Starting phenix.real_space_refine on Sun Aug 24 07:38:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9btj_44892/08_2025/9btj_44892.cif Found real_map, /net/cci-nas-00/data/ceres_data/9btj_44892/08_2025/9btj_44892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9btj_44892/08_2025/9btj_44892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9btj_44892/08_2025/9btj_44892.map" model { file = "/net/cci-nas-00/data/ceres_data/9btj_44892/08_2025/9btj_44892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9btj_44892/08_2025/9btj_44892.cif" } resolution = 4.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.053 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 115 5.16 5 C 11150 2.51 5 N 2876 2.21 5 O 3811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17952 Number of models: 1 Model: "" Number of chains: 47 Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 806 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "H" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1106 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3642 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 23, 'TRANS': 440} Chain breaks: 1 Chain: "B" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1013 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "A" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3630 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 23, 'TRANS': 438} Chain breaks: 1 Chain: "C" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1009 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "D" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3642 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 23, 'TRANS': 440} Chain breaks: 1 Chain: "E" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1004 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" 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: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "P" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: "U" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" 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: "e" 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: "f" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.28, per 1000 atoms: 0.24 Number of scatterers: 17952 At special positions: 0 Unit cell: (125.576, 126.649, 156.702, 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 115 16.00 O 3811 8.00 N 2876 7.00 C 11150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.04 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.04 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.05 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 201 " - pdb=" SG CYS D 433 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.04 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.04 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN P 4 " - " MAN P 5 " " MAN U 5 " - " MAN U 6 " " MAN U 8 " - " MAN U 9 " " MAN f 4 " - " MAN f 5 " ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 7 " " MAN O 4 " - " MAN O 5 " " BMA P 3 " - " MAN P 4 " " MAN P 6 " - " MAN P 7 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 8 " " MAN U 4 " - " MAN U 7 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " " BMA f 3 " - " MAN f 4 " " BMA n 3 " - " MAN n 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 4 " " MAN O 4 " - " MAN O 6 " " BMA P 3 " - " MAN P 6 " " MAN P 6 " - " MAN P 8 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 5 " " BMA d 3 " - " MAN d 5 " " BMA f 3 " - " MAN f 6 " " BMA n 3 " - " MAN n 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " 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 R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " NAG-ASN " NAG A 601 " - " ASN A 130 " " NAG A 602 " - " ASN A 230 " " NAG A 604 " - " ASN A 276 " " NAG A 606 " - " ASN A 301 " " NAG A 607 " - " ASN A 332 " " NAG A 608 " - " ASN A 386 " " NAG A 609 " - " ASN A 442 " " NAG A 610 " - " ASN A 448 " " NAG A 611 " - " ASN A 88 " " NAG A 612 " - " ASN A 133 " " NAG A 615 " - " ASN A 358 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 625 " " NAG B 703 " - " ASN B 616 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 625 " " NAG C 703 " - " ASN C 616 " " NAG D 601 " - " ASN D 130 " " NAG D 602 " - " ASN D 230 " " NAG D 604 " - " ASN D 276 " " NAG D 606 " - " ASN D 301 " " NAG D 607 " - " ASN D 332 " " NAG D 608 " - " ASN D 386 " " NAG D 610 " - " ASN D 448 " " NAG D 611 " - " ASN D 133 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 625 " " NAG E 703 " - " ASN E 616 " " NAG G 601 " - " ASN G 130 " " NAG G 602 " - " ASN G 230 " " NAG G 604 " - " ASN G 276 " " NAG G 606 " - " ASN G 301 " " NAG G 607 " - " ASN G 332 " " NAG G 608 " - " ASN G 386 " " NAG G 611 " - " ASN G 88 " " NAG G 612 " - " ASN G 133 " " NAG G 615 " - " ASN G 398 " " NAG I 1 " - " ASN G 262 " " NAG J 1 " - " ASN G 241 " " NAG K 1 " - " ASN G 358 " " NAG M 1 " - " ASN G 392 " " NAG N 1 " - " ASN G 339 " " NAG O 1 " - " ASN G 156 " " NAG P 1 " - " ASN G 160 " " NAG Q 1 " - " ASN B 637 " " NAG R 1 " - " ASN A 156 " " NAG S 1 " - " ASN A 197 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN A 241 " " NAG X 1 " - " ASN A 392 " " NAG Z 1 " - " ASN A 160 " " NAG a 1 " - " ASN C 637 " " NAG b 1 " - " ASN D 156 " " NAG d 1 " - " ASN D 262 " " NAG e 1 " - " ASN D 241 " " NAG f 1 " - " ASN D 88 " " NAG g 1 " - " ASN D 160 " " NAG j 1 " - " ASN D 398 " " NAG m 1 " - " ASN D 392 " " NAG o 1 " - " ASN E 637 " Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 463.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3736 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 32 sheets defined 20.9% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.036A pdb=" N GLU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.896A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 115 removed outlier: 4.009A pdb=" N ASP G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL G 108 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 335 through 353 removed outlier: 3.624A pdb=" N ASN G 339 " --> pdb=" O LYS G 335 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG G 340 " --> pdb=" O GLN G 336 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR G 341 " --> pdb=" O ASN G 337 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN G 344 " --> pdb=" O ARG G 340 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA G 350 " --> pdb=" O GLY G 346 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU G 351 " --> pdb=" O ARG G 347 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS G 352 " --> pdb=" O LYS G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.507A pdb=" N THR G 372 " --> pdb=" O ASP G 368 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 368 through 373' Processing helix chain 'G' and resid 402 through 406 removed outlier: 3.689A pdb=" N ALA G 405 " --> pdb=" O ASN G 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 481 removed outlier: 3.847A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 544 removed outlier: 3.922A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.969A pdb=" N ILE B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.587A pdb=" N ASN B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.530A pdb=" N TRP B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU B 632 " --> pdb=" O TRP B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.766A pdb=" N SER B 644 " --> pdb=" O HIS B 640 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 645 " --> pdb=" O THR B 641 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 655 " --> pdb=" O PHE B 651 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP B 659 " --> pdb=" O ILE B 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.047A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.666A pdb=" N GLY A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLU A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N HIS A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.650A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.647A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 536 removed outlier: 4.048A pdb=" N ASN C 535 " --> pdb=" O ALA C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 542 removed outlier: 4.312A pdb=" N ALA C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG C 542 " --> pdb=" O THR C 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 537 through 542' Processing helix chain 'C' and resid 570 through 596 Processing helix chain 'C' and resid 618 through 624 removed outlier: 3.560A pdb=" N ASN C 624 " --> pdb=" O GLU C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.528A pdb=" N TRP C 631 " --> pdb=" O THR C 627 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG C 633 " --> pdb=" O MET C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 662 removed outlier: 3.807A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU C 648 " --> pdb=" O SER C 644 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE C 655 " --> pdb=" O PHE C 651 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU C 657 " --> pdb=" O GLN C 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 117 removed outlier: 3.899A pdb=" N ASP D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 335 through 353 removed outlier: 3.515A pdb=" N GLN D 343 " --> pdb=" O ASN D 339 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN D 344 " --> pdb=" O ARG D 340 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU D 351 " --> pdb=" O ARG D 347 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N HIS D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.895A pdb=" N THR D 373 " --> pdb=" O LEU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 481 removed outlier: 3.779A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 536 removed outlier: 3.843A pdb=" N ASN E 535 " --> pdb=" O ALA E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 544 removed outlier: 3.782A pdb=" N ALA E 541 " --> pdb=" O LEU E 537 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 596 removed outlier: 3.596A pdb=" N LYS E 574 " --> pdb=" O VAL E 570 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU E 592 " --> pdb=" O GLU E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 624 removed outlier: 3.513A pdb=" N ASN E 624 " --> pdb=" O GLU E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 removed outlier: 3.653A pdb=" N GLU E 632 " --> pdb=" O TRP E 628 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG E 633 " --> pdb=" O MET E 629 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 662 removed outlier: 3.585A pdb=" N GLU E 654 " --> pdb=" O GLN E 650 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN E 656 " --> pdb=" O GLN E 652 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU E 657 " --> pdb=" O GLN E 653 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 3 through 5 removed outlier: 3.849A pdb=" N CYS L 23 " --> pdb=" O ARG L 71 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 45 through 49 removed outlier: 7.027A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN L 89 " --> pdb=" O ALA L 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.979A pdb=" N PHE H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 46 through 51 removed outlier: 3.831A pdb=" N LEU H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ASN H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TRP H 35 " --> pdb=" O ASN H 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 100I through 100K removed outlier: 3.577A pdb=" N GLU G 172 " --> pdb=" O PHE G 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 83 through 84 removed outlier: 3.917A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL G 44 " --> pdb=" O LYS G 492 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU G 494 " --> pdb=" O VAL G 42 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL G 42 " --> pdb=" O LEU G 494 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N ILE G 496 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 9.770A pdb=" N TYR G 40 " --> pdb=" O ILE G 496 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N VAL G 38 " --> pdb=" O PRO G 498 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS B 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 75 through 76 removed outlier: 3.891A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE G 53 " --> pdb=" O CYS G 218 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.636A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE G 93 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.395A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS G 296 " --> pdb=" O CYS G 445 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLY G 451 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 10.900A pdb=" N GLU G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.912A pdb=" N LEU G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 12.504A pdb=" N LEU G 288 " --> pdb=" O LEU G 453 " (cutoff:3.500A) removed outlier: 10.859A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 10.954A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N GLY G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N SER G 334 " --> pdb=" O GLY G 293 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL G 295 " --> pdb=" O ASN G 332 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN G 332 " --> pdb=" O VAL G 295 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR G 297 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.535A pdb=" N ILE G 271 " --> pdb=" O HIS G 287 " (cutoff:3.500A) removed outlier: 10.954A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 10.859A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 12.504A pdb=" N LEU G 288 " --> pdb=" O LEU G 453 " (cutoff:3.500A) removed outlier: 11.912A pdb=" N LEU G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 10.900A pdb=" N GLU G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLY G 451 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS G 296 " --> pdb=" O CYS G 445 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE G 359 " --> pdb=" O TYR G 395 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.752A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 494 through 499 removed outlier: 3.557A pdb=" N ALA A 497 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 37 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL A 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS C 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.925A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.531A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 129 through 132 removed outlier: 3.817A pdb=" N ASN A 156 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 172 " --> pdb=" O PHE A 159 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AB9, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.321A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.073A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.460A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ASN A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.987A pdb=" N VAL A 292 " --> pdb=" O ASN A 446 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 9.444A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 283 through 298 current: chain 'A' and resid 359 through 361 removed outlier: 3.508A pdb=" N ILE A 359 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.106A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.444A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.987A pdb=" N VAL A 292 " --> pdb=" O ASN A 446 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ASN A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.460A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.073A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 413 through 415 Processing sheet with id=AC2, first strand: chain 'A' and resid 302 through 312 removed outlier: 6.364A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.574A pdb=" N TYR A 384 " --> pdb=" O ARG A 419 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG A 419 " --> pdb=" O TYR A 384 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AC5, first strand: chain 'D' and resid 494 through 499 removed outlier: 3.556A pdb=" N ALA D 497 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL E 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N VAL D 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N THR E 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N TYR D 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N CYS E 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.818A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET D 84 " --> pdb=" O THR D 244 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'D' and resid 91 through 94 removed outlier: 3.506A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE D 93 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY D 237 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 130 through 133 Processing sheet with id=AD1, first strand: chain 'D' and resid 181 through 182 removed outlier: 3.592A pdb=" N ARG D 192 " --> pdb=" O VAL D 182 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 259 through 261 Processing sheet with id=AD3, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.206A pdb=" N ASN D 358 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N PHE D 468 " --> pdb=" O ASN D 358 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D 359 " --> pdb=" O TYR D 395 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY D 393 " --> pdb=" O PHE D 361 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 377 through 378 removed outlier: 4.402A pdb=" N HIS D 330 " --> pdb=" O THR D 297 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR D 297 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN D 332 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL D 295 " --> pdb=" O ASN D 332 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS D 296 " --> pdb=" O CYS D 445 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE D 443 " --> pdb=" O ARG D 298 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 302 through 308 removed outlier: 6.448A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS D 305 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA D 319 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE D 307 " --> pdb=" O PHE D 317 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.05 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5353 1.35 - 1.47: 4932 1.47 - 1.59: 7860 1.59 - 1.72: 2 1.72 - 1.84: 150 Bond restraints: 18297 Sorted by residual: bond pdb=" C LYS A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 1.339 1.386 -0.047 3.40e-02 8.65e+02 1.93e+00 bond pdb=" C ARG H 13 " pdb=" N PRO H 14 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.64e+00 bond pdb=" N PRO D 212 " pdb=" CA PRO D 212 " ideal model delta sigma weight residual 1.469 1.483 -0.014 1.28e-02 6.10e+03 1.23e+00 bond pdb=" C1 MAN N 4 " pdb=" O5 MAN N 4 " ideal model delta sigma weight residual 1.399 1.421 -0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" CA VAL G 430 " pdb=" CB VAL G 430 " ideal model delta sigma weight residual 1.527 1.541 -0.014 1.31e-02 5.83e+03 1.16e+00 ... (remaining 18292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 24483 2.43 - 4.85: 332 4.85 - 7.28: 34 7.28 - 9.70: 1 9.70 - 12.13: 6 Bond angle restraints: 24856 Sorted by residual: angle pdb=" C TYR H 33 " pdb=" CA TYR H 33 " pdb=" CB TYR H 33 " ideal model delta sigma weight residual 116.63 110.04 6.59 1.16e+00 7.43e-01 3.23e+01 angle pdb=" C CYS A 218 " pdb=" N ALA A 219 " pdb=" CA ALA A 219 " ideal model delta sigma weight residual 120.97 133.10 -12.13 2.84e+00 1.24e-01 1.82e+01 angle pdb=" N TYR H 33 " pdb=" CA TYR H 33 " pdb=" C TYR H 33 " ideal model delta sigma weight residual 108.08 114.56 -6.48 1.69e+00 3.50e-01 1.47e+01 angle pdb=" CA TYR H 33 " pdb=" C TYR H 33 " pdb=" N TYR H 34 " ideal model delta sigma weight residual 119.63 116.59 3.04 8.10e-01 1.52e+00 1.41e+01 angle pdb=" C2 NAG U 1 " pdb=" N2 NAG U 1 " pdb=" C7 NAG U 1 " ideal model delta sigma weight residual 124.56 135.48 -10.92 3.00e+00 1.11e-01 1.33e+01 ... (remaining 24851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 11759 17.93 - 35.86: 950 35.86 - 53.79: 187 53.79 - 71.72: 70 71.72 - 89.66: 18 Dihedral angle restraints: 12984 sinusoidal: 7187 harmonic: 5797 Sorted by residual: dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -152.58 66.58 1 1.00e+01 1.00e-02 5.78e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -150.69 64.69 1 1.00e+01 1.00e-02 5.50e+01 dihedral pdb=" CB CYS D 119 " pdb=" SG CYS D 119 " pdb=" SG CYS D 205 " pdb=" CB CYS D 205 " ideal model delta sinusoidal sigma weight residual -86.00 -143.10 57.10 1 1.00e+01 1.00e-02 4.38e+01 ... (remaining 12981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2884 0.077 - 0.155: 305 0.155 - 0.232: 23 0.232 - 0.310: 5 0.310 - 0.387: 4 Chirality restraints: 3221 Sorted by residual: chirality pdb=" C1 NAG j 1 " pdb=" ND2 ASN D 398 " pdb=" C2 NAG j 1 " pdb=" O5 NAG j 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" C1 NAG E 703 " pdb=" ND2 ASN E 616 " pdb=" C2 NAG E 703 " pdb=" O5 NAG E 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" C1 NAG C 703 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C 703 " pdb=" O5 NAG C 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 3218 not shown) Planarity restraints: 3011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO G 437 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO G 438 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO G 438 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 438 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 182 " 0.038 5.00e-02 4.00e+02 5.86e-02 5.50e+00 pdb=" N PRO D 183 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 183 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 183 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 427 " 0.012 2.00e-02 2.50e+03 1.43e-02 5.12e+00 pdb=" CG TRP G 427 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP G 427 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP G 427 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP G 427 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP G 427 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP G 427 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 427 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 427 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP G 427 " -0.001 2.00e-02 2.50e+03 ... (remaining 3008 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 376 2.68 - 3.24: 16635 3.24 - 3.79: 26072 3.79 - 4.35: 33429 4.35 - 4.90: 54359 Nonbonded interactions: 130871 Sorted by model distance: nonbonded pdb=" OD1 ASP H 100E" pdb=" N TYS H 100F" model vdw 2.131 3.120 nonbonded pdb=" OG1 THR G 297 " pdb=" O ILE G 443 " model vdw 2.140 3.040 nonbonded pdb=" O ARG A 347 " pdb=" NH1 ARG A 347 " model vdw 2.244 3.120 nonbonded pdb=" OG1 THR H 68 " pdb=" OG SER H 81 " model vdw 2.261 3.040 nonbonded pdb=" O VAL G 36 " pdb=" OG1 THR B 606 " model vdw 2.272 3.040 ... (remaining 130866 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 33 through 611) selection = (chain 'D' and (resid 33 through 137 or resid 147 through 611)) selection = (chain 'G' and (resid 33 through 137 or resid 147 through 611)) } ncs_group { reference = (chain 'B' and resid 518 through 703) selection = (chain 'C' and resid 518 through 703) selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'M' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'o' } ncs_group { reference = chain 'I' selection = chain 'N' selection = chain 'T' selection = chain 'd' selection = chain 'n' } ncs_group { reference = chain 'J' selection = chain 'X' selection = chain 'm' } ncs_group { reference = (chain 'O' and resid 5 through 7) selection = (chain 'P' and resid 6 through 8) selection = (chain 'f' and resid 4 through 6) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.050 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18470 Z= 0.132 Angle : 0.754 14.630 25337 Z= 0.343 Chirality : 0.048 0.387 3221 Planarity : 0.004 0.065 2951 Dihedral : 13.238 89.656 9134 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.76 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.18), residues: 1976 helix: -1.03 (0.26), residues: 342 sheet: 0.12 (0.27), residues: 400 loop : -1.36 (0.16), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 327 TYR 0.014 0.001 TYR G 217 PHE 0.019 0.001 PHE A 391 TRP 0.038 0.001 TRP G 427 HIS 0.007 0.001 HIS G 216 Details of bonding type rmsd covalent geometry : bond 0.00262 (18297) covalent geometry : angle 0.67024 (24856) SS BOND : bond 0.00421 ( 38) SS BOND : angle 1.10129 ( 76) hydrogen bonds : bond 0.29531 ( 434) hydrogen bonds : angle 9.57706 ( 1221) link_ALPHA1-2 : bond 0.00789 ( 4) link_ALPHA1-2 : angle 1.67044 ( 12) link_ALPHA1-3 : bond 0.01253 ( 13) link_ALPHA1-3 : angle 1.52323 ( 39) link_ALPHA1-6 : bond 0.00688 ( 12) link_ALPHA1-6 : angle 1.67378 ( 36) link_BETA1-4 : bond 0.00875 ( 46) link_BETA1-4 : angle 2.01516 ( 138) link_NAG-ASN : bond 0.00804 ( 60) link_NAG-ASN : angle 3.63528 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.656 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: L 77 ASN cc_start: 0.8906 (t0) cc_final: 0.8492 (t0) REVERT: H 100 ASP cc_start: 0.8695 (t0) cc_final: 0.8444 (m-30) REVERT: G 84 MET cc_start: 0.8843 (tpt) cc_final: 0.8085 (ttm) REVERT: G 100 MET cc_start: 0.9302 (mtp) cc_final: 0.8990 (mtt) REVERT: B 587 LEU cc_start: 0.9764 (mt) cc_final: 0.9112 (mm) REVERT: B 632 GLU cc_start: 0.9445 (tp30) cc_final: 0.9242 (tm-30) REVERT: A 95 MET cc_start: 0.8487 (ptt) cc_final: 0.7921 (ppp) REVERT: C 588 GLU cc_start: 0.9179 (tt0) cc_final: 0.8859 (pt0) REVERT: C 626 MET cc_start: 0.7159 (ppp) cc_final: 0.6225 (tmm) REVERT: C 632 GLU cc_start: 0.9653 (tp30) cc_final: 0.9426 (tm-30) REVERT: D 100 MET cc_start: 0.9591 (tpp) cc_final: 0.9197 (mtt) REVERT: D 104 MET cc_start: 0.9690 (ttm) cc_final: 0.9266 (ttt) REVERT: D 176 PHE cc_start: 0.9451 (m-80) cc_final: 0.8959 (m-10) REVERT: D 195 ASN cc_start: 0.9405 (m-40) cc_final: 0.9061 (t0) REVERT: D 207 LYS cc_start: 0.9351 (mppt) cc_final: 0.8886 (tttm) REVERT: D 302 MET cc_start: 0.8607 (mmm) cc_final: 0.8406 (mmm) REVERT: E 518 VAL cc_start: 0.4940 (p) cc_final: 0.3176 (p) REVERT: E 584 GLU cc_start: 0.8907 (tt0) cc_final: 0.8694 (tm-30) REVERT: E 585 ARG cc_start: 0.9215 (mmp-170) cc_final: 0.8965 (tpp-160) REVERT: E 632 GLU cc_start: 0.9478 (tp30) cc_final: 0.9086 (pp20) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1360 time to fit residues: 42.1423 Evaluate side-chains 99 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 37 GLN ** G 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS B 575 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN C 543 GLN C 619 GLN D 94 ASN D 186 ASN ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN D 396 HIS D 442 ASN E 619 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.041306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.032498 restraints weight = 160811.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.033368 restraints weight = 95880.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.033968 restraints weight = 69564.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.034372 restraints weight = 56224.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.034634 restraints weight = 48876.148| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 18470 Z= 0.248 Angle : 0.825 12.260 25337 Z= 0.380 Chirality : 0.047 0.350 3221 Planarity : 0.004 0.056 2951 Dihedral : 9.240 77.237 5403 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.86 % Favored : 94.99 % Rotamer: Outliers : 0.11 % Allowed : 4.93 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.18), residues: 1976 helix: 0.07 (0.27), residues: 375 sheet: -0.09 (0.24), residues: 448 loop : -1.27 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 105 TYR 0.016 0.002 TYR L 72 PHE 0.020 0.002 PHE E 522 TRP 0.015 0.002 TRP C 631 HIS 0.011 0.001 HIS G 216 Details of bonding type rmsd covalent geometry : bond 0.00524 (18297) covalent geometry : angle 0.75525 (24856) SS BOND : bond 0.00388 ( 38) SS BOND : angle 1.09762 ( 76) hydrogen bonds : bond 0.06057 ( 434) hydrogen bonds : angle 6.53923 ( 1221) link_ALPHA1-2 : bond 0.00737 ( 4) link_ALPHA1-2 : angle 1.55188 ( 12) link_ALPHA1-3 : bond 0.01143 ( 13) link_ALPHA1-3 : angle 1.79888 ( 39) link_ALPHA1-6 : bond 0.00547 ( 12) link_ALPHA1-6 : angle 1.84182 ( 36) link_BETA1-4 : bond 0.00846 ( 46) link_BETA1-4 : angle 2.00673 ( 138) link_NAG-ASN : bond 0.00677 ( 60) link_NAG-ASN : angle 3.44725 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.575 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: L 77 ASN cc_start: 0.9237 (t0) cc_final: 0.8827 (t0) REVERT: H 20 LEU cc_start: 0.9107 (tp) cc_final: 0.8892 (tp) REVERT: G 100 MET cc_start: 0.9439 (mtp) cc_final: 0.9172 (mtm) REVERT: B 632 GLU cc_start: 0.9509 (tp30) cc_final: 0.9158 (tm-30) REVERT: A 95 MET cc_start: 0.8823 (ptt) cc_final: 0.8070 (ppp) REVERT: C 588 GLU cc_start: 0.9269 (tt0) cc_final: 0.8927 (pt0) REVERT: C 626 MET cc_start: 0.7263 (ppp) cc_final: 0.6866 (tmm) REVERT: D 104 MET cc_start: 0.9732 (ttm) cc_final: 0.9316 (ttt) REVERT: D 195 ASN cc_start: 0.9426 (m-40) cc_final: 0.9040 (t0) REVERT: D 302 MET cc_start: 0.8585 (mmm) cc_final: 0.8191 (mmm) REVERT: E 530 MET cc_start: 0.4349 (tpt) cc_final: 0.4094 (tpt) REVERT: E 584 GLU cc_start: 0.9095 (tt0) cc_final: 0.8852 (tm-30) REVERT: E 585 ARG cc_start: 0.9393 (mmp-170) cc_final: 0.8521 (tpp80) REVERT: E 648 GLU cc_start: 0.9195 (tm-30) cc_final: 0.8908 (tm-30) outliers start: 2 outliers final: 2 residues processed: 129 average time/residue: 0.1397 time to fit residues: 27.1303 Evaluate side-chains 92 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 74 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 174 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 144 optimal weight: 20.0000 chunk 193 optimal weight: 0.8980 chunk 163 optimal weight: 9.9990 chunk 195 optimal weight: 5.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 36 HIS G 105 HIS ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 ASN G 478 ASN ** B 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN A 94 ASN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS C 652 GLN ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** 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 = 0.3084 r_free = 0.3084 target = 0.039452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.030951 restraints weight = 164642.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.031805 restraints weight = 99017.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.032400 restraints weight = 71403.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.032670 restraints weight = 57735.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.033004 restraints weight = 51242.930| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18470 Z= 0.238 Angle : 0.813 12.333 25337 Z= 0.372 Chirality : 0.048 0.312 3221 Planarity : 0.004 0.058 2951 Dihedral : 9.327 73.301 5403 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.62 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.19), residues: 1976 helix: 0.35 (0.27), residues: 379 sheet: -0.27 (0.23), residues: 478 loop : -1.24 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 40 TYR 0.020 0.002 TYR G 401 PHE 0.024 0.002 PHE C 522 TRP 0.026 0.002 TRP C 571 HIS 0.007 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00511 (18297) covalent geometry : angle 0.74119 (24856) SS BOND : bond 0.00443 ( 38) SS BOND : angle 1.26372 ( 76) hydrogen bonds : bond 0.05261 ( 434) hydrogen bonds : angle 5.87231 ( 1221) link_ALPHA1-2 : bond 0.00586 ( 4) link_ALPHA1-2 : angle 1.54034 ( 12) link_ALPHA1-3 : bond 0.00928 ( 13) link_ALPHA1-3 : angle 1.64527 ( 39) link_ALPHA1-6 : bond 0.00544 ( 12) link_ALPHA1-6 : angle 1.88574 ( 36) link_BETA1-4 : bond 0.00705 ( 46) link_BETA1-4 : angle 1.94069 ( 138) link_NAG-ASN : bond 0.00651 ( 60) link_NAG-ASN : angle 3.48108 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.685 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: L 77 ASN cc_start: 0.9194 (t0) cc_final: 0.8816 (t0) REVERT: H 5 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8666 (tm-30) REVERT: H 20 LEU cc_start: 0.9135 (tp) cc_final: 0.8879 (tp) REVERT: G 100 MET cc_start: 0.9488 (mtp) cc_final: 0.9213 (mtt) REVERT: B 530 MET cc_start: 0.8003 (mmp) cc_final: 0.7638 (mmm) REVERT: B 632 GLU cc_start: 0.9532 (tp30) cc_final: 0.9184 (tm-30) REVERT: A 95 MET cc_start: 0.8950 (ptt) cc_final: 0.8091 (ppp) REVERT: C 584 GLU cc_start: 0.9326 (pt0) cc_final: 0.9085 (pp20) REVERT: C 588 GLU cc_start: 0.9342 (tt0) cc_final: 0.8899 (pt0) REVERT: C 626 MET cc_start: 0.7589 (ppp) cc_final: 0.7160 (ppp) REVERT: C 659 ASP cc_start: 0.8920 (m-30) cc_final: 0.8642 (m-30) REVERT: D 100 MET cc_start: 0.9497 (mtt) cc_final: 0.9193 (mtt) REVERT: D 194 ILE cc_start: 0.9726 (tt) cc_final: 0.9510 (pt) REVERT: D 195 ASN cc_start: 0.9373 (m-40) cc_final: 0.8876 (t0) REVERT: D 302 MET cc_start: 0.8685 (mmm) cc_final: 0.8395 (mmm) REVERT: D 370 GLU cc_start: 0.9225 (mp0) cc_final: 0.9014 (mm-30) REVERT: E 585 ARG cc_start: 0.9373 (mmp-170) cc_final: 0.8516 (tpp80) REVERT: E 632 GLU cc_start: 0.9591 (tp30) cc_final: 0.9300 (pp20) REVERT: E 648 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8921 (tm-30) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1575 time to fit residues: 26.7190 Evaluate side-chains 90 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 50 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 185 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 163 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 54BHIS G 417 GLN B 543 GLN B 575 GLN ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN E 624 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.039861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.031273 restraints weight = 163578.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.032165 restraints weight = 95937.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.032775 restraints weight = 68422.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.033164 restraints weight = 54923.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.033428 restraints weight = 47569.461| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18470 Z= 0.154 Angle : 0.722 12.331 25337 Z= 0.326 Chirality : 0.046 0.336 3221 Planarity : 0.004 0.057 2951 Dihedral : 9.010 70.502 5403 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.21 % Favored : 94.64 % Rotamer: Outliers : 0.11 % Allowed : 2.61 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.19), residues: 1976 helix: 0.47 (0.27), residues: 379 sheet: -0.26 (0.24), residues: 473 loop : -1.17 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 49 TYR 0.015 0.001 TYR G 401 PHE 0.017 0.001 PHE C 522 TRP 0.016 0.001 TRP C 571 HIS 0.012 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00331 (18297) covalent geometry : angle 0.64690 (24856) SS BOND : bond 0.00396 ( 38) SS BOND : angle 1.13476 ( 76) hydrogen bonds : bond 0.04308 ( 434) hydrogen bonds : angle 5.52880 ( 1221) link_ALPHA1-2 : bond 0.00535 ( 4) link_ALPHA1-2 : angle 1.54066 ( 12) link_ALPHA1-3 : bond 0.01008 ( 13) link_ALPHA1-3 : angle 1.57806 ( 39) link_ALPHA1-6 : bond 0.00583 ( 12) link_ALPHA1-6 : angle 1.78756 ( 36) link_BETA1-4 : bond 0.00726 ( 46) link_BETA1-4 : angle 1.87801 ( 138) link_NAG-ASN : bond 0.00629 ( 60) link_NAG-ASN : angle 3.32413 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 115 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1 GLN cc_start: 0.8585 (pm20) cc_final: 0.8342 (pm20) REVERT: L 48 MET cc_start: 0.8511 (tmm) cc_final: 0.8307 (tmm) REVERT: L 77 ASN cc_start: 0.9241 (t0) cc_final: 0.8901 (t0) REVERT: L 91 TRP cc_start: 0.8610 (m-10) cc_final: 0.8385 (m-10) REVERT: H 20 LEU cc_start: 0.9136 (tp) cc_final: 0.8878 (tp) REVERT: H 29 ILE cc_start: 0.8976 (tt) cc_final: 0.8736 (pt) REVERT: G 100 MET cc_start: 0.9512 (mtp) cc_final: 0.9215 (mtt) REVERT: G 434 MET cc_start: 0.6978 (mtt) cc_final: 0.6714 (mtt) REVERT: B 530 MET cc_start: 0.8101 (mmp) cc_final: 0.7831 (mmm) REVERT: B 632 GLU cc_start: 0.9488 (tp30) cc_final: 0.9107 (tm-30) REVERT: A 95 MET cc_start: 0.8959 (ptt) cc_final: 0.8038 (ppp) REVERT: C 584 GLU cc_start: 0.9351 (pt0) cc_final: 0.9108 (pp20) REVERT: C 587 LEU cc_start: 0.9749 (mm) cc_final: 0.9452 (tt) REVERT: C 588 GLU cc_start: 0.9386 (tt0) cc_final: 0.9031 (pt0) REVERT: C 626 MET cc_start: 0.7718 (ppp) cc_final: 0.7226 (ppp) REVERT: C 659 ASP cc_start: 0.8934 (m-30) cc_final: 0.8707 (m-30) REVERT: D 100 MET cc_start: 0.9483 (mtt) cc_final: 0.9180 (mtt) REVERT: D 194 ILE cc_start: 0.9711 (tt) cc_final: 0.9485 (pt) REVERT: D 195 ASN cc_start: 0.9348 (m-40) cc_final: 0.8892 (t0) REVERT: D 370 GLU cc_start: 0.9253 (mp0) cc_final: 0.8957 (mm-30) REVERT: E 545 LEU cc_start: 0.8238 (tp) cc_final: 0.7404 (tp) REVERT: E 584 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8511 (tm-30) REVERT: E 585 ARG cc_start: 0.8990 (mmp-170) cc_final: 0.8615 (tpp80) REVERT: E 632 GLU cc_start: 0.9600 (tp30) cc_final: 0.9238 (pp20) REVERT: E 648 GLU cc_start: 0.9233 (tm-30) cc_final: 0.8979 (tm-30) outliers start: 2 outliers final: 0 residues processed: 117 average time/residue: 0.1632 time to fit residues: 28.0661 Evaluate side-chains 89 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 41 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 163 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 96 HIS ** G 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 396 HIS G 478 ASN B 543 GLN B 575 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN E 652 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.038144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.029835 restraints weight = 168947.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.030701 restraints weight = 99111.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.031290 restraints weight = 70700.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.031678 restraints weight = 56775.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.031926 restraints weight = 49209.205| |-----------------------------------------------------------------------------| r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 18470 Z= 0.278 Angle : 0.850 11.630 25337 Z= 0.388 Chirality : 0.047 0.320 3221 Planarity : 0.004 0.062 2951 Dihedral : 9.337 70.227 5403 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.43 % Favored : 93.42 % Rotamer: Outliers : 0.06 % Allowed : 4.36 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.19), residues: 1976 helix: 0.31 (0.27), residues: 391 sheet: -0.42 (0.25), residues: 432 loop : -1.33 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 71 TYR 0.035 0.002 TYR C 643 PHE 0.037 0.002 PHE C 522 TRP 0.021 0.002 TRP C 571 HIS 0.011 0.002 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00593 (18297) covalent geometry : angle 0.77745 (24856) SS BOND : bond 0.00772 ( 38) SS BOND : angle 1.30318 ( 76) hydrogen bonds : bond 0.04738 ( 434) hydrogen bonds : angle 5.63548 ( 1221) link_ALPHA1-2 : bond 0.00554 ( 4) link_ALPHA1-2 : angle 1.51221 ( 12) link_ALPHA1-3 : bond 0.00871 ( 13) link_ALPHA1-3 : angle 1.72226 ( 39) link_ALPHA1-6 : bond 0.00531 ( 12) link_ALPHA1-6 : angle 1.90905 ( 36) link_BETA1-4 : bond 0.00727 ( 46) link_BETA1-4 : angle 2.06489 ( 138) link_NAG-ASN : bond 0.00677 ( 60) link_NAG-ASN : angle 3.55040 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 MET cc_start: 0.8432 (tmm) cc_final: 0.8163 (tmm) REVERT: L 51 GLU cc_start: 0.8902 (tp30) cc_final: 0.8534 (tp30) REVERT: L 77 ASN cc_start: 0.9371 (t0) cc_final: 0.9096 (t0) REVERT: H 20 LEU cc_start: 0.9162 (tp) cc_final: 0.8913 (tp) REVERT: G 100 MET cc_start: 0.9500 (mtp) cc_final: 0.9203 (mtt) REVERT: G 210 PHE cc_start: 0.9366 (p90) cc_final: 0.9162 (p90) REVERT: G 302 MET cc_start: 0.9145 (mmp) cc_final: 0.8917 (mmm) REVERT: B 632 GLU cc_start: 0.9563 (tp30) cc_final: 0.9149 (tm-30) REVERT: A 95 MET cc_start: 0.9103 (ptt) cc_final: 0.8157 (ppp) REVERT: C 584 GLU cc_start: 0.9355 (pt0) cc_final: 0.9144 (pp20) REVERT: C 588 GLU cc_start: 0.9386 (tt0) cc_final: 0.8926 (pt0) REVERT: C 626 MET cc_start: 0.7740 (ppp) cc_final: 0.7264 (ppp) REVERT: D 100 MET cc_start: 0.9504 (mtt) cc_final: 0.9192 (mtt) REVERT: D 195 ASN cc_start: 0.9322 (m-40) cc_final: 0.8621 (t0) REVERT: D 370 GLU cc_start: 0.9278 (mp0) cc_final: 0.8952 (mm-30) REVERT: D 434 MET cc_start: 0.8227 (mpp) cc_final: 0.7850 (mpp) REVERT: E 632 GLU cc_start: 0.9661 (tp30) cc_final: 0.9326 (pp20) outliers start: 1 outliers final: 0 residues processed: 96 average time/residue: 0.1678 time to fit residues: 24.1492 Evaluate side-chains 80 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 51 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN G 478 ASN B 535 ASN ** B 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.038134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.029813 restraints weight = 167122.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.030691 restraints weight = 97996.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.031279 restraints weight = 69776.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.031674 restraints weight = 56105.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.031927 restraints weight = 48591.332| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18470 Z= 0.225 Angle : 0.797 11.347 25337 Z= 0.364 Chirality : 0.047 0.331 3221 Planarity : 0.004 0.060 2951 Dihedral : 9.219 66.260 5403 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.48 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.19), residues: 1976 helix: 0.33 (0.27), residues: 381 sheet: -0.41 (0.25), residues: 440 loop : -1.39 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 327 TYR 0.019 0.002 TYR G 401 PHE 0.027 0.002 PHE C 522 TRP 0.016 0.002 TRP A 479 HIS 0.008 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00480 (18297) covalent geometry : angle 0.72283 (24856) SS BOND : bond 0.00802 ( 38) SS BOND : angle 1.36430 ( 76) hydrogen bonds : bond 0.04412 ( 434) hydrogen bonds : angle 5.51349 ( 1221) link_ALPHA1-2 : bond 0.00534 ( 4) link_ALPHA1-2 : angle 1.49425 ( 12) link_ALPHA1-3 : bond 0.00902 ( 13) link_ALPHA1-3 : angle 1.64225 ( 39) link_ALPHA1-6 : bond 0.00519 ( 12) link_ALPHA1-6 : angle 1.80110 ( 36) link_BETA1-4 : bond 0.00686 ( 46) link_BETA1-4 : angle 1.97540 ( 138) link_NAG-ASN : bond 0.00699 ( 60) link_NAG-ASN : angle 3.48295 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 MET cc_start: 0.8513 (tmm) cc_final: 0.8134 (tmm) REVERT: L 51 GLU cc_start: 0.9067 (tp30) cc_final: 0.8648 (tp30) REVERT: L 77 ASN cc_start: 0.9344 (t0) cc_final: 0.9069 (t0) REVERT: H 20 LEU cc_start: 0.9132 (tp) cc_final: 0.8838 (tp) REVERT: G 434 MET cc_start: 0.7467 (mtt) cc_final: 0.6410 (mpp) REVERT: B 530 MET cc_start: 0.8196 (mmp) cc_final: 0.7809 (mmm) REVERT: B 632 GLU cc_start: 0.9475 (tp30) cc_final: 0.9062 (tm-30) REVERT: A 95 MET cc_start: 0.9018 (ptt) cc_final: 0.8081 (ppp) REVERT: A 104 MET cc_start: 0.9292 (ppp) cc_final: 0.9068 (ppp) REVERT: C 587 LEU cc_start: 0.9768 (mm) cc_final: 0.9467 (tt) REVERT: C 588 GLU cc_start: 0.9370 (tt0) cc_final: 0.9027 (pt0) REVERT: C 626 MET cc_start: 0.7885 (ppp) cc_final: 0.7416 (ppp) REVERT: D 100 MET cc_start: 0.9499 (mtt) cc_final: 0.9160 (mtt) REVERT: D 195 ASN cc_start: 0.9248 (m-40) cc_final: 0.8591 (t0) REVERT: D 370 GLU cc_start: 0.9311 (mp0) cc_final: 0.9008 (mm-30) REVERT: D 434 MET cc_start: 0.8355 (mpp) cc_final: 0.7878 (mpp) REVERT: D 475 MET cc_start: 0.8743 (tpp) cc_final: 0.8515 (tpp) REVERT: E 545 LEU cc_start: 0.8126 (tp) cc_final: 0.7324 (tp) REVERT: E 584 GLU cc_start: 0.9337 (mt-10) cc_final: 0.9104 (mt-10) REVERT: E 632 GLU cc_start: 0.9648 (tp30) cc_final: 0.9294 (pp20) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1581 time to fit residues: 24.0157 Evaluate side-chains 82 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 56 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 193 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN H 3 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 ASN B 543 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.038151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.029784 restraints weight = 168388.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.030693 restraints weight = 96509.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.031315 restraints weight = 67783.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.031703 restraints weight = 53908.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.031988 restraints weight = 46521.133| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18470 Z= 0.189 Angle : 0.766 11.137 25337 Z= 0.349 Chirality : 0.046 0.332 3221 Planarity : 0.004 0.064 2951 Dihedral : 8.899 58.991 5403 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.33 % Favored : 93.52 % Rotamer: Outliers : 0.11 % Allowed : 1.59 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.19), residues: 1976 helix: 0.50 (0.28), residues: 375 sheet: -0.49 (0.24), residues: 446 loop : -1.33 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 40 TYR 0.020 0.002 TYR C 643 PHE 0.024 0.002 PHE C 522 TRP 0.012 0.001 TRP A 479 HIS 0.008 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00410 (18297) covalent geometry : angle 0.69367 (24856) SS BOND : bond 0.00410 ( 38) SS BOND : angle 1.32320 ( 76) hydrogen bonds : bond 0.04079 ( 434) hydrogen bonds : angle 5.35099 ( 1221) link_ALPHA1-2 : bond 0.00537 ( 4) link_ALPHA1-2 : angle 1.49078 ( 12) link_ALPHA1-3 : bond 0.00910 ( 13) link_ALPHA1-3 : angle 1.59246 ( 39) link_ALPHA1-6 : bond 0.00519 ( 12) link_ALPHA1-6 : angle 1.76602 ( 36) link_BETA1-4 : bond 0.00716 ( 46) link_BETA1-4 : angle 1.99208 ( 138) link_NAG-ASN : bond 0.00668 ( 60) link_NAG-ASN : angle 3.33739 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1 GLN cc_start: 0.8922 (pm20) cc_final: 0.8562 (pm20) REVERT: L 48 MET cc_start: 0.8473 (tmm) cc_final: 0.8125 (tmm) REVERT: L 51 GLU cc_start: 0.9077 (tp30) cc_final: 0.8662 (tp30) REVERT: L 77 ASN cc_start: 0.9313 (t0) cc_final: 0.9004 (t0) REVERT: H 20 LEU cc_start: 0.9160 (tp) cc_final: 0.8877 (tp) REVERT: G 434 MET cc_start: 0.7351 (mtt) cc_final: 0.7085 (mtt) REVERT: B 530 MET cc_start: 0.8191 (mmp) cc_final: 0.7780 (mmm) REVERT: B 632 GLU cc_start: 0.9473 (tp30) cc_final: 0.9069 (tm-30) REVERT: A 95 MET cc_start: 0.9005 (ptt) cc_final: 0.8026 (ppp) REVERT: C 587 LEU cc_start: 0.9772 (mm) cc_final: 0.9494 (pp) REVERT: C 588 GLU cc_start: 0.9383 (tt0) cc_final: 0.8995 (pt0) REVERT: C 626 MET cc_start: 0.7907 (ppp) cc_final: 0.7426 (ppp) REVERT: C 657 GLU cc_start: 0.9494 (tt0) cc_final: 0.9188 (tp30) REVERT: D 100 MET cc_start: 0.9531 (mtt) cc_final: 0.9171 (mtt) REVERT: D 195 ASN cc_start: 0.9260 (m-40) cc_final: 0.8582 (t0) REVERT: E 632 GLU cc_start: 0.9631 (tp30) cc_final: 0.9245 (pp20) outliers start: 2 outliers final: 0 residues processed: 99 average time/residue: 0.1551 time to fit residues: 23.1233 Evaluate side-chains 81 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 180 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 185 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN H 3 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 ASN B 543 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 ASN D 478 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.037692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.029347 restraints weight = 171829.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.030237 restraints weight = 100696.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.030833 restraints weight = 71579.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.031221 restraints weight = 57565.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.031469 restraints weight = 50082.874| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18470 Z= 0.232 Angle : 0.814 10.942 25337 Z= 0.370 Chirality : 0.047 0.324 3221 Planarity : 0.004 0.063 2951 Dihedral : 8.985 59.158 5403 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.83 % Favored : 93.02 % Rotamer: Outliers : 0.06 % Allowed : 1.47 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.19), residues: 1976 helix: 0.32 (0.28), residues: 382 sheet: -0.44 (0.25), residues: 441 loop : -1.41 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 105 TYR 0.023 0.002 TYR G 401 PHE 0.027 0.002 PHE C 522 TRP 0.013 0.002 TRP G 427 HIS 0.014 0.001 HIS G 216 Details of bonding type rmsd covalent geometry : bond 0.00499 (18297) covalent geometry : angle 0.74197 (24856) SS BOND : bond 0.00424 ( 38) SS BOND : angle 1.43356 ( 76) hydrogen bonds : bond 0.04193 ( 434) hydrogen bonds : angle 5.47115 ( 1221) link_ALPHA1-2 : bond 0.00535 ( 4) link_ALPHA1-2 : angle 1.48860 ( 12) link_ALPHA1-3 : bond 0.00872 ( 13) link_ALPHA1-3 : angle 1.62858 ( 39) link_ALPHA1-6 : bond 0.00492 ( 12) link_ALPHA1-6 : angle 1.79535 ( 36) link_BETA1-4 : bond 0.00711 ( 46) link_BETA1-4 : angle 2.03306 ( 138) link_NAG-ASN : bond 0.00694 ( 60) link_NAG-ASN : angle 3.44019 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 MET cc_start: 0.8447 (tmm) cc_final: 0.8135 (tmm) REVERT: L 51 GLU cc_start: 0.9157 (tp30) cc_final: 0.8708 (tp30) REVERT: L 77 ASN cc_start: 0.9321 (t0) cc_final: 0.9026 (t0) REVERT: H 20 LEU cc_start: 0.9175 (tp) cc_final: 0.8829 (tp) REVERT: G 434 MET cc_start: 0.7617 (mtt) cc_final: 0.7334 (mtt) REVERT: B 632 GLU cc_start: 0.9467 (tp30) cc_final: 0.9033 (tm-30) REVERT: A 84 MET cc_start: 0.9037 (tpp) cc_final: 0.8663 (tpp) REVERT: A 95 MET cc_start: 0.9036 (ptt) cc_final: 0.8104 (ppp) REVERT: A 104 MET cc_start: 0.9336 (ppp) cc_final: 0.8819 (ppp) REVERT: C 587 LEU cc_start: 0.9749 (mm) cc_final: 0.9488 (pp) REVERT: C 588 GLU cc_start: 0.9369 (tt0) cc_final: 0.8917 (pt0) REVERT: C 657 GLU cc_start: 0.9491 (tt0) cc_final: 0.9195 (tp30) REVERT: D 100 MET cc_start: 0.9504 (mtt) cc_final: 0.9151 (mtt) REVERT: D 104 MET cc_start: 0.9669 (ttt) cc_final: 0.9424 (ttt) REVERT: D 195 ASN cc_start: 0.9073 (m-40) cc_final: 0.8440 (t0) REVERT: D 434 MET cc_start: 0.8480 (mpp) cc_final: 0.7640 (mpp) REVERT: D 475 MET cc_start: 0.8724 (tpp) cc_final: 0.8517 (tpp) REVERT: E 545 LEU cc_start: 0.7926 (tp) cc_final: 0.7516 (tp) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.1561 time to fit residues: 21.8526 Evaluate side-chains 79 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 95 optimal weight: 0.0470 chunk 186 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 overall best weight: 2.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN H 1 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 ASN B 543 GLN A 339 ASN ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.038335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.029975 restraints weight = 165150.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.030887 restraints weight = 95965.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.031479 restraints weight = 67486.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.031908 restraints weight = 53990.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.032192 restraints weight = 46330.937| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18470 Z= 0.149 Angle : 0.745 15.403 25337 Z= 0.338 Chirality : 0.047 0.493 3221 Planarity : 0.004 0.065 2951 Dihedral : 8.662 57.751 5403 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.87 % Favored : 93.98 % Rotamer: Outliers : 0.06 % Allowed : 0.68 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.19), residues: 1976 helix: 0.43 (0.28), residues: 381 sheet: -0.43 (0.25), residues: 439 loop : -1.33 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 45 TYR 0.018 0.001 TYR G 401 PHE 0.030 0.001 PHE E 522 TRP 0.013 0.001 TRP A 427 HIS 0.007 0.001 HIS G 216 Details of bonding type rmsd covalent geometry : bond 0.00321 (18297) covalent geometry : angle 0.66685 (24856) SS BOND : bond 0.00403 ( 38) SS BOND : angle 1.19863 ( 76) hydrogen bonds : bond 0.03761 ( 434) hydrogen bonds : angle 5.27260 ( 1221) link_ALPHA1-2 : bond 0.00532 ( 4) link_ALPHA1-2 : angle 1.49631 ( 12) link_ALPHA1-3 : bond 0.00884 ( 13) link_ALPHA1-3 : angle 1.50350 ( 39) link_ALPHA1-6 : bond 0.00510 ( 12) link_ALPHA1-6 : angle 1.68269 ( 36) link_BETA1-4 : bond 0.00686 ( 46) link_BETA1-4 : angle 1.94414 ( 138) link_NAG-ASN : bond 0.00652 ( 60) link_NAG-ASN : angle 3.46639 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1 GLN cc_start: 0.8827 (pm20) cc_final: 0.8174 (pm20) REVERT: L 48 MET cc_start: 0.8498 (tmm) cc_final: 0.8140 (tmm) REVERT: L 51 GLU cc_start: 0.9127 (tp30) cc_final: 0.8700 (tp30) REVERT: L 77 ASN cc_start: 0.9306 (t0) cc_final: 0.8991 (t0) REVERT: H 20 LEU cc_start: 0.9165 (tp) cc_final: 0.8825 (tp) REVERT: G 100 MET cc_start: 0.9364 (mtm) cc_final: 0.8961 (mtt) REVERT: G 210 PHE cc_start: 0.9381 (p90) cc_final: 0.9123 (p90) REVERT: G 434 MET cc_start: 0.7301 (mtt) cc_final: 0.7023 (mtt) REVERT: B 530 MET cc_start: 0.8180 (mmp) cc_final: 0.7669 (mmm) REVERT: B 632 GLU cc_start: 0.9428 (tp30) cc_final: 0.8897 (tm-30) REVERT: A 95 MET cc_start: 0.8963 (ptt) cc_final: 0.8025 (ppp) REVERT: C 587 LEU cc_start: 0.9748 (mm) cc_final: 0.9458 (tt) REVERT: C 588 GLU cc_start: 0.9367 (tt0) cc_final: 0.8988 (pt0) REVERT: C 657 GLU cc_start: 0.9494 (tt0) cc_final: 0.9197 (tp30) REVERT: D 100 MET cc_start: 0.9518 (mtt) cc_final: 0.9184 (mtt) REVERT: D 195 ASN cc_start: 0.9199 (m-40) cc_final: 0.8544 (t0) REVERT: D 434 MET cc_start: 0.8306 (mpp) cc_final: 0.7637 (mpp) REVERT: E 545 LEU cc_start: 0.8062 (tp) cc_final: 0.7269 (tp) REVERT: E 584 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8786 (tm-30) REVERT: E 632 GLU cc_start: 0.9583 (tp30) cc_final: 0.9194 (pp20) outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.1488 time to fit residues: 22.2337 Evaluate side-chains 80 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 69 optimal weight: 0.0570 chunk 124 optimal weight: 0.5980 chunk 129 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 overall best weight: 2.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN H 1 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 ASN B 543 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.038233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.029851 restraints weight = 167407.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.030753 restraints weight = 97245.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.031362 restraints weight = 68905.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.031749 restraints weight = 55071.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.032035 restraints weight = 47780.067| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18470 Z= 0.157 Angle : 0.740 13.645 25337 Z= 0.336 Chirality : 0.046 0.384 3221 Planarity : 0.004 0.065 2951 Dihedral : 8.515 58.481 5403 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.38 % Favored : 93.47 % Rotamer: Outliers : 0.06 % Allowed : 0.45 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.19), residues: 1976 helix: 0.41 (0.28), residues: 380 sheet: -0.52 (0.25), residues: 445 loop : -1.27 (0.18), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 49 TYR 0.019 0.001 TYR G 401 PHE 0.029 0.001 PHE E 522 TRP 0.017 0.001 TRP G 427 HIS 0.006 0.001 HIS G 216 Details of bonding type rmsd covalent geometry : bond 0.00338 (18297) covalent geometry : angle 0.66462 (24856) SS BOND : bond 0.00393 ( 38) SS BOND : angle 1.14823 ( 76) hydrogen bonds : bond 0.03689 ( 434) hydrogen bonds : angle 5.22498 ( 1221) link_ALPHA1-2 : bond 0.00530 ( 4) link_ALPHA1-2 : angle 1.48929 ( 12) link_ALPHA1-3 : bond 0.00850 ( 13) link_ALPHA1-3 : angle 1.51369 ( 39) link_ALPHA1-6 : bond 0.00507 ( 12) link_ALPHA1-6 : angle 1.69070 ( 36) link_BETA1-4 : bond 0.00701 ( 46) link_BETA1-4 : angle 1.97721 ( 138) link_NAG-ASN : bond 0.00655 ( 60) link_NAG-ASN : angle 3.35053 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1 GLN cc_start: 0.8768 (pm20) cc_final: 0.8136 (pm20) REVERT: L 48 MET cc_start: 0.8593 (tmm) cc_final: 0.8198 (tmm) REVERT: L 51 GLU cc_start: 0.9108 (tp30) cc_final: 0.8738 (tp30) REVERT: L 77 ASN cc_start: 0.9286 (t0) cc_final: 0.8964 (t0) REVERT: H 20 LEU cc_start: 0.9175 (tp) cc_final: 0.8842 (tp) REVERT: G 100 MET cc_start: 0.9346 (mtm) cc_final: 0.8882 (mtt) REVERT: G 434 MET cc_start: 0.7285 (mtt) cc_final: 0.6988 (mtt) REVERT: B 530 MET cc_start: 0.8180 (mmp) cc_final: 0.7671 (mmm) REVERT: B 632 GLU cc_start: 0.9462 (tp30) cc_final: 0.8956 (tm-30) REVERT: A 95 MET cc_start: 0.8904 (ptt) cc_final: 0.8020 (ppp) REVERT: C 587 LEU cc_start: 0.9749 (mm) cc_final: 0.9498 (tt) REVERT: C 588 GLU cc_start: 0.9313 (tt0) cc_final: 0.8864 (pt0) REVERT: C 657 GLU cc_start: 0.9485 (tt0) cc_final: 0.9185 (tp30) REVERT: D 100 MET cc_start: 0.9491 (mtt) cc_final: 0.9155 (mtt) REVERT: D 104 MET cc_start: 0.9664 (ttt) cc_final: 0.9438 (ttt) REVERT: D 195 ASN cc_start: 0.9119 (m-40) cc_final: 0.8647 (t0) REVERT: D 434 MET cc_start: 0.8266 (mpp) cc_final: 0.7443 (mpp) REVERT: E 545 LEU cc_start: 0.7857 (tp) cc_final: 0.7411 (tp) REVERT: E 584 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8721 (tm-30) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.1450 time to fit residues: 20.7876 Evaluate side-chains 78 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 119 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 194 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 GLN ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.038706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.030299 restraints weight = 163912.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.031212 restraints weight = 95110.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.031819 restraints weight = 66830.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.032253 restraints weight = 53225.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.032494 restraints weight = 45618.326| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18470 Z= 0.124 Angle : 0.709 12.089 25337 Z= 0.322 Chirality : 0.046 0.348 3221 Planarity : 0.004 0.132 2951 Dihedral : 8.301 58.033 5403 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.82 % Favored : 94.03 % Rotamer: Outliers : 0.06 % Allowed : 0.23 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.19), residues: 1976 helix: 0.47 (0.27), residues: 386 sheet: -0.47 (0.25), residues: 449 loop : -1.26 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 49 TYR 0.019 0.001 TYR G 401 PHE 0.026 0.001 PHE E 522 TRP 0.016 0.001 TRP G 427 HIS 0.005 0.001 HIS G 216 Details of bonding type rmsd covalent geometry : bond 0.00267 (18297) covalent geometry : angle 0.63658 (24856) SS BOND : bond 0.00396 ( 38) SS BOND : angle 1.02406 ( 76) hydrogen bonds : bond 0.03532 ( 434) hydrogen bonds : angle 5.08297 ( 1221) link_ALPHA1-2 : bond 0.00523 ( 4) link_ALPHA1-2 : angle 1.49655 ( 12) link_ALPHA1-3 : bond 0.00887 ( 13) link_ALPHA1-3 : angle 1.45907 ( 39) link_ALPHA1-6 : bond 0.00529 ( 12) link_ALPHA1-6 : angle 1.63098 ( 36) link_BETA1-4 : bond 0.00712 ( 46) link_BETA1-4 : angle 1.94542 ( 138) link_NAG-ASN : bond 0.00657 ( 60) link_NAG-ASN : angle 3.20805 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2193.96 seconds wall clock time: 39 minutes 24.43 seconds (2364.43 seconds total)