Starting phenix.real_space_refine on Sun Aug 24 15:06:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gje_40088/08_2025/8gje_40088.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gje_40088/08_2025/8gje_40088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gje_40088/08_2025/8gje_40088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gje_40088/08_2025/8gje_40088.map" model { file = "/net/cci-nas-00/data/ceres_data/8gje_40088/08_2025/8gje_40088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gje_40088/08_2025/8gje_40088.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.096 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 123 5.16 5 C 12855 2.51 5 N 3414 2.21 5 O 4221 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 20613 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3569 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 1 Chain: "B" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 975 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "H" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "L" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain: "C" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3569 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 1 Chain: "E" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 975 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "G" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "J" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain: "D" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3569 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 1 Chain: "F" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 975 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "I" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "K" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "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: 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: "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: 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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "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: 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: "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: 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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "F" 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: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.24, per 1000 atoms: 0.25 Number of scatterers: 20613 At special positions: 0 Unit cell: (141.48, 145.41, 121.83, 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 123 16.00 O 4221 8.00 N 3414 7.00 C 12855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 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=2.04 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 F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN a 4 " - " MAN a 5 " " MAN a 5 " - " MAN a 6 " " MAN j 4 " - " MAN j 5 " " MAN j 5 " - " MAN j 6 " ALPHA1-3 " BMA R 3 " - " MAN R 4 " " MAN R 7 " - " MAN R 8 " " BMA U 3 " - " MAN U 7 " " MAN U 4 " - " MAN U 5 " " BMA a 3 " - " MAN a 4 " " MAN a 7 " - " MAN a 8 " " BMA d 3 " - " MAN d 7 " " MAN d 4 " - " MAN d 5 " " BMA j 3 " - " MAN j 4 " " MAN j 7 " - " MAN j 8 " " BMA m 3 " - " MAN m 7 " " MAN m 4 " - " MAN m 5 " ALPHA1-6 " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 9 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 6 " " BMA a 3 " - " MAN a 7 " " MAN a 7 " - " MAN a 9 " " BMA d 3 " - " MAN d 4 " " MAN d 4 " - " MAN d 6 " " BMA j 3 " - " MAN j 7 " " MAN j 7 " - " MAN j 9 " " BMA m 3 " - " MAN m 4 " " MAN m 4 " - " MAN m 6 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " 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 f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " BETA1-6 " NAG O 1 " - " FUC O 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG X 1 " - " FUC X 4 " " NAG g 1 " - " FUC g 4 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 289 " " NAG A 604 " - " ASN A 301 " " NAG A 605 " - " ASN A 339 " " NAG A 606 " - " ASN A 442 " " NAG A 607 " - " ASN A 448 " " NAG B 700 " - " ASN B 611 " " NAG B 701 " - " ASN B 625 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 289 " " NAG C 604 " - " ASN C 301 " " NAG C 605 " - " ASN C 339 " " NAG C 606 " - " ASN C 442 " " NAG C 607 " - " ASN C 448 " " NAG D 601 " - " ASN D 88 " " NAG D 602 " - " ASN D 133 " " NAG D 603 " - " ASN D 289 " " NAG D 604 " - " ASN D 301 " " NAG D 605 " - " ASN D 339 " " NAG D 606 " - " ASN D 442 " " NAG D 607 " - " ASN D 448 " " NAG E 700 " - " ASN E 611 " " NAG E 701 " - " ASN E 625 " " NAG E 702 " - " ASN E 637 " " NAG F 700 " - " ASN F 611 " " NAG F 701 " - " ASN F 625 " " NAG F 702 " - " ASN F 637 " " NAG J 600 " - " ASN J 72 " " NAG K 600 " - " ASN K 72 " " NAG L 600 " - " ASN L 72 " " NAG M 1 " - " ASN A 156 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 197 " " NAG P 1 " - " ASN A 230 " " NAG Q 1 " - " ASN A 241 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 276 " " NAG V 1 " - " ASN C 156 " " NAG W 1 " - " ASN C 160 " " NAG X 1 " - " ASN C 197 " " NAG Y 1 " - " ASN C 230 " " NAG Z 1 " - " ASN C 241 " " NAG a 1 " - " ASN C 262 " " NAG b 1 " - " ASN C 332 " " NAG c 1 " - " ASN C 386 " " NAG d 1 " - " ASN C 276 " " NAG e 1 " - " ASN D 156 " " NAG f 1 " - " ASN D 160 " " NAG g 1 " - " ASN D 197 " " NAG h 1 " - " ASN D 230 " " NAG i 1 " - " ASN D 241 " " NAG j 1 " - " ASN D 262 " " NAG k 1 " - " ASN D 332 " " NAG l 1 " - " ASN D 386 " " NAG m 1 " - " ASN D 276 " Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 847.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4446 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 45 sheets defined 22.3% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.690A pdb=" N HIS A 72 " --> pdb=" O TRP A 69 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N CYS A 74 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 143 through 152 removed outlier: 3.574A pdb=" N LYS A 152 " --> pdb=" O ASP A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 143 through 152' Processing helix chain 'A' and resid 185E through 189 removed outlier: 3.513A pdb=" N SER A 189 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.531A pdb=" N ASN A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 484 removed outlier: 4.055A pdb=" N ASN A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.557A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.758A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 653 Processing helix chain 'B' and resid 658 through 663 removed outlier: 3.507A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 71D through 73 No H-bonds generated for 'chain 'H' and resid 71D through 73' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.602A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 69 through 74 removed outlier: 3.690A pdb=" N HIS C 72 " --> pdb=" O TRP C 69 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N CYS C 74 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 143 through 152 removed outlier: 3.574A pdb=" N LYS C 152 " --> pdb=" O ASP C 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 143 through 152' Processing helix chain 'C' and resid 185E through 189 removed outlier: 3.513A pdb=" N SER C 189 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 352 removed outlier: 3.531A pdb=" N ASN C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 474 through 484 removed outlier: 4.055A pdb=" N ASN C 478 " --> pdb=" O ASN C 474 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 removed outlier: 3.557A pdb=" N SER E 534 " --> pdb=" O MET E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 542 Processing helix chain 'E' and resid 570 through 596 Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.759A pdb=" N MET E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 653 Processing helix chain 'E' and resid 658 through 663 removed outlier: 3.507A pdb=" N LEU E 663 " --> pdb=" O ASP E 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 60 through 64 Processing helix chain 'G' and resid 71D through 73 No H-bonds generated for 'chain 'G' and resid 71D through 73' Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.602A pdb=" N THR G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'D' and resid 69 through 74 removed outlier: 3.690A pdb=" N HIS D 72 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N CYS D 74 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 117 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 143 through 152 removed outlier: 3.574A pdb=" N LYS D 152 " --> pdb=" O ASP D 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 143 through 152' Processing helix chain 'D' and resid 185E through 189 removed outlier: 3.513A pdb=" N SER D 189 " --> pdb=" O SER D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 352 removed outlier: 3.531A pdb=" N ASN D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 474 through 484 removed outlier: 4.054A pdb=" N ASN D 478 " --> pdb=" O ASN D 474 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.557A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 570 through 596 Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.758A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 653 Processing helix chain 'F' and resid 658 through 663 removed outlier: 3.507A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 60 through 64 Processing helix chain 'I' and resid 71D through 73 No H-bonds generated for 'chain 'I' and resid 71D through 73' Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.602A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.210A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.623A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 5.424A pdb=" N ILE A 215 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY A 250 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR A 217 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 184 Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.522A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.216A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.614A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 9.803A pdb=" N LYS A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.924A pdb=" N VAL A 292 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ASN A 448 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N LYS A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.879A 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 284 through 298 current: chain 'A' and resid 358 through 361 Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.879A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N LYS A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ASN A 448 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 10.924A pdb=" N VAL A 292 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 9.803A pdb=" N LYS A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.614A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.216A 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 421 removed outlier: 4.152A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 303 through 312 removed outlier: 6.850A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 11 removed outlier: 4.054A pdb=" N PHE H 33 " --> pdb=" O GLN H 95 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 11 removed outlier: 5.012A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.586A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS L 88 " --> pdb=" O VAL L 99 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY L 101 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR L 86 " --> pdb=" O GLY L 101 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.210A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.623A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 55 removed outlier: 5.423A pdb=" N ILE C 215 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY C 250 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR C 217 " --> pdb=" O THR C 248 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'C' and resid 129 through 133 Processing sheet with id=AC3, first strand: chain 'C' and resid 181 through 184 Processing sheet with id=AC4, first strand: chain 'C' and resid 201 through 203 Processing sheet with id=AC5, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.522A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N THR C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.614A pdb=" N ILE C 294 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 9.803A pdb=" N LYS C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.924A pdb=" N VAL C 292 " --> pdb=" O LYS C 446 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ASN C 448 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N LYS C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 298 current: chain 'C' and resid 358 through 361 Processing sheet with id=AC6, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.879A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N LYS C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ASN C 448 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 10.924A pdb=" N VAL C 292 " --> pdb=" O LYS C 446 " (cutoff:3.500A) removed outlier: 9.803A pdb=" N LYS C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.614A pdb=" N ILE C 294 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N THR C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 443 through 456 current: chain 'C' and resid 413 through 421 removed outlier: 4.152A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 303 through 312 removed outlier: 6.850A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 11 removed outlier: 4.055A pdb=" N PHE G 33 " --> pdb=" O GLN G 95 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 10 through 11 removed outlier: 5.013A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.587A pdb=" N LEU J 11 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS J 88 " --> pdb=" O VAL J 99 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY J 101 " --> pdb=" O TYR J 86 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR J 86 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.210A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.623A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 53 through 55 removed outlier: 5.423A pdb=" N ILE D 215 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY D 250 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR D 217 " --> pdb=" O THR D 248 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'D' and resid 129 through 133 Processing sheet with id=AD9, first strand: chain 'D' and resid 181 through 184 Processing sheet with id=AE1, first strand: chain 'D' and resid 201 through 203 Processing sheet with id=AE2, first strand: chain 'D' and resid 259 through 261 removed outlier: 3.522A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N THR D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.614A pdb=" N ILE D 294 " --> pdb=" O THR D 444 " (cutoff:3.500A) removed outlier: 9.803A pdb=" N LYS D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.925A pdb=" N VAL D 292 " --> pdb=" O LYS D 446 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ASN D 448 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N LYS D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 284 through 298 current: chain 'D' and resid 358 through 361 Processing sheet with id=AE3, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.879A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N LYS D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ASN D 448 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 10.925A pdb=" N VAL D 292 " --> pdb=" O LYS D 446 " (cutoff:3.500A) removed outlier: 9.803A pdb=" N LYS D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.614A pdb=" N ILE D 294 " --> pdb=" O THR D 444 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N THR D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 443 through 456 current: chain 'D' and resid 413 through 421 removed outlier: 4.152A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 303 through 312 removed outlier: 6.850A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'I' and resid 10 through 11 removed outlier: 4.054A pdb=" N PHE I 33 " --> pdb=" O GLN I 95 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 10 through 11 removed outlier: 5.012A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.586A pdb=" N LEU K 11 " --> pdb=" O ASP K 105 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS K 88 " --> pdb=" O VAL K 99 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY K 101 " --> pdb=" O TYR K 86 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR K 86 " --> pdb=" O GLY K 101 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 705 hydrogen bonds defined for protein. 1809 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: 3.71 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6308 1.34 - 1.46: 5422 1.46 - 1.59: 9126 1.59 - 1.71: 3 1.71 - 1.84: 168 Bond restraints: 21027 Sorted by residual: bond pdb=" C1 FUC g 4 " pdb=" C2 FUC g 4 " ideal model delta sigma weight residual 1.528 1.657 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C1 FUC O 4 " pdb=" C2 FUC O 4 " ideal model delta sigma weight residual 1.528 1.657 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C1 FUC X 4 " pdb=" C2 FUC X 4 " ideal model delta sigma weight residual 1.528 1.657 -0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" C1 FUC g 4 " pdb=" O5 FUC g 4 " ideal model delta sigma weight residual 1.400 1.494 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" C1 FUC O 4 " pdb=" O5 FUC O 4 " ideal model delta sigma weight residual 1.400 1.494 -0.094 2.00e-02 2.50e+03 2.21e+01 ... (remaining 21022 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 26927 2.08 - 4.16: 1354 4.16 - 6.23: 243 6.23 - 8.31: 33 8.31 - 10.39: 3 Bond angle restraints: 28560 Sorted by residual: angle pdb=" N ALA D 70 " pdb=" CA ALA D 70 " pdb=" C ALA D 70 " ideal model delta sigma weight residual 108.08 114.78 -6.70 1.69e+00 3.50e-01 1.57e+01 angle pdb=" N ASN C 138 " pdb=" CA ASN C 138 " pdb=" C ASN C 138 " ideal model delta sigma weight residual 107.37 115.55 -8.18 2.07e+00 2.33e-01 1.56e+01 angle pdb=" N ALA C 70 " pdb=" CA ALA C 70 " pdb=" C ALA C 70 " ideal model delta sigma weight residual 108.08 114.75 -6.67 1.69e+00 3.50e-01 1.56e+01 angle pdb=" N ASN D 138 " pdb=" CA ASN D 138 " pdb=" C ASN D 138 " ideal model delta sigma weight residual 107.37 115.52 -8.15 2.07e+00 2.33e-01 1.55e+01 angle pdb=" N ALA A 70 " pdb=" CA ALA A 70 " pdb=" C ALA A 70 " ideal model delta sigma weight residual 108.08 114.73 -6.65 1.69e+00 3.50e-01 1.55e+01 ... (remaining 28555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.21: 13577 21.21 - 42.42: 406 42.42 - 63.62: 168 63.62 - 84.83: 72 84.83 - 106.04: 45 Dihedral angle restraints: 14268 sinusoidal: 7374 harmonic: 6894 Sorted by residual: dihedral pdb=" CA PHE D 376 " pdb=" C PHE D 376 " pdb=" N ASN D 377 " pdb=" CA ASN D 377 " ideal model delta harmonic sigma weight residual 180.00 159.74 20.26 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PHE A 376 " pdb=" C PHE A 376 " pdb=" N ASN A 377 " pdb=" CA ASN A 377 " ideal model delta harmonic sigma weight residual 180.00 159.74 20.26 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PHE C 376 " pdb=" C PHE C 376 " pdb=" N ASN C 377 " pdb=" CA ASN C 377 " ideal model delta harmonic sigma weight residual 180.00 159.75 20.25 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 14265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2873 0.078 - 0.156: 587 0.156 - 0.234: 53 0.234 - 0.311: 24 0.311 - 0.389: 6 Chirality restraints: 3543 Sorted by residual: chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.42e+02 chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.41e+02 chirality pdb=" C1 NAG m 2 " pdb=" O4 NAG m 1 " pdb=" C2 NAG m 2 " pdb=" O5 NAG m 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.39e+02 ... (remaining 3540 not shown) Planarity restraints: 3534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 1 " 0.039 2.00e-02 2.50e+03 3.19e-02 1.28e+01 pdb=" C7 NAG d 1 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG d 1 " 0.030 2.00e-02 2.50e+03 pdb=" N2 NAG d 1 " -0.050 2.00e-02 2.50e+03 pdb=" O7 NAG d 1 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG U 1 " 0.039 2.00e-02 2.50e+03 3.19e-02 1.28e+01 pdb=" C7 NAG U 1 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG U 1 " 0.030 2.00e-02 2.50e+03 pdb=" N2 NAG U 1 " -0.050 2.00e-02 2.50e+03 pdb=" O7 NAG U 1 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG m 1 " 0.039 2.00e-02 2.50e+03 3.19e-02 1.28e+01 pdb=" C7 NAG m 1 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG m 1 " 0.030 2.00e-02 2.50e+03 pdb=" N2 NAG m 1 " -0.050 2.00e-02 2.50e+03 pdb=" O7 NAG m 1 " -0.007 2.00e-02 2.50e+03 ... (remaining 3531 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 9 2.28 - 2.94: 9028 2.94 - 3.59: 26930 3.59 - 4.25: 47408 4.25 - 4.90: 77014 Nonbonded interactions: 160389 Sorted by model distance: nonbonded pdb=" OD1 ASN A 67 " pdb=" CB ASN A 209 " model vdw 1.626 3.440 nonbonded pdb=" OD1 ASN D 67 " pdb=" CB ASN D 209 " model vdw 1.626 3.440 nonbonded pdb=" OD1 ASN C 67 " pdb=" CB ASN C 209 " model vdw 1.626 3.440 nonbonded pdb=" OD1 ASN A 67 " pdb=" CG ASN A 209 " model vdw 2.133 3.270 nonbonded pdb=" OD1 ASN D 67 " pdb=" CG ASN D 209 " model vdw 2.133 3.270 ... (remaining 160384 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' } ncs_group { reference = chain 'O' selection = chain 'X' selection = chain 'g' } ncs_group { reference = chain 'R' selection = chain 'a' selection = chain 'j' } ncs_group { reference = chain 'U' selection = chain 'd' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 20.200 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.129 21195 Z= 0.349 Angle : 1.126 15.348 29025 Z= 0.572 Chirality : 0.066 0.389 3543 Planarity : 0.007 0.115 3474 Dihedral : 14.032 106.041 9705 Min Nonbonded Distance : 1.626 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.29 % Allowed : 2.00 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.00 (0.17), residues: 2343 helix: 1.22 (0.27), residues: 381 sheet: 0.76 (0.19), residues: 681 loop : 0.58 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 298 TYR 0.029 0.003 TYR K 71 PHE 0.035 0.003 PHE A 233 TRP 0.025 0.003 TRP I 50 HIS 0.007 0.002 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00726 (21027) covalent geometry : angle 1.05825 (28560) SS BOND : bond 0.00590 ( 39) SS BOND : angle 1.87473 ( 78) hydrogen bonds : bond 0.14664 ( 672) hydrogen bonds : angle 7.76708 ( 1809) link_ALPHA1-2 : bond 0.00259 ( 6) link_ALPHA1-2 : angle 1.54179 ( 18) link_ALPHA1-3 : bond 0.00539 ( 12) link_ALPHA1-3 : angle 1.76908 ( 36) link_ALPHA1-6 : bond 0.01929 ( 12) link_ALPHA1-6 : angle 5.73661 ( 36) link_BETA1-4 : bond 0.01013 ( 36) link_BETA1-4 : angle 3.20007 ( 108) link_BETA1-6 : bond 0.04877 ( 3) link_BETA1-6 : angle 10.21223 ( 9) link_NAG-ASN : bond 0.00556 ( 60) link_NAG-ASN : angle 2.50702 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 648 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7269 (m-80) cc_final: 0.6855 (m-80) REVERT: A 150 MET cc_start: 0.8296 (mmm) cc_final: 0.8029 (tpp) REVERT: A 376 PHE cc_start: 0.7755 (m-80) cc_final: 0.7070 (m-80) REVERT: B 584 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8145 (mt-10) REVERT: B 589 ASP cc_start: 0.8391 (m-30) cc_final: 0.8116 (m-30) REVERT: B 625 ASN cc_start: 0.7866 (OUTLIER) cc_final: 0.7592 (t0) REVERT: B 639 THR cc_start: 0.8929 (m) cc_final: 0.8701 (p) REVERT: B 648 ASP cc_start: 0.8761 (m-30) cc_final: 0.8463 (t0) REVERT: B 652 GLN cc_start: 0.8391 (tp40) cc_final: 0.7950 (tp40) REVERT: H 83 ARG cc_start: 0.8094 (mtm180) cc_final: 0.7781 (mtm180) REVERT: H 84 SER cc_start: 0.9109 (p) cc_final: 0.8711 (t) REVERT: L 70 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7786 (pt0) REVERT: C 42 VAL cc_start: 0.8322 (t) cc_final: 0.7982 (p) REVERT: C 53 PHE cc_start: 0.7583 (m-80) cc_final: 0.6792 (m-10) REVERT: C 152 LYS cc_start: 0.8970 (mttt) cc_final: 0.8751 (mtmm) REVERT: C 185 LYS cc_start: 0.8622 (mttt) cc_final: 0.8250 (tptp) REVERT: C 302 ASN cc_start: 0.8101 (m110) cc_final: 0.7807 (m110) REVERT: C 432 ARG cc_start: 0.8518 (mtt90) cc_final: 0.8301 (mtm-85) REVERT: E 584 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8316 (mt-10) REVERT: E 652 GLN cc_start: 0.8413 (tp40) cc_final: 0.7921 (tp40) REVERT: G 84 SER cc_start: 0.8805 (p) cc_final: 0.8339 (t) REVERT: J 50 ASP cc_start: 0.6066 (t0) cc_final: 0.5820 (t0) REVERT: J 53 LYS cc_start: 0.8086 (mttt) cc_final: 0.7805 (mttt) REVERT: J 61 ARG cc_start: 0.7790 (mtm-85) cc_final: 0.7090 (ptp90) REVERT: J 70 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7878 (pt0) REVERT: J 82 ASP cc_start: 0.6310 (m-30) cc_final: 0.6055 (m-30) REVERT: D 53 PHE cc_start: 0.7677 (m-80) cc_final: 0.6832 (m-10) REVERT: D 111 LEU cc_start: 0.8905 (mt) cc_final: 0.8596 (mt) REVERT: D 150 MET cc_start: 0.8068 (mmm) cc_final: 0.7764 (tpp) REVERT: D 349 LEU cc_start: 0.9324 (mt) cc_final: 0.9007 (mt) REVERT: D 432 ARG cc_start: 0.8677 (mtt90) cc_final: 0.8377 (mtm-85) REVERT: F 584 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8103 (mt-10) REVERT: F 589 ASP cc_start: 0.8636 (m-30) cc_final: 0.8356 (m-30) REVERT: F 625 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7658 (t0) REVERT: F 639 THR cc_start: 0.8850 (m) cc_final: 0.8620 (p) REVERT: K 61 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.7155 (ptp90) REVERT: K 70 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8084 (pt0) REVERT: K 104 LEU cc_start: 0.7746 (tt) cc_final: 0.7425 (tp) outliers start: 6 outliers final: 3 residues processed: 654 average time/residue: 0.1915 time to fit residues: 178.6225 Evaluate side-chains 348 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 343 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain F residue 625 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 GLN L 24 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN J 24 GLN D 138 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 ASN F 543 GLN F 577 GLN I 62 GLN K 77 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.103251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.082032 restraints weight = 48420.095| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.63 r_work: 0.3191 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21195 Z= 0.198 Angle : 0.754 10.762 29025 Z= 0.365 Chirality : 0.049 0.294 3543 Planarity : 0.004 0.034 3474 Dihedral : 10.920 73.423 5197 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.09 % Allowed : 9.18 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.88 (0.17), residues: 2343 helix: 1.62 (0.26), residues: 390 sheet: 0.59 (0.18), residues: 738 loop : 0.36 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 480 TYR 0.028 0.002 TYR L 49 PHE 0.018 0.002 PHE J 62 TRP 0.026 0.002 TRP B 571 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00453 (21027) covalent geometry : angle 0.70602 (28560) SS BOND : bond 0.00231 ( 39) SS BOND : angle 1.13621 ( 78) hydrogen bonds : bond 0.04709 ( 672) hydrogen bonds : angle 6.39049 ( 1809) link_ALPHA1-2 : bond 0.00071 ( 6) link_ALPHA1-2 : angle 1.81574 ( 18) link_ALPHA1-3 : bond 0.00502 ( 12) link_ALPHA1-3 : angle 1.84741 ( 36) link_ALPHA1-6 : bond 0.00658 ( 12) link_ALPHA1-6 : angle 2.62741 ( 36) link_BETA1-4 : bond 0.00650 ( 36) link_BETA1-4 : angle 2.07520 ( 108) link_BETA1-6 : bond 0.03550 ( 3) link_BETA1-6 : angle 4.72970 ( 9) link_NAG-ASN : bond 0.00388 ( 60) link_NAG-ASN : angle 2.41228 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 347 time to evaluate : 0.724 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: A 53 PHE cc_start: 0.7480 (m-80) cc_final: 0.7049 (m-10) REVERT: A 95 MET cc_start: 0.8673 (ptm) cc_final: 0.8354 (ptm) REVERT: A 150 MET cc_start: 0.8231 (mmm) cc_final: 0.7897 (tpp) REVERT: A 277 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8693 (tt) REVERT: A 376 PHE cc_start: 0.7980 (m-80) cc_final: 0.7109 (m-80) REVERT: B 576 LEU cc_start: 0.8967 (tp) cc_final: 0.8754 (mm) REVERT: B 577 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8219 (tm-30) REVERT: B 584 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8457 (mt-10) REVERT: B 589 ASP cc_start: 0.8630 (m-30) cc_final: 0.8230 (m-30) REVERT: B 625 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7783 (t0) REVERT: B 648 ASP cc_start: 0.8860 (m-30) cc_final: 0.8435 (t0) REVERT: H 23 GLU cc_start: 0.8211 (mt-10) cc_final: 0.8007 (mp0) REVERT: H 28 ASN cc_start: 0.7864 (t0) cc_final: 0.7561 (t0) REVERT: H 84 SER cc_start: 0.9140 (p) cc_final: 0.8682 (t) REVERT: L 11 LEU cc_start: 0.8645 (mt) cc_final: 0.8307 (mt) REVERT: L 50 ASP cc_start: 0.7272 (t0) cc_final: 0.6145 (t0) REVERT: L 70 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7724 (pt0) REVERT: C 98 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8433 (t0) REVERT: C 152 LYS cc_start: 0.9200 (mttt) cc_final: 0.8840 (mtmm) REVERT: C 185 LYS cc_start: 0.8734 (mttt) cc_final: 0.8172 (tptp) REVERT: C 302 ASN cc_start: 0.8116 (m110) cc_final: 0.7641 (m110) REVERT: C 486 TYR cc_start: 0.7661 (p90) cc_final: 0.7055 (p90) REVERT: E 652 GLN cc_start: 0.8689 (tp40) cc_final: 0.8315 (tp40) REVERT: E 657 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8300 (mm-30) REVERT: G 28 ASN cc_start: 0.7937 (t0) cc_final: 0.7581 (t0) REVERT: G 84 SER cc_start: 0.8813 (p) cc_final: 0.8333 (t) REVERT: J 50 ASP cc_start: 0.6966 (t0) cc_final: 0.6726 (t0) REVERT: J 53 LYS cc_start: 0.8249 (mttt) cc_final: 0.8048 (mttm) REVERT: J 70 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7797 (pt0) REVERT: J 82 ASP cc_start: 0.7270 (m-30) cc_final: 0.6864 (m-30) REVERT: D 53 PHE cc_start: 0.7636 (m-80) cc_final: 0.6914 (m-10) REVERT: D 95 MET cc_start: 0.8534 (ptm) cc_final: 0.8285 (ptm) REVERT: D 150 MET cc_start: 0.8117 (mmm) cc_final: 0.7846 (tpp) REVERT: D 486 TYR cc_start: 0.8021 (OUTLIER) cc_final: 0.7366 (p90) REVERT: F 575 GLN cc_start: 0.9028 (tt0) cc_final: 0.8704 (mm-40) REVERT: F 576 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8675 (mm) REVERT: F 581 LEU cc_start: 0.9276 (tt) cc_final: 0.8735 (pp) REVERT: F 584 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8515 (mt-10) REVERT: F 589 ASP cc_start: 0.8852 (m-30) cc_final: 0.8641 (m-30) REVERT: F 625 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.8026 (t0) REVERT: F 630 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7696 (mp0) REVERT: K 24 GLN cc_start: 0.7608 (tt0) cc_final: 0.7365 (tt0) REVERT: K 50 ASP cc_start: 0.7163 (t0) cc_final: 0.5934 (t0) REVERT: K 62 PHE cc_start: 0.7343 (m-80) cc_final: 0.7078 (m-80) REVERT: K 70 GLU cc_start: 0.8531 (mt-10) cc_final: 0.7919 (pt0) outliers start: 65 outliers final: 40 residues processed: 394 average time/residue: 0.1701 time to fit residues: 99.2818 Evaluate side-chains 342 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 295 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 307 MET Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 482 GLU Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 69 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 117 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 171 optimal weight: 0.8980 chunk 169 optimal weight: 0.0870 chunk 216 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS A 302 ASN L 24 GLN C 130 HIS C 425 ASN E 543 GLN E 577 GLN J 24 GLN D 130 HIS ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 ASN ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN I 28 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.098925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.080232 restraints weight = 43822.374| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.02 r_work: 0.3130 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21195 Z= 0.178 Angle : 0.693 9.717 29025 Z= 0.333 Chirality : 0.047 0.292 3543 Planarity : 0.004 0.035 3474 Dihedral : 9.519 68.327 5197 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.14 % Allowed : 10.46 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.75 (0.17), residues: 2343 helix: 1.63 (0.26), residues: 390 sheet: 0.43 (0.18), residues: 738 loop : 0.30 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 30 TYR 0.026 0.002 TYR L 49 PHE 0.017 0.001 PHE D 376 TRP 0.030 0.002 TRP I 71D HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00404 (21027) covalent geometry : angle 0.64874 (28560) SS BOND : bond 0.00213 ( 39) SS BOND : angle 1.04149 ( 78) hydrogen bonds : bond 0.04174 ( 672) hydrogen bonds : angle 5.96087 ( 1809) link_ALPHA1-2 : bond 0.00072 ( 6) link_ALPHA1-2 : angle 1.78079 ( 18) link_ALPHA1-3 : bond 0.00683 ( 12) link_ALPHA1-3 : angle 1.58808 ( 36) link_ALPHA1-6 : bond 0.00628 ( 12) link_ALPHA1-6 : angle 2.58916 ( 36) link_BETA1-4 : bond 0.00659 ( 36) link_BETA1-4 : angle 1.78394 ( 108) link_BETA1-6 : bond 0.03813 ( 3) link_BETA1-6 : angle 4.29245 ( 9) link_NAG-ASN : bond 0.00350 ( 60) link_NAG-ASN : angle 2.29597 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 309 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8391 (mmm) cc_final: 0.8145 (tpp) REVERT: A 376 PHE cc_start: 0.8158 (m-80) cc_final: 0.7474 (m-80) REVERT: B 589 ASP cc_start: 0.8321 (m-30) cc_final: 0.8011 (m-30) REVERT: B 625 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7651 (t0) REVERT: B 630 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7460 (mp0) REVERT: B 648 ASP cc_start: 0.8580 (m-30) cc_final: 0.8218 (t0) REVERT: B 653 GLN cc_start: 0.7520 (tt0) cc_final: 0.7238 (tt0) REVERT: H 28 ASN cc_start: 0.8091 (t0) cc_final: 0.7887 (t0) REVERT: H 84 SER cc_start: 0.9146 (p) cc_final: 0.8707 (t) REVERT: L 3 GLN cc_start: 0.8153 (pp30) cc_final: 0.7803 (pp30) REVERT: L 24 GLN cc_start: 0.7849 (tt0) cc_final: 0.7593 (tt0) REVERT: L 50 ASP cc_start: 0.8123 (t0) cc_final: 0.7576 (t0) REVERT: L 70 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7818 (pt0) REVERT: L 77 ASN cc_start: 0.7743 (t0) cc_final: 0.7497 (t0) REVERT: C 98 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8585 (t0) REVERT: C 185 LYS cc_start: 0.8609 (mttt) cc_final: 0.8252 (tptp) REVERT: E 579 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8367 (mpp80) REVERT: E 652 GLN cc_start: 0.8391 (tp40) cc_final: 0.8156 (tp40) REVERT: G 84 SER cc_start: 0.8754 (p) cc_final: 0.8356 (t) REVERT: J 50 ASP cc_start: 0.7357 (t0) cc_final: 0.7104 (t0) REVERT: J 70 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7895 (pt0) REVERT: D 150 MET cc_start: 0.8341 (mmm) cc_final: 0.8106 (tpp) REVERT: D 320 THR cc_start: 0.9228 (m) cc_final: 0.8994 (p) REVERT: D 486 TYR cc_start: 0.7991 (OUTLIER) cc_final: 0.7384 (p90) REVERT: F 581 LEU cc_start: 0.9210 (tt) cc_final: 0.8750 (pp) REVERT: F 625 ASN cc_start: 0.8045 (OUTLIER) cc_final: 0.7801 (t0) REVERT: F 638 TYR cc_start: 0.8831 (m-10) cc_final: 0.8537 (m-10) REVERT: K 50 ASP cc_start: 0.8065 (t0) cc_final: 0.7855 (t0) REVERT: K 70 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8082 (pt0) outliers start: 66 outliers final: 45 residues processed: 353 average time/residue: 0.1661 time to fit residues: 87.9224 Evaluate side-chains 327 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 277 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 579 ARG Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 588 LYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 69 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 177 optimal weight: 0.0980 chunk 223 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 230 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 207 optimal weight: 0.3980 chunk 118 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 ASN E 543 GLN ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 ASN K 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.099910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.081610 restraints weight = 44044.333| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.97 r_work: 0.3156 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21195 Z= 0.127 Angle : 0.640 8.915 29025 Z= 0.304 Chirality : 0.046 0.291 3543 Planarity : 0.003 0.043 3474 Dihedral : 8.158 57.925 5197 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.09 % Allowed : 11.65 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.70 (0.17), residues: 2343 helix: 1.60 (0.27), residues: 393 sheet: 0.40 (0.18), residues: 738 loop : 0.25 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 579 TYR 0.022 0.001 TYR L 49 PHE 0.008 0.001 PHE I 91 TRP 0.027 0.001 TRP I 71D HIS 0.003 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00271 (21027) covalent geometry : angle 0.59593 (28560) SS BOND : bond 0.00204 ( 39) SS BOND : angle 0.96480 ( 78) hydrogen bonds : bond 0.03680 ( 672) hydrogen bonds : angle 5.65972 ( 1809) link_ALPHA1-2 : bond 0.00162 ( 6) link_ALPHA1-2 : angle 1.70884 ( 18) link_ALPHA1-3 : bond 0.00763 ( 12) link_ALPHA1-3 : angle 1.65285 ( 36) link_ALPHA1-6 : bond 0.00646 ( 12) link_ALPHA1-6 : angle 2.32820 ( 36) link_BETA1-4 : bond 0.00620 ( 36) link_BETA1-4 : angle 1.69382 ( 108) link_BETA1-6 : bond 0.03815 ( 3) link_BETA1-6 : angle 4.67179 ( 9) link_NAG-ASN : bond 0.00361 ( 60) link_NAG-ASN : angle 2.11187 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 316 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7763 (m-10) cc_final: 0.6573 (m-10) REVERT: A 104 MET cc_start: 0.8895 (ttm) cc_final: 0.8430 (ttm) REVERT: A 376 PHE cc_start: 0.8065 (m-80) cc_final: 0.7451 (m-80) REVERT: B 589 ASP cc_start: 0.8274 (m-30) cc_final: 0.7897 (m-30) REVERT: B 625 ASN cc_start: 0.7877 (OUTLIER) cc_final: 0.7532 (t0) REVERT: B 648 ASP cc_start: 0.8327 (m-30) cc_final: 0.7974 (t0) REVERT: H 72 ASP cc_start: 0.7894 (m-30) cc_final: 0.5102 (m-30) REVERT: H 84 SER cc_start: 0.9117 (p) cc_final: 0.8693 (t) REVERT: L 3 GLN cc_start: 0.8274 (pp30) cc_final: 0.7967 (pp30) REVERT: L 24 GLN cc_start: 0.7748 (tt0) cc_final: 0.7491 (tt0) REVERT: L 50 ASP cc_start: 0.8363 (t0) cc_final: 0.7891 (t0) REVERT: L 70 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7826 (pt0) REVERT: C 185 LYS cc_start: 0.8568 (mttt) cc_final: 0.8363 (tptp) REVERT: E 579 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8416 (mpp80) REVERT: E 652 GLN cc_start: 0.8438 (tp40) cc_final: 0.8230 (tp40) REVERT: G 84 SER cc_start: 0.8680 (p) cc_final: 0.8287 (t) REVERT: J 50 ASP cc_start: 0.7816 (t0) cc_final: 0.7556 (t0) REVERT: J 70 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7922 (pt0) REVERT: J 104 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7997 (mp) REVERT: D 150 MET cc_start: 0.8400 (mmm) cc_final: 0.8178 (tpp) REVERT: D 320 THR cc_start: 0.9238 (m) cc_final: 0.9000 (p) REVERT: D 486 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.7395 (p90) REVERT: F 575 GLN cc_start: 0.8841 (mt0) cc_final: 0.8628 (mm110) REVERT: F 577 GLN cc_start: 0.8636 (tp-100) cc_final: 0.8078 (mm-40) REVERT: F 584 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8024 (mt-10) REVERT: F 625 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7774 (t0) REVERT: F 630 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7475 (mp0) REVERT: K 70 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8089 (pt0) outliers start: 65 outliers final: 43 residues processed: 357 average time/residue: 0.1749 time to fit residues: 92.5327 Evaluate side-chains 326 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 278 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 579 ARG Chi-restraints excluded: chain E residue 588 LYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 425 ASN Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain K residue 63 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 5 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 220 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 ASN J 24 GLN ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN K 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.098128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.079805 restraints weight = 44091.570| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.96 r_work: 0.3108 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21195 Z= 0.167 Angle : 0.657 9.057 29025 Z= 0.311 Chirality : 0.046 0.292 3543 Planarity : 0.004 0.045 3474 Dihedral : 7.223 52.556 5197 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.19 % Allowed : 13.12 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.58 (0.17), residues: 2343 helix: 1.62 (0.27), residues: 393 sheet: 0.31 (0.18), residues: 741 loop : 0.14 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 94 TYR 0.020 0.001 TYR K 49 PHE 0.017 0.001 PHE D 376 TRP 0.037 0.002 TRP H 71D HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00381 (21027) covalent geometry : angle 0.61389 (28560) SS BOND : bond 0.00230 ( 39) SS BOND : angle 1.09568 ( 78) hydrogen bonds : bond 0.03800 ( 672) hydrogen bonds : angle 5.53088 ( 1809) link_ALPHA1-2 : bond 0.00113 ( 6) link_ALPHA1-2 : angle 1.74468 ( 18) link_ALPHA1-3 : bond 0.00664 ( 12) link_ALPHA1-3 : angle 1.80310 ( 36) link_ALPHA1-6 : bond 0.00629 ( 12) link_ALPHA1-6 : angle 2.44030 ( 36) link_BETA1-4 : bond 0.00588 ( 36) link_BETA1-4 : angle 1.70789 ( 108) link_BETA1-6 : bond 0.03574 ( 3) link_BETA1-6 : angle 4.25536 ( 9) link_NAG-ASN : bond 0.00379 ( 60) link_NAG-ASN : angle 2.13174 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 287 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 PHE cc_start: 0.8118 (m-80) cc_final: 0.7393 (m-80) REVERT: B 589 ASP cc_start: 0.8296 (m-30) cc_final: 0.7952 (m-30) REVERT: B 625 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7519 (t0) REVERT: B 630 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7446 (mp0) REVERT: B 648 ASP cc_start: 0.8335 (m-30) cc_final: 0.7995 (t0) REVERT: H 84 SER cc_start: 0.9100 (p) cc_final: 0.8682 (t) REVERT: L 3 GLN cc_start: 0.8229 (pp30) cc_final: 0.7917 (pp30) REVERT: L 50 ASP cc_start: 0.8682 (t0) cc_final: 0.8173 (t0) REVERT: L 70 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7859 (pt0) REVERT: C 42 VAL cc_start: 0.8272 (t) cc_final: 0.8070 (m) REVERT: E 625 ASN cc_start: 0.7888 (OUTLIER) cc_final: 0.7642 (t0) REVERT: E 652 GLN cc_start: 0.8453 (tp40) cc_final: 0.8109 (tp40) REVERT: E 657 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7433 (mm-30) REVERT: G 84 SER cc_start: 0.8662 (p) cc_final: 0.8207 (t) REVERT: J 70 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7907 (pt0) REVERT: D 150 MET cc_start: 0.8350 (mmm) cc_final: 0.8086 (tpt) REVERT: D 320 THR cc_start: 0.9245 (m) cc_final: 0.9035 (p) REVERT: D 486 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7539 (p90) REVERT: F 577 GLN cc_start: 0.8668 (tp-100) cc_final: 0.8108 (mm-40) REVERT: F 584 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8057 (mt-10) REVERT: F 630 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7545 (mp0) REVERT: F 652 GLN cc_start: 0.8492 (tt0) cc_final: 0.8282 (tt0) REVERT: K 70 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8055 (pt0) outliers start: 67 outliers final: 49 residues processed: 332 average time/residue: 0.1682 time to fit residues: 83.6401 Evaluate side-chains 322 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 270 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 91 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 136 optimal weight: 0.2980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 24 GLN C 425 ASN J 24 GLN ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.098197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.079998 restraints weight = 43918.567| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.95 r_work: 0.3135 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21195 Z= 0.142 Angle : 0.641 9.103 29025 Z= 0.304 Chirality : 0.046 0.292 3543 Planarity : 0.004 0.041 3474 Dihedral : 6.740 52.643 5195 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.28 % Allowed : 13.55 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.50 (0.17), residues: 2343 helix: 1.60 (0.27), residues: 393 sheet: 0.24 (0.18), residues: 741 loop : 0.09 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 579 TYR 0.021 0.001 TYR K 49 PHE 0.013 0.001 PHE D 376 TRP 0.032 0.001 TRP I 71D HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00318 (21027) covalent geometry : angle 0.59856 (28560) SS BOND : bond 0.00221 ( 39) SS BOND : angle 0.98648 ( 78) hydrogen bonds : bond 0.03670 ( 672) hydrogen bonds : angle 5.40511 ( 1809) link_ALPHA1-2 : bond 0.00130 ( 6) link_ALPHA1-2 : angle 1.70031 ( 18) link_ALPHA1-3 : bond 0.00694 ( 12) link_ALPHA1-3 : angle 1.72047 ( 36) link_ALPHA1-6 : bond 0.00572 ( 12) link_ALPHA1-6 : angle 2.31878 ( 36) link_BETA1-4 : bond 0.00570 ( 36) link_BETA1-4 : angle 1.66950 ( 108) link_BETA1-6 : bond 0.03611 ( 3) link_BETA1-6 : angle 4.39333 ( 9) link_NAG-ASN : bond 0.00304 ( 60) link_NAG-ASN : angle 2.11641 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 298 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8388 (p) REVERT: A 376 PHE cc_start: 0.8097 (m-80) cc_final: 0.7340 (m-80) REVERT: B 577 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: B 589 ASP cc_start: 0.8269 (m-30) cc_final: 0.7935 (m-30) REVERT: B 625 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.7474 (t0) REVERT: B 630 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7386 (mp0) REVERT: B 648 ASP cc_start: 0.8268 (m-30) cc_final: 0.7969 (t0) REVERT: H 84 SER cc_start: 0.9087 (p) cc_final: 0.8651 (t) REVERT: L 3 GLN cc_start: 0.8223 (pp30) cc_final: 0.7870 (pp30) REVERT: L 50 ASP cc_start: 0.8809 (t0) cc_final: 0.8359 (t0) REVERT: L 70 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7851 (pt0) REVERT: E 579 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8423 (mpp80) REVERT: E 652 GLN cc_start: 0.8291 (tp40) cc_final: 0.8086 (tp40) REVERT: E 657 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7359 (mm-30) REVERT: G 84 SER cc_start: 0.8737 (p) cc_final: 0.8453 (t) REVERT: J 50 ASP cc_start: 0.8493 (t0) cc_final: 0.8166 (t0) REVERT: J 70 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7926 (pt0) REVERT: D 150 MET cc_start: 0.8378 (mmm) cc_final: 0.8081 (tpt) REVERT: D 320 THR cc_start: 0.9228 (m) cc_final: 0.9021 (p) REVERT: D 486 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.7553 (p90) REVERT: F 584 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8009 (mt-10) REVERT: F 652 GLN cc_start: 0.8520 (tt0) cc_final: 0.8295 (tt0) REVERT: I 38 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7094 (ttp80) REVERT: K 62 PHE cc_start: 0.7268 (m-80) cc_final: 0.7040 (m-80) REVERT: K 70 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8013 (pt0) outliers start: 69 outliers final: 48 residues processed: 344 average time/residue: 0.1666 time to fit residues: 86.1794 Evaluate side-chains 323 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 269 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 579 ARG Chi-restraints excluded: chain E residue 588 LYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 233 optimal weight: 3.9990 chunk 207 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 37 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 24 GLN J 24 GLN ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN K 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.098458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.079678 restraints weight = 44444.182| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.07 r_work: 0.3117 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21195 Z= 0.133 Angle : 0.637 11.463 29025 Z= 0.301 Chirality : 0.046 0.389 3543 Planarity : 0.003 0.042 3474 Dihedral : 6.383 52.534 5195 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.00 % Allowed : 14.60 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.44 (0.17), residues: 2343 helix: 1.62 (0.27), residues: 393 sheet: 0.22 (0.18), residues: 750 loop : -0.00 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 542 TYR 0.023 0.001 TYR J 49 PHE 0.016 0.001 PHE D 376 TRP 0.033 0.001 TRP I 71D HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00294 (21027) covalent geometry : angle 0.59197 (28560) SS BOND : bond 0.00207 ( 39) SS BOND : angle 0.89628 ( 78) hydrogen bonds : bond 0.03551 ( 672) hydrogen bonds : angle 5.32529 ( 1809) link_ALPHA1-2 : bond 0.00146 ( 6) link_ALPHA1-2 : angle 1.67690 ( 18) link_ALPHA1-3 : bond 0.00687 ( 12) link_ALPHA1-3 : angle 1.67716 ( 36) link_ALPHA1-6 : bond 0.00533 ( 12) link_ALPHA1-6 : angle 2.26513 ( 36) link_BETA1-4 : bond 0.00585 ( 36) link_BETA1-4 : angle 1.63938 ( 108) link_BETA1-6 : bond 0.03700 ( 3) link_BETA1-6 : angle 4.44049 ( 9) link_NAG-ASN : bond 0.00310 ( 60) link_NAG-ASN : angle 2.21973 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 288 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8405 (p) REVERT: A 376 PHE cc_start: 0.8089 (m-80) cc_final: 0.7397 (m-80) REVERT: B 589 ASP cc_start: 0.8339 (m-30) cc_final: 0.7947 (m-30) REVERT: B 625 ASN cc_start: 0.7856 (OUTLIER) cc_final: 0.7538 (t0) REVERT: B 630 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7430 (mp0) REVERT: B 648 ASP cc_start: 0.8187 (m-30) cc_final: 0.7898 (t0) REVERT: H 84 SER cc_start: 0.9092 (p) cc_final: 0.8630 (t) REVERT: L 3 GLN cc_start: 0.8195 (pp30) cc_final: 0.7928 (pp30) REVERT: L 50 ASP cc_start: 0.8859 (t0) cc_final: 0.8457 (t0) REVERT: L 70 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7800 (pt0) REVERT: C 66 HIS cc_start: 0.7302 (OUTLIER) cc_final: 0.7047 (t-90) REVERT: E 543 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8236 (tm-30) REVERT: E 625 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7452 (t0) REVERT: E 652 GLN cc_start: 0.8336 (tp40) cc_final: 0.8009 (tp40) REVERT: E 657 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7365 (mm-30) REVERT: G 84 SER cc_start: 0.8746 (p) cc_final: 0.8454 (t) REVERT: J 40 ARG cc_start: 0.6904 (mmp80) cc_final: 0.6695 (mmp80) REVERT: J 50 ASP cc_start: 0.8566 (t0) cc_final: 0.8287 (t0) REVERT: J 70 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7926 (pt0) REVERT: D 320 THR cc_start: 0.9244 (m) cc_final: 0.9020 (p) REVERT: D 486 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.7598 (p90) REVERT: F 577 GLN cc_start: 0.8574 (tp-100) cc_final: 0.8035 (mm-40) REVERT: F 584 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8022 (mt-10) REVERT: F 630 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7523 (mp0) REVERT: F 638 TYR cc_start: 0.8781 (m-10) cc_final: 0.8507 (m-10) REVERT: I 38 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7169 (ttp80) REVERT: K 62 PHE cc_start: 0.7267 (m-80) cc_final: 0.7051 (m-80) REVERT: K 70 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8033 (pt0) outliers start: 63 outliers final: 47 residues processed: 329 average time/residue: 0.1522 time to fit residues: 74.9065 Evaluate side-chains 322 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 269 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain E residue 588 LYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 85 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 155 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 131 optimal weight: 0.8980 chunk 193 optimal weight: 0.0870 chunk 145 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 160 optimal weight: 0.0020 overall best weight: 0.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 24 GLN C 170 GLN ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.100553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.081462 restraints weight = 44435.517| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.17 r_work: 0.3130 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21195 Z= 0.112 Angle : 0.612 10.434 29025 Z= 0.292 Chirality : 0.045 0.299 3543 Planarity : 0.003 0.036 3474 Dihedral : 5.899 52.241 5195 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.71 % Allowed : 15.31 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.54 (0.17), residues: 2343 helix: 1.64 (0.27), residues: 396 sheet: 0.29 (0.19), residues: 735 loop : 0.07 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 542 TYR 0.021 0.001 TYR K 49 PHE 0.011 0.001 PHE D 376 TRP 0.033 0.001 TRP G 71D HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00235 (21027) covalent geometry : angle 0.57104 (28560) SS BOND : bond 0.00199 ( 39) SS BOND : angle 0.88132 ( 78) hydrogen bonds : bond 0.03357 ( 672) hydrogen bonds : angle 5.22972 ( 1809) link_ALPHA1-2 : bond 0.00223 ( 6) link_ALPHA1-2 : angle 1.59882 ( 18) link_ALPHA1-3 : bond 0.00731 ( 12) link_ALPHA1-3 : angle 1.55069 ( 36) link_ALPHA1-6 : bond 0.00523 ( 12) link_ALPHA1-6 : angle 2.16879 ( 36) link_BETA1-4 : bond 0.00595 ( 36) link_BETA1-4 : angle 1.60256 ( 108) link_BETA1-6 : bond 0.03825 ( 3) link_BETA1-6 : angle 4.64300 ( 9) link_NAG-ASN : bond 0.00346 ( 60) link_NAG-ASN : angle 2.00693 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 300 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 PHE cc_start: 0.8060 (m-80) cc_final: 0.7327 (m-80) REVERT: B 589 ASP cc_start: 0.8388 (m-30) cc_final: 0.7988 (m-30) REVERT: B 625 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7749 (t0) REVERT: B 648 ASP cc_start: 0.8159 (m-30) cc_final: 0.7922 (t0) REVERT: H 84 SER cc_start: 0.9139 (p) cc_final: 0.8696 (t) REVERT: L 3 GLN cc_start: 0.8152 (pp30) cc_final: 0.7874 (pp30) REVERT: L 50 ASP cc_start: 0.8873 (t0) cc_final: 0.8515 (t0) REVERT: L 70 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7760 (pt0) REVERT: C 66 HIS cc_start: 0.7214 (OUTLIER) cc_final: 0.6960 (t-90) REVERT: C 150 MET cc_start: 0.8164 (mmm) cc_final: 0.7592 (mmt) REVERT: E 577 GLN cc_start: 0.8822 (tp40) cc_final: 0.8602 (tp40) REVERT: E 584 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8295 (mt-10) REVERT: E 625 ASN cc_start: 0.7805 (OUTLIER) cc_final: 0.7494 (t0) REVERT: E 652 GLN cc_start: 0.8389 (tp40) cc_final: 0.7999 (tp40) REVERT: E 657 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7367 (mm-30) REVERT: G 84 SER cc_start: 0.8789 (p) cc_final: 0.8468 (t) REVERT: J 50 ASP cc_start: 0.8563 (t0) cc_final: 0.8306 (t0) REVERT: J 70 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7900 (pt0) REVERT: D 320 THR cc_start: 0.9272 (m) cc_final: 0.9012 (p) REVERT: D 486 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.7562 (p90) REVERT: F 577 GLN cc_start: 0.8588 (tp-100) cc_final: 0.8010 (mm-40) REVERT: F 584 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8026 (mt-10) REVERT: F 630 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7580 (mp0) REVERT: F 634 GLU cc_start: 0.8736 (tp30) cc_final: 0.8532 (tt0) REVERT: K 70 GLU cc_start: 0.8438 (mt-10) cc_final: 0.7995 (pt0) outliers start: 57 outliers final: 45 residues processed: 333 average time/residue: 0.1728 time to fit residues: 85.8147 Evaluate side-chains 322 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 272 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 85 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 116 optimal weight: 0.0870 chunk 185 optimal weight: 0.7980 chunk 36 optimal weight: 0.1980 chunk 109 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.098678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.080424 restraints weight = 43994.933| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.98 r_work: 0.3149 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21195 Z= 0.122 Angle : 0.627 10.514 29025 Z= 0.299 Chirality : 0.045 0.291 3543 Planarity : 0.003 0.040 3474 Dihedral : 5.717 52.149 5195 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.52 % Allowed : 15.98 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.53 (0.17), residues: 2343 helix: 1.68 (0.26), residues: 393 sheet: 0.31 (0.19), residues: 735 loop : 0.04 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 542 TYR 0.023 0.001 TYR F 638 PHE 0.013 0.001 PHE L 87 TRP 0.038 0.001 TRP G 71D HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00267 (21027) covalent geometry : angle 0.58763 (28560) SS BOND : bond 0.00201 ( 39) SS BOND : angle 0.87987 ( 78) hydrogen bonds : bond 0.03355 ( 672) hydrogen bonds : angle 5.18033 ( 1809) link_ALPHA1-2 : bond 0.00161 ( 6) link_ALPHA1-2 : angle 1.61355 ( 18) link_ALPHA1-3 : bond 0.00680 ( 12) link_ALPHA1-3 : angle 1.57586 ( 36) link_ALPHA1-6 : bond 0.00466 ( 12) link_ALPHA1-6 : angle 2.11189 ( 36) link_BETA1-4 : bond 0.00584 ( 36) link_BETA1-4 : angle 1.60590 ( 108) link_BETA1-6 : bond 0.03753 ( 3) link_BETA1-6 : angle 4.51397 ( 9) link_NAG-ASN : bond 0.00316 ( 60) link_NAG-ASN : angle 1.98883 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 290 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 589 ASP cc_start: 0.8274 (m-30) cc_final: 0.7909 (m-30) REVERT: B 625 ASN cc_start: 0.8047 (OUTLIER) cc_final: 0.7751 (t0) REVERT: B 630 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7390 (mp0) REVERT: H 84 SER cc_start: 0.9026 (p) cc_final: 0.8594 (t) REVERT: L 3 GLN cc_start: 0.8059 (pp30) cc_final: 0.7788 (pp30) REVERT: L 50 ASP cc_start: 0.8885 (t0) cc_final: 0.8600 (t0) REVERT: L 70 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7812 (pt0) REVERT: E 584 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8236 (mt-10) REVERT: E 652 GLN cc_start: 0.8355 (tp40) cc_final: 0.8011 (tp40) REVERT: E 657 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7375 (mm-30) REVERT: G 84 SER cc_start: 0.8684 (p) cc_final: 0.8382 (t) REVERT: J 50 ASP cc_start: 0.8521 (t0) cc_final: 0.8253 (t0) REVERT: J 70 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7934 (pt0) REVERT: D 320 THR cc_start: 0.9238 (m) cc_final: 0.8996 (p) REVERT: D 486 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.7455 (p90) REVERT: F 577 GLN cc_start: 0.8512 (tp-100) cc_final: 0.7978 (mm-40) REVERT: F 579 ARG cc_start: 0.8674 (mtm-85) cc_final: 0.8230 (ttm170) REVERT: F 584 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8002 (mt-10) REVERT: K 50 ASP cc_start: 0.8558 (t0) cc_final: 0.7893 (t0) REVERT: K 70 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8109 (pt0) outliers start: 53 outliers final: 44 residues processed: 323 average time/residue: 0.1812 time to fit residues: 86.9488 Evaluate side-chains 323 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 276 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 588 LYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 221 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN C 66 HIS J 24 GLN ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.099119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.081164 restraints weight = 44465.411| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.95 r_work: 0.3142 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21195 Z= 0.132 Angle : 0.639 12.132 29025 Z= 0.306 Chirality : 0.046 0.479 3543 Planarity : 0.004 0.039 3474 Dihedral : 5.664 52.224 5195 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.33 % Allowed : 16.64 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.50 (0.17), residues: 2343 helix: 1.65 (0.27), residues: 393 sheet: 0.34 (0.19), residues: 744 loop : -0.02 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 542 TYR 0.021 0.001 TYR K 49 PHE 0.020 0.001 PHE C 376 TRP 0.041 0.001 TRP G 71D HIS 0.008 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00294 (21027) covalent geometry : angle 0.59747 (28560) SS BOND : bond 0.00205 ( 39) SS BOND : angle 0.88172 ( 78) hydrogen bonds : bond 0.03431 ( 672) hydrogen bonds : angle 5.15303 ( 1809) link_ALPHA1-2 : bond 0.00148 ( 6) link_ALPHA1-2 : angle 1.62472 ( 18) link_ALPHA1-3 : bond 0.00649 ( 12) link_ALPHA1-3 : angle 1.57508 ( 36) link_ALPHA1-6 : bond 0.00433 ( 12) link_ALPHA1-6 : angle 2.07599 ( 36) link_BETA1-4 : bond 0.00576 ( 36) link_BETA1-4 : angle 1.60072 ( 108) link_BETA1-6 : bond 0.03676 ( 3) link_BETA1-6 : angle 4.41231 ( 9) link_NAG-ASN : bond 0.00344 ( 60) link_NAG-ASN : angle 2.16781 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 280 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 589 ASP cc_start: 0.8252 (m-30) cc_final: 0.7889 (m-30) REVERT: B 625 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.7720 (t0) REVERT: B 630 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7422 (mp0) REVERT: H 84 SER cc_start: 0.9012 (p) cc_final: 0.8575 (t) REVERT: L 3 GLN cc_start: 0.8121 (pp30) cc_final: 0.7846 (pp30) REVERT: L 50 ASP cc_start: 0.8867 (t0) cc_final: 0.8568 (t0) REVERT: L 70 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7821 (pt0) REVERT: E 584 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8214 (mt-10) REVERT: E 652 GLN cc_start: 0.8351 (tp40) cc_final: 0.8015 (tp40) REVERT: E 657 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7338 (mm-30) REVERT: G 84 SER cc_start: 0.8680 (p) cc_final: 0.8379 (t) REVERT: J 50 ASP cc_start: 0.8527 (t0) cc_final: 0.8241 (t0) REVERT: J 70 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7915 (pt0) REVERT: D 320 THR cc_start: 0.9204 (m) cc_final: 0.8961 (p) REVERT: D 486 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.7486 (p90) REVERT: F 577 GLN cc_start: 0.8511 (tp-100) cc_final: 0.7972 (mm-40) REVERT: F 579 ARG cc_start: 0.8710 (mtm-85) cc_final: 0.8254 (ttm170) REVERT: F 584 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7993 (mt-10) REVERT: K 50 ASP cc_start: 0.8539 (t0) cc_final: 0.7862 (t0) REVERT: K 70 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8084 (pt0) outliers start: 49 outliers final: 42 residues processed: 310 average time/residue: 0.1720 time to fit residues: 79.7947 Evaluate side-chains 318 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 273 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 588 LYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 620 THR Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 25 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 196 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 209 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN D 138 ASN ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.098149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.080075 restraints weight = 44382.536| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.02 r_work: 0.3102 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21195 Z= 0.151 Angle : 0.651 10.653 29025 Z= 0.313 Chirality : 0.046 0.395 3543 Planarity : 0.004 0.041 3474 Dihedral : 5.686 52.344 5195 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.47 % Allowed : 16.60 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.46 (0.17), residues: 2343 helix: 1.72 (0.27), residues: 393 sheet: 0.28 (0.19), residues: 750 loop : -0.07 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 542 TYR 0.021 0.001 TYR K 49 PHE 0.016 0.001 PHE C 376 TRP 0.044 0.001 TRP I 71D HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00343 (21027) covalent geometry : angle 0.61258 (28560) SS BOND : bond 0.00209 ( 39) SS BOND : angle 0.87752 ( 78) hydrogen bonds : bond 0.03545 ( 672) hydrogen bonds : angle 5.16915 ( 1809) link_ALPHA1-2 : bond 0.00124 ( 6) link_ALPHA1-2 : angle 1.68731 ( 18) link_ALPHA1-3 : bond 0.00594 ( 12) link_ALPHA1-3 : angle 1.60269 ( 36) link_ALPHA1-6 : bond 0.00394 ( 12) link_ALPHA1-6 : angle 2.04403 ( 36) link_BETA1-4 : bond 0.00568 ( 36) link_BETA1-4 : angle 1.60367 ( 108) link_BETA1-6 : bond 0.03549 ( 3) link_BETA1-6 : angle 4.24503 ( 9) link_NAG-ASN : bond 0.00311 ( 60) link_NAG-ASN : angle 2.08881 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4035.15 seconds wall clock time: 70 minutes 26.91 seconds (4226.91 seconds total)