: chain f residue 26 SER Chi-restraints excluded: chain f residue 67 ILE Chi-restraints excluded: chain f residue 141 LEU Chi-restraints excluded: chain f residue 170 GLU Chi-restraints excluded: chain g residue 29 LEU Chi-restraints excluded: chain g residue 63 VAL Chi-restraints excluded: chain g residue 67 ILE Chi-restraints excluded: chain g residue 76 PHE Chi-restraints excluded: chain g residue 81 PHE Chi-restraints excluded: chain g residue 82 TYR Chi-restraints excluded: chain g residue 93 CYS Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain g residue 132 SER Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain g residue 154 VAL Chi-restraints excluded: chain g residue 164 THR Chi-restraints excluded: chain g residue 180 TYR Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 94 MET Chi-restraints excluded: chain h residue 109 LEU Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 183 THR Chi-restraints excluded: chain h residue 186 LEU Chi-restraints excluded: chain i residue 31 ASP Chi-restraints excluded: chain i residue 53 VAL Chi-restraints excluded: chain i residue 199 ILE Chi-restraints excluded: chain i residue 201 ASN Chi-restraints excluded: chain i residue 213 LYS Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 114 THR Chi-restraints excluded: chain j residue 141 LEU Chi-restraints excluded: chain j residue 176 SER Chi-restraints excluded: chain k residue 29 LEU Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 67 ILE Chi-restraints excluded: chain k residue 76 PHE Chi-restraints excluded: chain k residue 93 CYS Chi-restraints excluded: chain k residue 100 VAL Chi-restraints excluded: chain k residue 103 GLU Chi-restraints excluded: chain k residue 112 LEU Chi-restraints excluded: chain k residue 132 SER Chi-restraints excluded: chain k residue 154 VAL Chi-restraints excluded: chain k residue 164 THR Chi-restraints excluded: chain k residue 180 TYR Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 45 ARG Chi-restraints excluded: chain l residue 94 MET Chi-restraints excluded: chain l residue 109 LEU Chi-restraints excluded: chain l residue 114 THR Chi-restraints excluded: chain l residue 122 ILE Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 183 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 531 random chunks: chunk 408 optimal weight: 6.9990 chunk 210 optimal weight: 30.0000 chunk 220 optimal weight: 20.0000 chunk 506 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 199 optimal weight: 10.0000 chunk 371 optimal weight: 7.9990 chunk 397 optimal weight: 0.0980 chunk 209 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 overall best weight: 6.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 ASN A 22 ASN C 22 ASN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 HIS ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 GLN I 120 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 52 ASN f 129 GLN ** h 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 204 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.088549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.077315 restraints weight = 408294.875| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 8.67 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 43927 Z= 0.286 Angle : 0.853 17.766 59898 Z= 0.422 Chirality : 0.049 0.319 6934 Planarity : 0.006 0.172 7545 Dihedral : 12.871 114.839 7536 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 26.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.96 % Favored : 90.86 % Rotamer: Outliers : 3.90 % Allowed : 21.20 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.12), residues: 5370 helix: 1.42 (0.25), residues: 459 sheet: -0.61 (0.12), residues: 2021 loop : -1.40 (0.12), residues: 2890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG h 45 TYR 0.036 0.003 TYR l 54 PHE 0.021 0.003 PHE B 63 TRP 0.028 0.003 TRP E 127 HIS 0.014 0.002 HIS f 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.29 (43794) covalent geometry : angle 0.82769 / 0.42 (59553) SS BOND : bond 0.00988 / 0.53 ( 54) SS BOND : angle 1.61740 / 0.97 ( 108) hydrogen bonds : bond 0.04289 / 2.92 ( 1428) hydrogen bonds : angle 6.91931 / 4.81 ( 3801) link_ALPHA1-3 : bond 0.02428 / 1.14 ( 9) link_ALPHA1-3 : angle 3.47254 / 2.22 ( 27) link_ALPHA1-6 : bond 0.01330 / 0.73 ( 7) link_ALPHA1-6 : angle 1.73473 / 1.15 ( 21) link_BETA1-4 : bond 0.00957 / 0.55 ( 42) link_BETA1-4 : angle 3.26569 / 2.21 ( 126) link_NAG-ASN : bond 0.00728 / 0.38 ( 21) link_NAG-ASN : angle 3.37796 / 2.42 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10740 Ramachandran restraints generated. 5370 Oldfield, 0 Emsley, 5370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10740 Ramachandran restraints generated. 5370 Oldfield, 0 Emsley, 5370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 4704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 298 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8406 (tm-30) REVERT: A 63 ASN cc_start: 0.7877 (OUTLIER) cc_final: 0.6977 (p0) REVERT: A 176 LYS cc_start: 0.5755 (OUTLIER) cc_final: 0.4973 (pttp) REVERT: A 208 ARG cc_start: 0.6891 (ptt180) cc_final: 0.6383 (ptp-170) REVERT: C 62 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8395 (tp30) REVERT: C 244 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8577 (tt) REVERT: D 78 GLN cc_start: 0.8778 (tt0) cc_final: 0.8473 (pt0) REVERT: E 63 ASN cc_start: 0.6471 (OUTLIER) cc_final: 0.6231 (p0) REVERT: E 141 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.6824 (tpp80) REVERT: E 302 TYR cc_start: 0.5296 (OUTLIER) cc_final: 0.3728 (m-80) REVERT: F 56 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.9044 (tp) REVERT: G 123 MET cc_start: 0.9398 (tpp) cc_final: 0.9134 (tpp) REVERT: G 159 ASP cc_start: 0.9735 (m-30) cc_final: 0.9495 (p0) REVERT: G 191 TYR cc_start: 0.9550 (OUTLIER) cc_final: 0.9136 (t80) REVERT: H 161 GLU cc_start: 0.9383 (pm20) cc_final: 0.9111 (tp30) REVERT: I 137 PHE cc_start: 0.9556 (m-80) cc_final: 0.9315 (m-80) REVERT: I 159 ASP cc_start: 0.9697 (m-30) cc_final: 0.9373 (p0) REVERT: I 191 TYR cc_start: 0.9719 (m-80) cc_final: 0.9286 (t80) REVERT: J 70 ASP cc_start: 0.9531 (m-30) cc_final: 0.9191 (p0) REVERT: K 191 TYR cc_start: 0.9642 (m-80) cc_final: 0.9203 (m-80) REVERT: L 70 ASP cc_start: 0.9531 (m-30) cc_final: 0.9099 (p0) REVERT: a 7 TRP cc_start: 0.8433 (p-90) cc_final: 0.7885 (p-90) REVERT: a 65 MET cc_start: 0.7283 (tmm) cc_final: 0.6388 (tmm) REVERT: a 220 CYS cc_start: 0.0906 (OUTLIER) cc_final: 0.0401 (t) REVERT: b 47 GLN cc_start: 0.8426 (tp-100) cc_final: 0.8224 (mt0) REVERT: b 59 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7866 (ptt90) REVERT: c 75 GLN cc_start: 0.9038 (mt0) cc_final: 0.8694 (mm-40) REVERT: d 2 ILE cc_start: 0.7410 (mp) cc_final: 0.7079 (tp) REVERT: d 174 LYS cc_start: 0.7303 (mttt) cc_final: 0.6754 (tmtt) REVERT: e 7 TRP cc_start: 0.8713 (p-90) cc_final: 0.8189 (p-90) REVERT: f 94 MET cc_start: 0.8588 (mpp) cc_final: 0.8117 (mpp) REVERT: g 25 TYR cc_start: 0.8754 (m-10) cc_final: 0.8451 (m-80) REVERT: g 76 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8314 (p90) REVERT: g 127 PRO cc_start: 0.8518 (Cg_endo) cc_final: 0.8277 (Cg_exo) REVERT: g 180 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.8075 (t80) REVERT: h 59 ARG cc_start: 0.5829 (mmt180) cc_final: 0.5427 (mmt180) REVERT: j 171 GLN cc_start: 0.7386 (mm-40) cc_final: 0.6966 (mm110) REVERT: k 25 TYR cc_start: 0.8556 (m-80) cc_final: 0.8259 (m-80) REVERT: k 76 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8552 (p90) REVERT: l 109 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.7915 (tt) REVERT: l 113 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.5581 (ptm160) REVERT: l 215 ASN cc_start: 0.8496 (m-40) cc_final: 0.7338 (t0) outliers start: 183 outliers final: 123 residues processed: 453 average time/residue: 0.2352 time to fit residues: 182.6559 Evaluate side-chains 420 residues out of total 4704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 280 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain C residue 1 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain E residue 1 GLN Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain E residue 127 TRP Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 178 TYR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 193 PHE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 302 TYR Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 191 TYR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain I residue 37 ASN Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain K residue 37 ASN Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 210 ILE Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain a residue 37 VAL Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain a residue 67 ILE Chi-restraints excluded: chain a residue 93 CYS Chi-restraints excluded: chain a residue 144 CYS Chi-restraints excluded: chain a residue 220 CYS Chi-restraints excluded: chain b residue 4 LEU Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain b residue 59 ARG Chi-restraints excluded: chain b residue 79 ASP Chi-restraints excluded: chain b residue 115 VAL Chi-restraints excluded: chain b residue 176 SER Chi-restraints excluded: chain b residue 193 LYS Chi-restraints excluded: chain c residue 34 TRP Chi-restraints excluded: chain c residue 51 ILE Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 90 THR Chi-restraints excluded: chain c residue 112 LEU Chi-restraints excluded: chain c residue 144 CYS Chi-restraints excluded: chain c residue 180 TYR Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 94 MET Chi-restraints excluded: chain d residue 97 THR Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain d residue 151 VAL Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain e residue 65 MET Chi-restraints excluded: chain e residue 103 GLU Chi-restraints excluded: chain e residue 120 THR Chi-restraints excluded: chain e residue 144 CYS Chi-restraints excluded: chain e residue 182 LEU Chi-restraints excluded: chain e residue 199 ILE Chi-restraints excluded: chain f residue 20 SER Chi-restraints excluded: chain f residue 26 SER Chi-restraints excluded: chain f residue 80 ILE Chi-restraints excluded: chain f residue 114 THR Chi-restraints excluded: chain f residue 176 SER Chi-restraints excluded: chain g residue 29 LEU Chi-restraints excluded: chain g residue 55 LEU Chi-restraints excluded: chain g residue 63 VAL Chi-restraints excluded: chain g residue 67 ILE Chi-restraints excluded: chain g residue 76 PHE Chi-restraints excluded: chain g residue 81 PHE Chi-restraints excluded: chain g residue 93 CYS Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 132 SER Chi-restraints excluded: chain g residue 164 THR Chi-restraints excluded: chain g residue 180 TYR Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 83 VAL Chi-restraints excluded: chain h residue 94 MET Chi-restraints excluded: chain h residue 109 LEU Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 186 LEU Chi-restraints excluded: chain i residue 31 ASP Chi-restraints excluded: chain i residue 53 VAL Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain i residue 144 CYS Chi-restraints excluded: chain i residue 199 ILE Chi-restraints excluded: chain i residue 201 ASN Chi-restraints excluded: chain i residue 213 LYS Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 41 LEU Chi-restraints excluded: chain j residue 70 ARG Chi-restraints excluded: chain j residue 108 VAL Chi-restraints excluded: chain j residue 114 THR Chi-restraints excluded: chain j residue 115 VAL Chi-restraints excluded: chain j residue 176 SER Chi-restraints excluded: chain j residue 202 THR Chi-restraints excluded: chain k residue 29 LEU Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 67 ILE Chi-restraints excluded: chain k residue 76 PHE Chi-restraints excluded: chain k residue 93 CYS Chi-restraints excluded: chain k residue 100 VAL Chi-restraints excluded: chain k residue 112 LEU Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain k residue 132 SER Chi-restraints excluded: chain k residue 164 THR Chi-restraints excluded: chain k residue 180 TYR Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 45 ARG Chi-restraints excluded: chain l residue 109 LEU Chi-restraints excluded: chain l residue 113 ARG Chi-restraints excluded: chain l residue 114 THR Chi-restraints excluded: chain l residue 122 ILE Chi-restraints excluded: chain l residue 183 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 531 random chunks: chunk 365 optimal weight: 20.0000 chunk 498 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 382 optimal weight: 9.9990 chunk 464 optimal weight: 0.0570 chunk 130 optimal weight: 40.0000 chunk 299 optimal weight: 0.6980 chunk 449 optimal weight: 0.6980 chunk 369 optimal weight: 2.9990 chunk 318 optimal weight: 0.4980 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 250 ASN B 12 ASN B 34 GLN B 78 GLN B 159 HIS C 170 ASN ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 250 ASN H 90 GLN I 6 GLN ** I 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN ** K 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 201 ASN b 55 HIS ** b 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 129 GLN f 157 ASN ** h 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 30 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.093853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.082851 restraints weight = 405333.055| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 8.80 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 43927 Z= 0.138 Angle : 0.740 17.059 59898 Z= 0.354 Chirality : 0.047 0.284 6934 Planarity : 0.005 0.169 7545 Dihedral : 12.099 109.702 7536 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.37 % Favored : 93.46 % Rotamer: Outliers : 2.92 % Allowed : 22.35 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.12), residues: 5370 helix: 1.63 (0.25), residues: 454 sheet: -0.34 (0.12), residues: 1927 loop : -1.26 (0.12), residues: 2989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG h 45 TYR 0.021 0.001 TYR D 162 PHE 0.019 0.002 PHE k 92 TRP 0.019 0.001 TRP E 127 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (43794) covalent geometry : angle 0.71322 / 0.35 (59553) SS BOND : bond 0.00424 / 0.27 ( 54) SS BOND : angle 1.24449 / 0.77 ( 108) hydrogen bonds : bond 0.03074 / 2.09 ( 1428) hydrogen bonds : angle 6.12733 / 4.27 ( 3801) link_ALPHA1-3 : bond 0.02296 / 1.07 ( 9) link_ALPHA1-3 : angle 3.90581 / 2.51 ( 27) link_ALPHA1-6 : bond 0.00967 / 0.51 ( 7) link_ALPHA1-6 : angle 1.77194 / 1.18 ( 21) link_BETA1-4 : bond 0.00894 / 0.50 ( 42) link_BETA1-4 : angle 3.10435 / 2.11 ( 126) link_NAG-ASN : bond 0.00609 / 0.33 ( 21) link_NAG-ASN : angle 3.23690 / 2.33 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10740 Ramachandran restraints generated. 5370 Oldfield, 0 Emsley, 5370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10740 Ramachandran restraints generated. 5370 Oldfield, 0 Emsley, 5370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 4704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 308 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8396 (tm-30) REVERT: A 63 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7031 (p0) REVERT: A 208 ARG cc_start: 0.6995 (ptt180) cc_final: 0.6656 (ptp-170) REVERT: B 56 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.8993 (tp) REVERT: C 62 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8395 (tp30) REVERT: C 244 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8562 (tt) REVERT: C 268 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.5476 (tmm) REVERT: D 78 GLN cc_start: 0.8865 (tt0) cc_final: 0.8491 (pt0) REVERT: E 63 ASN cc_start: 0.6584 (OUTLIER) cc_final: 0.6227 (p0) REVERT: E 268 MET cc_start: 0.4285 (OUTLIER) cc_final: 0.3874 (mmm) REVERT: F 56 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8891 (tp) REVERT: G 191 TYR cc_start: 0.9617 (OUTLIER) cc_final: 0.9232 (t80) REVERT: H 70 ASP cc_start: 0.9357 (m-30) cc_final: 0.9012 (p0) REVERT: H 161 GLU cc_start: 0.9351 (pm20) cc_final: 0.9111 (tp30) REVERT: I 159 ASP cc_start: 0.9699 (m-30) cc_final: 0.9429 (p0) REVERT: J 70 ASP cc_start: 0.9496 (m-30) cc_final: 0.9161 (p0) REVERT: K 163 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8380 (mm-30) REVERT: K 191 TYR cc_start: 0.9633 (m-80) cc_final: 0.9208 (m-80) REVERT: L 70 ASP cc_start: 0.9447 (m-30) cc_final: 0.8966 (p0) REVERT: a 7 TRP cc_start: 0.8397 (p-90) cc_final: 0.7958 (p-90) REVERT: a 46 GLN cc_start: 0.7999 (tp-100) cc_final: 0.7311 (tm-30) REVERT: a 65 MET cc_start: 0.6818 (tmm) cc_final: 0.5691 (tmm) REVERT: a 199 ILE cc_start: 0.7716 (mm) cc_final: 0.7272 (mm) REVERT: a 220 CYS cc_start: 0.0525 (OUTLIER) cc_final: -0.0076 (t) REVERT: b 59 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7810 (ptt90) REVERT: d 2 ILE cc_start: 0.7719 (mp) cc_final: 0.7412 (tp) REVERT: d 119 SER cc_start: 0.4943 (p) cc_final: 0.4577 (p) REVERT: d 153 TRP cc_start: 0.3192 (m100) cc_final: 0.2562 (m100) REVERT: d 171 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8370 (mt0) REVERT: e 203 ASN cc_start: 0.8143 (t0) cc_final: 0.7799 (t0) REVERT: f 94 MET cc_start: 0.8301 (mpp) cc_final: 0.7999 (mpp) REVERT: f 109 LEU cc_start: 0.8458 (tt) cc_final: 0.8207 (tt) REVERT: g 25 TYR cc_start: 0.8713 (m-10) cc_final: 0.8441 (m-80) REVERT: g 76 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8381 (p90) REVERT: g 106 MET cc_start: 0.6986 (tmm) cc_final: 0.6518 (tmm) REVERT: h 109 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7712 (tp) REVERT: i 7 TRP cc_start: 0.8538 (p-90) cc_final: 0.8000 (p-90) REVERT: k 76 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8257 (p90) REVERT: k 106 MET cc_start: 0.7035 (tmt) cc_final: 0.6393 (tmm) REVERT: l 59 ARG cc_start: 0.5755 (mmt180) cc_final: 0.5110 (mmt180) REVERT: l 109 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.7927 (tt) REVERT: l 215 ASN cc_start: 0.8571 (m-40) cc_final: 0.7583 (p0) outliers start: 137 outliers final: 98 residues processed: 423 average time/residue: 0.2414 time to fit residues: 172.7583 Evaluate side-chains 402 residues out of total 4704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 287 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain C residue 1 GLN Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain E residue 1 GLN Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain E residue 127 TRP Chi-restraints excluded: chain E residue 178 TYR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain G residue 191 TYR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain I residue 37 ASN Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain K residue 37 ASN Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 210 ILE Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain a residue 67 ILE Chi-restraints excluded: chain a residue 93 CYS Chi-restraints excluded: chain a residue 144 CYS Chi-restraints excluded: chain a residue 170 PHE Chi-restraints excluded: chain a residue 220 CYS Chi-restraints excluded: chain b residue 4 LEU Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain b residue 59 ARG Chi-restraints excluded: chain b residue 107 THR Chi-restraints excluded: chain b residue 115 VAL Chi-restraints excluded: chain b residue 193 LYS Chi-restraints excluded: chain c residue 34 TRP Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 90 THR Chi-restraints excluded: chain c residue 112 LEU Chi-restraints excluded: chain c residue 144 CYS Chi-restraints excluded: chain c residue 180 TYR Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 94 MET Chi-restraints excluded: chain d residue 97 THR Chi-restraints excluded: chain d residue 151 VAL Chi-restraints excluded: chain d residue 171 GLN Chi-restraints excluded: chain e residue 103 GLU Chi-restraints excluded: chain e residue 144 CYS Chi-restraints excluded: chain e residue 186 VAL Chi-restraints excluded: chain e residue 199 ILE Chi-restraints excluded: chain f residue 26 SER Chi-restraints excluded: chain f residue 67 ILE Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 141 LEU Chi-restraints excluded: chain f residue 157 ASN Chi-restraints excluded: chain f residue 170 GLU Chi-restraints excluded: chain g residue 29 LEU Chi-restraints excluded: chain g residue 55 LEU Chi-restraints excluded: chain g residue 63 VAL Chi-restraints excluded: chain g residue 67 ILE Chi-restraints excluded: chain g residue 76 PHE Chi-restraints excluded: chain g residue 81 PHE Chi-restraints excluded: chain g residue 82 TYR Chi-restraints excluded: chain g residue 93 CYS Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain g residue 132 SER Chi-restraints excluded: chain g residue 164 THR Chi-restraints excluded: chain h residue 94 MET Chi-restraints excluded: chain h residue 109 LEU Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 183 THR Chi-restraints excluded: chain h residue 186 LEU Chi-restraints excluded: chain i residue 31 ASP Chi-restraints excluded: chain i residue 53 VAL Chi-restraints excluded: chain i residue 144 CYS Chi-restraints excluded: chain i residue 201 ASN Chi-restraints excluded: chain j residue 108 VAL Chi-restraints excluded: chain j residue 114 THR Chi-restraints excluded: chain j residue 176 SER Chi-restraints excluded: chain k residue 29 LEU Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 67 ILE Chi-restraints excluded: chain k residue 76 PHE Chi-restraints excluded: chain k residue 93 CYS Chi-restraints excluded: chain k residue 100 VAL Chi-restraints excluded: chain k residue 112 LEU Chi-restraints excluded: chain k residue 132 SER Chi-restraints excluded: chain k residue 164 THR Chi-restraints excluded: chain k residue 180 TYR Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 45 ARG Chi-restraints excluded: chain l residue 94 MET Chi-restraints excluded: chain l residue 109 LEU Chi-restraints excluded: chain l residue 114 THR Chi-restraints excluded: chain l residue 122 ILE Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 183 THR Chi-restraints excluded: chain l residue 186 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 531 random chunks: chunk 143 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 486 optimal weight: 0.4980 chunk 201 optimal weight: 50.0000 chunk 315 optimal weight: 5.9990 chunk 240 optimal weight: 6.9990 chunk 452 optimal weight: 0.6980 chunk 503 optimal weight: 0.4980 chunk 467 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 473 optimal weight: 1.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 GLN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 GLN ** a 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 47 GLN ** b 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 47 GLN f 157 ASN ** i 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.088720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.073079 restraints weight = 311240.662| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 10.29 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 43927 Z= 0.145 Angle : 0.736 16.783 59898 Z= 0.351 Chirality : 0.047 0.301 6934 Planarity : 0.005 0.168 7545 Dihedral : 11.814 109.148 7532 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.21 % Favored : 92.64 % Rotamer: Outliers : 2.89 % Allowed : 22.65 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.12), residues: 5370 helix: 1.77 (0.25), residues: 451 sheet: -0.31 (0.12), residues: 1963 loop : -1.23 (0.12), residues: 2956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG j 70 TYR 0.021 0.001 TYR F 162 PHE 0.023 0.002 PHE I 137 TRP 0.022 0.002 TRP E 127 HIS 0.007 0.001 HIS f 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (43794) covalent geometry : angle 0.71006 / 0.34 (59553) SS BOND : bond 0.00428 / 0.26 ( 54) SS BOND : angle 1.25353 / 0.75 ( 108) hydrogen bonds : bond 0.03138 / 2.13 ( 1428) hydrogen bonds : angle 6.08153 / 4.25 ( 3801) link_ALPHA1-3 : bond 0.02364 / 1.10 ( 9) link_ALPHA1-3 : angle 3.74912 / 2.44 ( 27) link_ALPHA1-6 : bond 0.00992 / 0.54 ( 7) link_ALPHA1-6 : angle 1.47061 / 0.97 ( 21) link_BETA1-4 : bond 0.00890 / 0.51 ( 42) link_BETA1-4 : angle 3.06785 / 2.09 ( 126) link_NAG-ASN : bond 0.00535 / 0.29 ( 21) link_NAG-ASN : angle 3.24028 / 2.33 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10740 Ramachandran restraints generated. 5370 Oldfield, 0 Emsley, 5370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10740 Ramachandran restraints generated. 5370 Oldfield, 0 Emsley, 5370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 4704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 296 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8432 (tm-30) REVERT: A 63 ASN cc_start: 0.7406 (OUTLIER) cc_final: 0.6619 (p0) REVERT: A 208 ARG cc_start: 0.7263 (ptt180) cc_final: 0.7001 (ptp-170) REVERT: B 56 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.9034 (tp) REVERT: C 62 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8379 (tp30) REVERT: C 104 ASP cc_start: 0.8601 (t0) cc_final: 0.8119 (t0) REVERT: C 201 ARG cc_start: 0.7929 (ptt-90) cc_final: 0.7716 (ptt-90) REVERT: C 244 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8469 (tt) REVERT: C 268 MET cc_start: 0.6048 (OUTLIER) cc_final: 0.5030 (tmm) REVERT: D 78 GLN cc_start: 0.8839 (tt0) cc_final: 0.8462 (pt0) REVERT: E 63 ASN cc_start: 0.6026 (OUTLIER) cc_final: 0.5690 (p0) REVERT: E 268 MET cc_start: 0.4251 (OUTLIER) cc_final: 0.3700 (mmm) REVERT: F 56 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8979 (tp) REVERT: G 123 MET cc_start: 0.9152 (tpp) cc_final: 0.8819 (tpp) REVERT: G 191 TYR cc_start: 0.9695 (OUTLIER) cc_final: 0.9395 (t80) REVERT: H 70 ASP cc_start: 0.9430 (m-30) cc_final: 0.9082 (p0) REVERT: H 161 GLU cc_start: 0.9299 (pm20) cc_final: 0.9089 (tp30) REVERT: I 191 TYR cc_start: 0.9806 (m-80) cc_final: 0.9528 (t80) REVERT: J 70 ASP cc_start: 0.9588 (m-30) cc_final: 0.9236 (p0) REVERT: K 163 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8268 (mm-30) REVERT: K 191 TYR cc_start: 0.9666 (m-80) cc_final: 0.9321 (m-80) REVERT: L 70 ASP cc_start: 0.9530 (m-30) cc_final: 0.9066 (p0) REVERT: a 7 TRP cc_start: 0.8564 (p-90) cc_final: 0.8018 (p-90) REVERT: a 46 GLN cc_start: 0.8010 (tp-100) cc_final: 0.7418 (tm-30) REVERT: a 145 LEU cc_start: 0.8995 (tt) cc_final: 0.8715 (tt) REVERT: b 59 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7825 (ptt90) REVERT: c 180 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.7407 (t80) REVERT: d 2 ILE cc_start: 0.7681 (mp) cc_final: 0.7377 (tp) REVERT: d 153 TRP cc_start: 0.4243 (m100) cc_final: 0.3637 (m100) REVERT: e 203 ASN cc_start: 0.8099 (t0) cc_final: 0.7785 (t0) REVERT: f 47 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.9067 (pm20) REVERT: f 94 MET cc_start: 0.8269 (mpp) cc_final: 0.7923 (mpp) REVERT: g 76 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8460 (p90) REVERT: g 106 MET cc_start: 0.6856 (tmm) cc_final: 0.6476 (tmm) REVERT: h 109 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7808 (tp) REVERT: i 7 TRP cc_start: 0.8650 (p-90) cc_final: 0.8117 (p-90) REVERT: k 65 MET cc_start: 0.6183 (ptp) cc_final: 0.5918 (ptp) REVERT: k 76 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.8372 (p90) REVERT: k 106 MET cc_start: 0.6948 (tmt) cc_final: 0.6399 (tmm) REVERT: l 59 ARG cc_start: 0.5818 (mmt180) cc_final: 0.5053 (mmt180) REVERT: l 109 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.7959 (tt) REVERT: l 215 ASN cc_start: 0.8663 (m-40) cc_final: 0.7876 (p0) outliers start: 136 outliers final: 106 residues processed: 406 average time/residue: 0.2281 time to fit residues: 158.9398 Evaluate side-chains 404 residues out of total 4704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 281 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain C residue 1 GLN Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain E residue 1 GLN Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain E residue 127 TRP Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 178 TYR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain G residue 191 TYR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain I residue 37 ASN Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 207 GLN Chi-restraints excluded: chain K residue 210 ILE Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain a residue 67 ILE Chi-restraints excluded: chain a residue 93 CYS Chi-restraints excluded: chain a residue 144 CYS Chi-restraints excluded: chain a residue 170 PHE Chi-restraints excluded: chain b residue 4 LEU Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain b residue 59 ARG Chi-restraints excluded: chain b residue 79 ASP Chi-restraints excluded: chain b residue 107 THR Chi-restraints excluded: chain b residue 115 VAL Chi-restraints excluded: chain b residue 193 LYS Chi-restraints excluded: chain c residue 34 TRP Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 90 THR Chi-restraints excluded: chain c residue 112 LEU Chi-restraints excluded: chain c residue 144 CYS Chi-restraints excluded: chain c residue 154 VAL Chi-restraints excluded: chain c residue 180 TYR Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 94 MET Chi-restraints excluded: chain d residue 97 THR Chi-restraints excluded: chain d residue 151 VAL Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain e residue 65 MET Chi-restraints excluded: chain e residue 103 GLU Chi-restraints excluded: chain e residue 144 CYS Chi-restraints excluded: chain e residue 186 VAL Chi-restraints excluded: chain e residue 199 ILE Chi-restraints excluded: chain e residue 201 ASN Chi-restraints excluded: chain f residue 26 SER Chi-restraints excluded: chain f residue 47 GLN Chi-restraints excluded: chain f residue 51 LEU Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 115 VAL Chi-restraints excluded: chain f residue 141 LEU Chi-restraints excluded: chain f residue 157 ASN Chi-restraints excluded: chain g residue 29 LEU Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain g residue 55 LEU Chi-restraints excluded: chain g residue 63 VAL Chi-restraints excluded: chain g residue 67 ILE Chi-restraints excluded: chain g residue 76 PHE Chi-restraints excluded: chain g residue 93 CYS Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain g residue 132 SER Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain g residue 164 THR Chi-restraints excluded: chain h residue 94 MET Chi-restraints excluded: chain h residue 109 LEU Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 140 LEU Chi-restraints excluded: chain h residue 183 THR Chi-restraints excluded: chain h residue 186 LEU Chi-restraints excluded: chain i residue 53 VAL Chi-restraints excluded: chain i residue 65 MET Chi-restraints excluded: chain i residue 199 ILE Chi-restraints excluded: chain i residue 201 ASN Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 114 THR Chi-restraints excluded: chain j residue 176 SER Chi-restraints excluded: chain k residue 29 LEU Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 67 ILE Chi-restraints excluded: chain k residue 76 PHE Chi-restraints excluded: chain k residue 93 CYS Chi-restraints excluded: chain k residue 100 VAL Chi-restraints excluded: chain k residue 104 LEU Chi-restraints excluded: chain k residue 112 LEU Chi-restraints excluded: chain k residue 132 SER Chi-restraints excluded: chain k residue 164 THR Chi-restraints excluded: chain k residue 180 TYR Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 45 ARG Chi-restraints excluded: chain l residue 94 MET Chi-restraints excluded: chain l residue 109 LEU Chi-restraints excluded: chain l residue 114 THR Chi-restraints excluded: chain l residue 122 ILE Chi-restraints excluded: chain l residue 183 THR Chi-restraints excluded: chain l residue 186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 531 random chunks: chunk 297 optimal weight: 0.9990 chunk 174 optimal weight: 0.7980 chunk 302 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 251 optimal weight: 6.9990 chunk 342 optimal weight: 2.9990 chunk 375 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 444 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 GLN ** a 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 HIS ** b 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 129 GLN ** d 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 47 GLN f 157 ASN ** i 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.087941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.072330 restraints weight = 313059.948| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 10.30 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 43927 Z= 0.160 Angle : 0.745 16.737 59898 Z= 0.357 Chirality : 0.047 0.303 6934 Planarity : 0.006 0.167 7545 Dihedral : 11.686 107.665 7532 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.39 % Favored : 92.48 % Rotamer: Outliers : 2.94 % Allowed : 22.58 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.12), residues: 5370 helix: 1.79 (0.25), residues: 451 sheet: -0.31 (0.12), residues: 1967 loop : -1.26 (0.12), residues: 2952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG j 70 TYR 0.020 0.002 TYR D 162 PHE 0.036 0.002 PHE l 123 TRP 0.021 0.002 TRP E 127 HIS 0.007 0.001 HIS f 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (43794) covalent geometry : angle 0.71828 / 0.35 (59553) SS BOND : bond 0.00444 / 0.28 ( 54) SS BOND : angle 1.55643 / 1.15 ( 108) hydrogen bonds : bond 0.03205 / 2.18 ( 1428) hydrogen bonds : angle 6.13296 / 4.28 ( 3801) link_ALPHA1-3 : bond 0.02282 / 1.05 ( 9) link_ALPHA1-3 : angle 3.87731 / 2.53 ( 27) link_ALPHA1-6 : bond 0.00865 / 0.48 ( 7) link_ALPHA1-6 : angle 1.37518 / 0.88 ( 21) link_BETA1-4 : bond 0.00896 / 0.52 ( 42) link_BETA1-4 : angle 3.06269 / 2.09 ( 126) link_NAG-ASN : bond 0.00513 / 0.27 ( 21) link_NAG-ASN : angle 3.21887 / 2.32 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10740 Ramachandran restraints generated. 5370 Oldfield, 0 Emsley, 5370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10740 Ramachandran restraints generated. 5370 Oldfield, 0 Emsley, 5370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 4704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 290 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8437 (tm-30) REVERT: A 63 ASN cc_start: 0.7416 (OUTLIER) cc_final: 0.6631 (p0) REVERT: B 56 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.9107 (tp) REVERT: C 62 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8414 (tp30) REVERT: C 104 ASP cc_start: 0.8642 (t0) cc_final: 0.8155 (t0) REVERT: C 201 ARG cc_start: 0.7990 (ptt-90) cc_final: 0.7745 (ptt-90) REVERT: C 244 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8462 (tt) REVERT: C 268 MET cc_start: 0.6002 (OUTLIER) cc_final: 0.5009 (tmm) REVERT: D 78 GLN cc_start: 0.8848 (tt0) cc_final: 0.8427 (pt0) REVERT: E 63 ASN cc_start: 0.6063 (OUTLIER) cc_final: 0.5719 (p0) REVERT: E 268 MET cc_start: 0.4089 (OUTLIER) cc_final: 0.3543 (mmm) REVERT: F 56 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8977 (tp) REVERT: G 123 MET cc_start: 0.9173 (tpp) cc_final: 0.8848 (tpp) REVERT: G 191 TYR cc_start: 0.9705 (OUTLIER) cc_final: 0.9417 (t80) REVERT: H 70 ASP cc_start: 0.9428 (m-30) cc_final: 0.9076 (p0) REVERT: H 161 GLU cc_start: 0.9296 (pm20) cc_final: 0.9087 (tp30) REVERT: I 191 TYR cc_start: 0.9827 (m-80) cc_final: 0.9569 (t80) REVERT: J 70 ASP cc_start: 0.9583 (m-30) cc_final: 0.9226 (p0) REVERT: K 163 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8368 (mm-30) REVERT: K 191 TYR cc_start: 0.9671 (m-80) cc_final: 0.9325 (m-80) REVERT: L 70 ASP cc_start: 0.9521 (m-30) cc_final: 0.9055 (p0) REVERT: a 7 TRP cc_start: 0.8596 (p-90) cc_final: 0.8011 (p-90) REVERT: a 46 GLN cc_start: 0.8002 (tp-100) cc_final: 0.7392 (tm-30) REVERT: b 59 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7892 (ptt90) REVERT: b 76 PHE cc_start: 0.8259 (m-10) cc_final: 0.7918 (m-10) REVERT: d 2 ILE cc_start: 0.7662 (mp) cc_final: 0.7395 (tp) REVERT: d 153 TRP cc_start: 0.4339 (m100) cc_final: 0.3780 (m100) REVERT: e 203 ASN cc_start: 0.8142 (t0) cc_final: 0.7835 (t0) REVERT: f 94 MET cc_start: 0.8307 (mpp) cc_final: 0.7868 (mpp) REVERT: g 18 LEU cc_start: 0.8284 (tt) cc_final: 0.7988 (tt) REVERT: g 76 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8500 (p90) REVERT: g 106 MET cc_start: 0.7046 (tmm) cc_final: 0.6560 (tmm) REVERT: h 109 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.7846 (tp) REVERT: i 7 TRP cc_start: 0.8719 (p-90) cc_final: 0.8140 (p-90) REVERT: k 76 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8436 (p90) REVERT: k 106 MET cc_start: 0.6892 (tmt) cc_final: 0.6336 (tmm) REVERT: l 59 ARG cc_start: 0.5908 (mmt180) cc_final: 0.5093 (mmt180) REVERT: l 109 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.7985 (tt) REVERT: l 215 ASN cc_start: 0.8671 (m-40) cc_final: 0.7904 (p0) outliers start: 138 outliers final: 111 residues processed: 402 average time/residue: 0.2196 time to fit residues: 152.3634 Evaluate side-chains 405 residues out of total 4704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 279 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain C residue 1 GLN Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain E residue 1 GLN Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain E residue 127 TRP Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 178 TYR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain G residue 191 TYR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain I residue 37 ASN Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain K residue 37 ASN Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 207 GLN Chi-restraints excluded: chain K residue 210 ILE Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain a residue 67 ILE Chi-restraints excluded: chain a residue 93 CYS Chi-restraints excluded: chain a residue 144 CYS Chi-restraints excluded: chain a residue 170 PHE Chi-restraints excluded: chain b residue 4 LEU Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain b residue 59 ARG Chi-restraints excluded: chain b residue 79 ASP Chi-restraints excluded: chain b residue 107 THR Chi-restraints excluded: chain b residue 115 VAL Chi-restraints excluded: chain b residue 193 LYS Chi-restraints excluded: chain c residue 34 TRP Chi-restraints excluded: chain c residue 51 ILE Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 90 THR Chi-restraints excluded: chain c residue 112 LEU Chi-restraints excluded: chain c residue 144 CYS Chi-restraints excluded: chain c residue 154 VAL Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 94 MET Chi-restraints excluded: chain d residue 97 THR Chi-restraints excluded: chain d residue 151 VAL Chi-restraints excluded: chain d residue 171 GLN Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain e residue 65 MET Chi-restraints excluded: chain e residue 103 GLU Chi-restraints excluded: chain e residue 144 CYS Chi-restraints excluded: chain e residue 186 VAL Chi-restraints excluded: chain e residue 199 ILE Chi-restraints excluded: chain e residue 201 ASN Chi-restraints excluded: chain f residue 26 SER Chi-restraints excluded: chain f residue 80 ILE Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 115 VAL Chi-restraints excluded: chain f residue 141 LEU Chi-restraints excluded: chain g residue 29 LEU Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain g residue 55 LEU Chi-restraints excluded: chain g residue 63 VAL Chi-restraints excluded: chain g residue 67 ILE Chi-restraints excluded: chain g residue 76 PHE Chi-restraints excluded: chain g residue 93 CYS Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain g residue 132 SER Chi-restraints excluded: chain g residue 164 THR Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 94 MET Chi-restraints excluded: chain h residue 109 LEU Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 140 LEU Chi-restraints excluded: chain h residue 183 THR Chi-restraints excluded: chain h residue 186 LEU Chi-restraints excluded: chain i residue 4 LEU Chi-restraints excluded: chain i residue 53 VAL Chi-restraints excluded: chain i residue 65 MET Chi-restraints excluded: chain i residue 199 ILE Chi-restraints excluded: chain i residue 201 ASN Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 114 THR Chi-restraints excluded: chain j residue 176 SER Chi-restraints excluded: chain k residue 29 LEU Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 67 ILE Chi-restraints excluded: chain k residue 76 PHE Chi-restraints excluded: chain k residue 93 CYS Chi-restraints excluded: chain k residue 100 VAL Chi-restraints excluded: chain k residue 104 LEU Chi-restraints excluded: chain k residue 112 LEU Chi-restraints excluded: chain k residue 132 SER Chi-restraints excluded: chain k residue 164 THR Chi-restraints excluded: chain k residue 180 TYR Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 45 ARG Chi-restraints excluded: chain l residue 94 MET Chi-restraints excluded: chain l residue 109 LEU Chi-restraints excluded: chain l residue 114 THR Chi-restraints excluded: chain l residue 122 ILE Chi-restraints excluded: chain l residue 183 THR Chi-restraints excluded: chain l residue 186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 531 random chunks: chunk 70 optimal weight: 6.9990 chunk 359 optimal weight: 3.9990 chunk 81 optimal weight: 30.0000 chunk 308 optimal weight: 5.9990 chunk 400 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 chunk 351 optimal weight: 2.9990 chunk 301 optimal weight: 0.8980 chunk 398 optimal weight: 7.9990 chunk 307 optimal weight: 0.8980 chunk 261 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 ASN ** I 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 GLN ** a 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 157 ASN ** i 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.091691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.080390 restraints weight = 406515.804| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 9.56 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 43927 Z= 0.166 Angle : 0.754 16.682 59898 Z= 0.362 Chirality : 0.047 0.307 6934 Planarity : 0.005 0.167 7545 Dihedral : 11.556 106.136 7532 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.60 % Favored : 92.27 % Rotamer: Outliers : 2.87 % Allowed : 22.69 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.12), residues: 5370 helix: 1.69 (0.25), residues: 454 sheet: -0.31 (0.12), residues: 1958 loop : -1.29 (0.12), residues: 2958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG j 70 TYR 0.028 0.002 TYR c 180 PHE 0.030 0.002 PHE l 123 TRP 0.022 0.002 TRP E 127 HIS 0.006 0.001 HIS j 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (43794) covalent geometry : angle 0.72763 / 0.36 (59553) SS BOND : bond 0.00440 / 0.27 ( 54) SS BOND : angle 1.46053 / 1.02 ( 108) hydrogen bonds : bond 0.03217 / 2.19 ( 1428) hydrogen bonds : angle 6.21216 / 4.33 ( 3801) link_ALPHA1-3 : bond 0.02301 / 1.05 ( 9) link_ALPHA1-3 : angle 3.93526 / 2.57 ( 27) link_ALPHA1-6 : bond 0.00827 / 0.46 ( 7) link_ALPHA1-6 : angle 1.34342 / 0.86 ( 21) link_BETA1-4 : bond 0.00898 / 0.52 ( 42) link_BETA1-4 : angle 3.06044 / 2.09 ( 126) link_NAG-ASN : bond 0.00500 / 0.26 ( 21) link_NAG-ASN : angle 3.21238 / 2.32 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11455.60 seconds wall clock time: 198 minutes 32.72 seconds (11912.72 seconds total)