Starting phenix.real_space_refine on Sat Jul 4 12:27:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gje_40088/07_2026/8gje_40088.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gje_40088/07_2026/8gje_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8gje_40088/07_2026/8gje_40088.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gje_40088/07_2026/8gje_40088.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gje_40088/07_2026/8gje_40088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gje_40088/07_2026/8gje_40088.map" model { file = "/net/cci-nas-00/data/ceres_data/8gje_40088/07_2026/8gje_40088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gje_40088/07_2026/8gje_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 4.43, per 1000 atoms: 0.21 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: 2.14 Conformation dependent library (CDL) restraints added in 784.1 milliseconds 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: 0.42 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: 3.96 Time building geometry restraints manager: 2.60 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 - 17.82: 11089 17.82 - 35.65: 383 35.65 - 53.47: 109 53.47 - 71.29: 56 71.29 - 89.12: 12 Dihedral angle restraints: 11649 sinusoidal: 4755 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 11646 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: 0.04 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: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.950 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 11.423 89.118 7086 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 are 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/Z covalent geometry : bond 0.00726 / 0.35 (21027) covalent geometry : angle 1.05825 / 0.56 (28560) SS BOND : bond 0.00590 / 0.36 ( 39) SS BOND : angle 1.87473 / 1.45 ( 78) hydrogen bonds : bond 0.14664 / 9.85 ( 672) hydrogen bonds : angle 7.76708 / 5.50 ( 1809) link_ALPHA1-2 : bond 0.00259 / 0.13 ( 6) link_ALPHA1-2 : angle 1.54179 / 1.02 ( 18) link_ALPHA1-3 : bond 0.00539 / 0.32 ( 12) link_ALPHA1-3 : angle 1.76908 / 1.28 ( 36) link_ALPHA1-6 : bond 0.01929 / 1.16 ( 12) link_ALPHA1-6 : angle 5.73661 / 4.75 ( 36) link_BETA1-4 : bond 0.01013 / 0.66 ( 36) link_BETA1-4 : angle 3.20007 / 2.12 ( 108) link_BETA1-6 : bond 0.04877 / 2.44 ( 3) link_BETA1-6 : angle 10.21223 / 7.21 ( 9) link_NAG-ASN : bond 0.00556 / 0.36 ( 60) link_NAG-ASN : angle 2.50702 / 1.74 ( 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 : 0.788 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: 0.1885 time to fit residues: 177.2500 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 : 0.836 ------------------------------------------------------------------------------- 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... 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 = 0.3691 r_free = 0.3691 target = 0.103103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.081922 restraints weight = 48464.831| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.63 r_work: 0.3257 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21195 Z= 0.200 Angle : 0.748 11.455 29025 Z= 0.363 Chirality : 0.048 0.273 3543 Planarity : 0.004 0.036 3474 Dihedral : 5.097 50.986 2578 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.00 % Allowed : 9.18 % Favored : 87.83 % 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 are not related in a simple way. whole: 0.88 (0.17), residues: 2343 helix: 1.59 (0.26), residues: 390 sheet: 0.60 (0.18), residues: 738 loop : 0.37 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 480 TYR 0.029 0.002 TYR L 49 PHE 0.019 0.002 PHE F 522 TRP 0.027 0.002 TRP B 571 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (21027) covalent geometry : angle 0.70739 / 0.36 (28560) SS BOND : bond 0.00242 / 0.13 ( 39) SS BOND : angle 1.10031 / 0.86 ( 78) hydrogen bonds : bond 0.04504 / 3.01 ( 672) hydrogen bonds : angle 6.31233 / 4.45 ( 1809) link_ALPHA1-2 : bond 0.00064 / 0.04 ( 6) link_ALPHA1-2 : angle 1.73747 / 1.11 ( 18) link_ALPHA1-3 : bond 0.00275 / 0.17 ( 12) link_ALPHA1-3 : angle 1.64598 / 1.17 ( 36) link_ALPHA1-6 : bond 0.00743 / 0.43 ( 12) link_ALPHA1-6 : angle 2.46086 / 1.88 ( 36) link_BETA1-4 : bond 0.00632 / 0.39 ( 36) link_BETA1-4 : angle 1.75196 / 1.17 ( 108) link_BETA1-6 : bond 0.02718 / 1.37 ( 3) link_BETA1-6 : angle 4.45831 / 2.93 ( 9) link_NAG-ASN : bond 0.00475 / 0.27 ( 60) link_NAG-ASN : angle 2.34190 / 1.75 ( 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 416 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 353 time to evaluate : 1.047 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: A 53 PHE cc_start: 0.7482 (m-80) cc_final: 0.7080 (m-10) REVERT: A 95 MET cc_start: 0.8633 (ptm) cc_final: 0.8330 (ptm) REVERT: A 150 MET cc_start: 0.8230 (mmm) cc_final: 0.7916 (tpp) REVERT: A 376 PHE cc_start: 0.7952 (m-80) cc_final: 0.7177 (m-80) REVERT: B 576 LEU cc_start: 0.9027 (tp) cc_final: 0.8820 (mm) REVERT: B 584 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8425 (mt-10) REVERT: B 588 LYS cc_start: 0.8726 (mttt) cc_final: 0.8315 (mttm) REVERT: B 589 ASP cc_start: 0.8523 (m-30) cc_final: 0.8137 (m-30) REVERT: B 625 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7811 (t0) REVERT: B 648 ASP cc_start: 0.8769 (m-30) cc_final: 0.8353 (t0) REVERT: H 28 ASN cc_start: 0.7878 (t0) cc_final: 0.7567 (t0) REVERT: H 82 LYS cc_start: 0.8939 (mttm) cc_final: 0.8536 (mtpp) REVERT: H 84 SER cc_start: 0.9143 (p) cc_final: 0.8699 (t) REVERT: L 11 LEU cc_start: 0.8661 (mt) cc_final: 0.8314 (mt) REVERT: L 50 ASP cc_start: 0.7311 (t0) cc_final: 0.6202 (t0) REVERT: L 70 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7735 (pt0) REVERT: C 98 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8451 (t0) REVERT: C 152 LYS cc_start: 0.9161 (mttt) cc_final: 0.8849 (mtmm) REVERT: C 185 LYS cc_start: 0.8683 (mttt) cc_final: 0.8178 (tptp) REVERT: C 302 ASN cc_start: 0.8104 (m110) cc_final: 0.7661 (m110) REVERT: C 482 GLU cc_start: 0.8295 (mp0) cc_final: 0.7826 (mp0) REVERT: C 486 TYR cc_start: 0.7698 (p90) cc_final: 0.7092 (p90) REVERT: E 652 GLN cc_start: 0.8693 (tp40) cc_final: 0.8367 (tp40) REVERT: E 657 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8349 (mm-30) REVERT: G 28 ASN cc_start: 0.8003 (t0) cc_final: 0.7666 (t0) REVERT: G 84 SER cc_start: 0.8825 (p) cc_final: 0.8379 (t) REVERT: J 50 ASP cc_start: 0.6998 (t0) cc_final: 0.6739 (t0) REVERT: J 70 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7814 (pt0) REVERT: J 82 ASP cc_start: 0.7351 (m-30) cc_final: 0.6902 (m-30) REVERT: D 53 PHE cc_start: 0.7644 (m-80) cc_final: 0.7195 (m-10) REVERT: D 95 MET cc_start: 0.8507 (ptm) cc_final: 0.8270 (ptm) REVERT: D 150 MET cc_start: 0.8122 (mmm) cc_final: 0.7840 (tpp) REVERT: D 486 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.7329 (p90) REVERT: F 576 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8706 (mm) REVERT: F 584 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8624 (mt-10) REVERT: F 589 ASP cc_start: 0.8781 (m-30) cc_final: 0.8572 (m-30) REVERT: F 625 ASN cc_start: 0.8323 (OUTLIER) cc_final: 0.8007 (t0) REVERT: K 50 ASP cc_start: 0.7227 (t0) cc_final: 0.6025 (t0) REVERT: K 62 PHE cc_start: 0.7389 (m-80) cc_final: 0.7153 (m-80) REVERT: K 70 GLU cc_start: 0.8517 (mt-10) cc_final: 0.7924 (pt0) outliers start: 63 outliers final: 35 residues processed: 401 average time/residue: 0.1684 time to fit residues: 101.2288 Evaluate side-chains 338 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 298 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 425 ASN 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 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 444 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 110 THR 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 486 TYR Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 576 LEU 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 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: 1.9990 chunk 122 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 chunk 169 optimal weight: 0.0030 chunk 216 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 HIS A 302 ASN L 24 GLN 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 I 28 ASN K 24 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.100229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.081828 restraints weight = 43812.698| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.98 r_work: 0.3154 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21195 Z= 0.140 Angle : 0.662 10.395 29025 Z= 0.318 Chirality : 0.045 0.271 3543 Planarity : 0.004 0.038 3474 Dihedral : 4.856 51.524 2578 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.90 % Allowed : 10.98 % Favored : 86.12 % 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 are not related in a simple way. whole: 0.82 (0.17), residues: 2343 helix: 1.74 (0.27), residues: 390 sheet: 0.45 (0.18), residues: 738 loop : 0.34 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 61 TYR 0.024 0.001 TYR L 49 PHE 0.016 0.001 PHE D 376 TRP 0.029 0.001 TRP I 71D HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (21027) covalent geometry : angle 0.62247 / 0.31 (28560) SS BOND : bond 0.00205 / 0.12 ( 39) SS BOND : angle 1.02096 / 0.81 ( 78) hydrogen bonds : bond 0.03975 / 2.66 ( 672) hydrogen bonds : angle 5.89449 / 4.16 ( 1809) link_ALPHA1-2 : bond 0.00127 / 0.06 ( 6) link_ALPHA1-2 : angle 1.61235 / 1.03 ( 18) link_ALPHA1-3 : bond 0.00447 / 0.27 ( 12) link_ALPHA1-3 : angle 1.38359 / 0.95 ( 36) link_ALPHA1-6 : bond 0.00799 / 0.46 ( 12) link_ALPHA1-6 : angle 2.51500 / 1.97 ( 36) link_BETA1-4 : bond 0.00580 / 0.36 ( 36) link_BETA1-4 : angle 1.52628 / 1.02 ( 108) link_BETA1-6 : bond 0.02431 / 1.21 ( 3) link_BETA1-6 : angle 3.47524 / 2.29 ( 9) link_NAG-ASN : bond 0.00369 / 0.20 ( 60) link_NAG-ASN : angle 2.17959 / 1.62 ( 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 377 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 316 time to evaluate : 0.734 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 150 MET cc_start: 0.8357 (mmm) cc_final: 0.8119 (tpp) REVERT: A 376 PHE cc_start: 0.7954 (m-80) cc_final: 0.7267 (m-80) REVERT: B 589 ASP cc_start: 0.8329 (m-30) cc_final: 0.8025 (m-30) REVERT: B 625 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7602 (t0) REVERT: B 630 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7413 (mp0) REVERT: B 648 ASP cc_start: 0.8424 (m-30) cc_final: 0.8153 (t0) REVERT: H 3 GLN cc_start: 0.8784 (tt0) cc_final: 0.8032 (mt0) REVERT: H 84 SER cc_start: 0.9148 (p) cc_final: 0.8713 (t) REVERT: L 3 GLN cc_start: 0.8247 (pp30) cc_final: 0.7947 (pp30) REVERT: L 24 GLN cc_start: 0.7868 (tt0) cc_final: 0.7555 (tt0) REVERT: L 50 ASP cc_start: 0.7825 (t0) cc_final: 0.7246 (t0) REVERT: L 70 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7814 (pt0) REVERT: L 77 ASN cc_start: 0.7638 (t0) cc_final: 0.7407 (t0) REVERT: C 98 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8578 (t0) REVERT: C 185 LYS cc_start: 0.8562 (mttt) cc_final: 0.8334 (tptp) REVERT: C 434 MET cc_start: 0.8904 (ttp) cc_final: 0.8623 (ttp) REVERT: E 579 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8420 (mpp80) REVERT: E 657 GLU cc_start: 0.8232 (mm-30) cc_final: 0.8020 (mm-30) REVERT: G 31 ASP cc_start: 0.8852 (m-30) cc_final: 0.8651 (m-30) REVERT: G 84 SER cc_start: 0.8707 (p) cc_final: 0.8324 (t) REVERT: J 50 ASP cc_start: 0.7556 (t0) cc_final: 0.7312 (t0) REVERT: J 70 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7945 (pt0) REVERT: D 53 PHE cc_start: 0.7801 (m-80) cc_final: 0.7296 (m-10) REVERT: D 150 MET cc_start: 0.8321 (mmm) cc_final: 0.8103 (tpp) REVERT: D 320 THR cc_start: 0.9211 (m) cc_final: 0.8989 (p) REVERT: D 425 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.7884 (p0) REVERT: D 486 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.7331 (p90) REVERT: F 575 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8797 (mm110) REVERT: F 589 ASP cc_start: 0.8529 (m-30) cc_final: 0.8318 (m-30) REVERT: F 625 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7741 (t0) REVERT: F 638 TYR cc_start: 0.8800 (m-10) cc_final: 0.8493 (m-10) REVERT: K 50 ASP cc_start: 0.7853 (t0) cc_final: 0.7550 (t0) REVERT: K 70 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8075 (pt0) outliers start: 61 outliers final: 39 residues processed: 355 average time/residue: 0.1660 time to fit residues: 88.9521 Evaluate side-chains 322 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 277 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 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 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 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 595 ILE 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 276 ASN Chi-restraints excluded: chain D residue 277 LEU 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 574 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 72 ASP Chi-restraints excluded: chain I residue 99 TYR 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: 0.2980 chunk 223 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 230 optimal weight: 10.0000 chunk 131 optimal weight: 0.4980 chunk 133 optimal weight: 0.8980 chunk 160 optimal weight: 0.0570 chunk 140 optimal weight: 1.9990 chunk 207 optimal weight: 0.0070 chunk 118 optimal weight: 3.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN C 130 HIS C 170 GLN C 425 ASN ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 ASN I 3 GLN K 24 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.101358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.083078 restraints weight = 43986.134| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.99 r_work: 0.3181 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 21195 Z= 0.107 Angle : 0.610 8.274 29025 Z= 0.293 Chirality : 0.044 0.271 3543 Planarity : 0.003 0.041 3474 Dihedral : 4.692 50.391 2578 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.62 % Allowed : 12.13 % 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 are not related in a simple way. whole: 0.78 (0.17), residues: 2343 helix: 1.60 (0.26), residues: 393 sheet: 0.47 (0.18), residues: 738 loop : 0.31 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 579 TYR 0.022 0.001 TYR L 49 PHE 0.010 0.001 PHE C 376 TRP 0.027 0.001 TRP I 71D HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (21027) covalent geometry : angle 0.57356 / 0.29 (28560) SS BOND : bond 0.00250 / 0.16 ( 39) SS BOND : angle 1.03322 / 0.80 ( 78) hydrogen bonds : bond 0.03538 / 2.37 ( 672) hydrogen bonds : angle 5.61426 / 3.96 ( 1809) link_ALPHA1-2 : bond 0.00183 / 0.09 ( 6) link_ALPHA1-2 : angle 1.54169 / 0.99 ( 18) link_ALPHA1-3 : bond 0.00460 / 0.27 ( 12) link_ALPHA1-3 : angle 1.37354 / 0.95 ( 36) link_ALPHA1-6 : bond 0.00778 / 0.45 ( 12) link_ALPHA1-6 : angle 2.25732 / 1.74 ( 36) link_BETA1-4 : bond 0.00564 / 0.35 ( 36) link_BETA1-4 : angle 1.44933 / 0.97 ( 108) link_BETA1-6 : bond 0.01884 / 0.94 ( 3) link_BETA1-6 : angle 2.47800 / 1.59 ( 9) link_NAG-ASN : bond 0.00349 / 0.19 ( 60) link_NAG-ASN : angle 2.02218 / 1.49 ( 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 368 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 313 time to evaluate : 0.865 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: A 95 MET cc_start: 0.8465 (ptm) cc_final: 0.8245 (ptm) REVERT: A 150 MET cc_start: 0.8336 (mmm) cc_final: 0.8136 (tpp) REVERT: A 376 PHE cc_start: 0.7958 (m-80) cc_final: 0.7331 (m-80) REVERT: B 589 ASP cc_start: 0.8272 (m-30) cc_final: 0.7943 (m-30) REVERT: B 625 ASN cc_start: 0.7849 (OUTLIER) cc_final: 0.7514 (t0) REVERT: B 648 ASP cc_start: 0.8397 (m-30) cc_final: 0.8006 (t0) REVERT: H 3 GLN cc_start: 0.8728 (tt0) cc_final: 0.7957 (mt0) REVERT: H 84 SER cc_start: 0.9111 (p) cc_final: 0.8684 (t) REVERT: L 3 GLN cc_start: 0.8272 (pp30) cc_final: 0.7957 (pp30) REVERT: L 50 ASP cc_start: 0.8145 (t0) cc_final: 0.7633 (t0) REVERT: L 70 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7875 (pt0) REVERT: E 579 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8415 (mpp80) REVERT: E 625 ASN cc_start: 0.7797 (OUTLIER) cc_final: 0.7595 (t0) REVERT: G 84 SER cc_start: 0.8694 (p) cc_final: 0.8233 (t) REVERT: J 70 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7937 (pt0) REVERT: J 104 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7955 (mp) REVERT: D 53 PHE cc_start: 0.7658 (m-80) cc_final: 0.7443 (m-10) REVERT: D 150 MET cc_start: 0.8370 (mmm) cc_final: 0.8135 (tpp) REVERT: D 209 ASN cc_start: 0.8787 (t0) cc_final: 0.8586 (t0) REVERT: D 320 THR cc_start: 0.9222 (m) cc_final: 0.8982 (p) REVERT: D 426 MET cc_start: 0.5923 (OUTLIER) cc_final: 0.5665 (mtm) REVERT: D 482 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8006 (mm-30) REVERT: D 486 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.7343 (p90) REVERT: F 575 GLN cc_start: 0.9020 (mt0) cc_final: 0.8791 (mm-40) REVERT: F 577 GLN cc_start: 0.8673 (tp-100) cc_final: 0.8124 (mm-40) REVERT: F 584 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8008 (mt-10) REVERT: F 625 ASN cc_start: 0.8010 (OUTLIER) cc_final: 0.7730 (t0) REVERT: F 630 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7437 (mp0) REVERT: K 70 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8074 (pt0) outliers start: 55 outliers final: 36 residues processed: 347 average time/residue: 0.1704 time to fit residues: 88.2081 Evaluate side-chains 324 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 280 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 120 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 625 ASN 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 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 579 ARG 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 104 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 426 MET 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 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 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: 6.9990 chunk 186 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** K 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.095929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.077463 restraints weight = 44346.941| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.98 r_work: 0.3058 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 21195 Z= 0.246 Angle : 0.699 9.381 29025 Z= 0.339 Chirality : 0.047 0.273 3543 Planarity : 0.004 0.049 3474 Dihedral : 4.929 51.382 2578 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.19 % Allowed : 13.46 % Favored : 83.36 % 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 are not related in a simple way. whole: 0.51 (0.17), residues: 2343 helix: 1.60 (0.27), residues: 393 sheet: 0.26 (0.18), residues: 741 loop : 0.09 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 40 TYR 0.018 0.002 TYR K 49 PHE 0.020 0.002 PHE A 53 TRP 0.030 0.002 TRP I 71D HIS 0.008 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.25 (21027) covalent geometry : angle 0.66480 / 0.33 (28560) SS BOND : bond 0.00252 / 0.17 ( 39) SS BOND : angle 1.08749 / 0.82 ( 78) hydrogen bonds : bond 0.04206 / 2.80 ( 672) hydrogen bonds : angle 5.57757 / 3.95 ( 1809) link_ALPHA1-2 : bond 0.00342 / 0.20 ( 6) link_ALPHA1-2 : angle 1.88047 / 1.24 ( 18) link_ALPHA1-3 : bond 0.00325 / 0.19 ( 12) link_ALPHA1-3 : angle 1.61364 / 1.12 ( 36) link_ALPHA1-6 : bond 0.00668 / 0.38 ( 12) link_ALPHA1-6 : angle 2.27353 / 1.71 ( 36) link_BETA1-4 : bond 0.00531 / 0.33 ( 36) link_BETA1-4 : angle 1.57916 / 1.06 ( 108) link_BETA1-6 : bond 0.02046 / 1.02 ( 3) link_BETA1-6 : angle 2.66552 / 1.84 ( 9) link_NAG-ASN : bond 0.00332 / 0.21 ( 60) link_NAG-ASN : angle 2.08041 / 1.51 ( 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 353 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 286 time to evaluate : 0.843 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 150 MET cc_start: 0.8472 (mmm) cc_final: 0.8166 (tpp) REVERT: A 376 PHE cc_start: 0.8180 (m-80) cc_final: 0.7474 (m-80) REVERT: A 425 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8230 (p0) REVERT: B 589 ASP cc_start: 0.8360 (m-30) cc_final: 0.8133 (m-30) REVERT: B 625 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7547 (t0) REVERT: B 630 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7514 (mp0) REVERT: B 648 ASP cc_start: 0.8409 (m-30) cc_final: 0.8044 (t0) REVERT: H 3 GLN cc_start: 0.8756 (tt0) cc_final: 0.7950 (mt0) REVERT: H 84 SER cc_start: 0.9117 (p) cc_final: 0.8710 (t) REVERT: L 3 GLN cc_start: 0.8181 (pp30) cc_final: 0.7903 (pp30) REVERT: L 50 ASP cc_start: 0.8830 (t0) cc_final: 0.8375 (t0) REVERT: L 70 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7833 (pt0) REVERT: C 302 ASN cc_start: 0.8014 (m110) cc_final: 0.7576 (m110) REVERT: C 425 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.7906 (p0) REVERT: E 579 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8546 (mpp80) REVERT: E 625 ASN cc_start: 0.7857 (OUTLIER) cc_final: 0.7545 (t0) REVERT: G 84 SER cc_start: 0.8834 (p) cc_final: 0.8547 (t) REVERT: J 50 ASP cc_start: 0.8646 (t0) cc_final: 0.8267 (t0) REVERT: J 70 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7909 (pt0) REVERT: D 53 PHE cc_start: 0.7772 (m-80) cc_final: 0.7449 (m-10) REVERT: D 150 MET cc_start: 0.8376 (mmm) cc_final: 0.8093 (tpt) REVERT: D 209 ASN cc_start: 0.8874 (t0) cc_final: 0.8635 (t0) REVERT: D 486 TYR cc_start: 0.8204 (OUTLIER) cc_final: 0.7559 (p90) REVERT: F 575 GLN cc_start: 0.8986 (mt0) cc_final: 0.8646 (mm-40) REVERT: F 577 GLN cc_start: 0.8770 (tp-100) cc_final: 0.8265 (mm-40) REVERT: F 584 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8088 (mt-10) REVERT: F 630 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7609 (mp0) REVERT: F 651 THR cc_start: 0.7976 (m) cc_final: 0.7670 (p) REVERT: F 652 GLN cc_start: 0.8672 (tt0) cc_final: 0.8456 (tt0) REVERT: K 50 ASP cc_start: 0.8501 (t0) cc_final: 0.8033 (t0) REVERT: K 70 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8051 (pt0) outliers start: 67 outliers final: 46 residues processed: 329 average time/residue: 0.1624 time to fit residues: 81.3571 Evaluate side-chains 316 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 264 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 425 ASN Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 619 GLN 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 60 SER 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 425 ASN 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 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 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 17 SER Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain K residue 22 THR 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: 0.0370 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 129 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 191 optimal weight: 0.0000 chunk 136 optimal weight: 0.0570 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** K 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.099284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.081015 restraints weight = 43681.663| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.98 r_work: 0.3145 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21195 Z= 0.107 Angle : 0.610 11.260 29025 Z= 0.293 Chirality : 0.044 0.310 3543 Planarity : 0.003 0.037 3474 Dihedral : 4.633 51.193 2576 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.85 % Allowed : 14.69 % Favored : 82.45 % 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 are not related in a simple way. whole: 0.58 (0.17), residues: 2343 helix: 1.70 (0.27), residues: 396 sheet: 0.32 (0.18), residues: 735 loop : 0.09 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 94 TYR 0.022 0.001 TYR J 49 PHE 0.020 0.001 PHE H 73 TRP 0.040 0.001 TRP H 71D HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (21027) covalent geometry : angle 0.57500 / 0.29 (28560) SS BOND : bond 0.00224 / 0.15 ( 39) SS BOND : angle 0.93675 / 0.74 ( 78) hydrogen bonds : bond 0.03409 / 2.29 ( 672) hydrogen bonds : angle 5.36667 / 3.80 ( 1809) link_ALPHA1-2 : bond 0.00254 / 0.12 ( 6) link_ALPHA1-2 : angle 1.54586 / 1.01 ( 18) link_ALPHA1-3 : bond 0.00496 / 0.30 ( 12) link_ALPHA1-3 : angle 1.32585 / 0.91 ( 36) link_ALPHA1-6 : bond 0.00786 / 0.45 ( 12) link_ALPHA1-6 : angle 2.06623 / 1.58 ( 36) link_BETA1-4 : bond 0.00517 / 0.32 ( 36) link_BETA1-4 : angle 1.37454 / 0.93 ( 108) link_BETA1-6 : bond 0.01864 / 0.93 ( 3) link_BETA1-6 : angle 2.51423 / 1.72 ( 9) link_NAG-ASN : bond 0.00358 / 0.20 ( 60) link_NAG-ASN : angle 2.06043 / 1.55 ( 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: 60 poor density : 307 time to evaluate : 0.795 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: 0.8289 (mmm) cc_final: 0.8045 (tpp) REVERT: A 376 PHE cc_start: 0.8089 (m-80) cc_final: 0.7380 (m-80) REVERT: B 577 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8055 (tm-30) REVERT: B 589 ASP cc_start: 0.8247 (m-30) cc_final: 0.7935 (m-30) REVERT: B 625 ASN cc_start: 0.7865 (OUTLIER) cc_final: 0.7497 (t0) REVERT: B 630 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7351 (mp0) REVERT: B 648 ASP cc_start: 0.8294 (m-30) cc_final: 0.7973 (t0) REVERT: H 3 GLN cc_start: 0.8708 (tt0) cc_final: 0.7985 (mt0) REVERT: H 84 SER cc_start: 0.9083 (p) cc_final: 0.8630 (t) REVERT: L 3 GLN cc_start: 0.8155 (pp30) cc_final: 0.7866 (pp30) REVERT: L 50 ASP cc_start: 0.8692 (t0) cc_final: 0.8104 (t0) REVERT: L 53 LYS cc_start: 0.8185 (mttm) cc_final: 0.7857 (mttm) REVERT: L 70 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7831 (pt0) REVERT: C 425 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.7769 (p0) REVERT: E 579 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8493 (mpp80) REVERT: E 625 ASN cc_start: 0.7702 (OUTLIER) cc_final: 0.7423 (t0) REVERT: G 84 SER cc_start: 0.8788 (p) cc_final: 0.8517 (t) REVERT: J 50 ASP cc_start: 0.8498 (t0) cc_final: 0.8204 (t0) REVERT: J 70 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7908 (pt0) REVERT: D 53 PHE cc_start: 0.7525 (m-80) cc_final: 0.7006 (m-10) REVERT: D 150 MET cc_start: 0.8302 (mmm) cc_final: 0.7986 (tpt) REVERT: D 209 ASN cc_start: 0.8872 (t0) cc_final: 0.8532 (t0) REVERT: D 217 TYR cc_start: 0.9105 (m-80) cc_final: 0.8716 (m-80) REVERT: D 486 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.7527 (p90) REVERT: F 575 GLN cc_start: 0.8822 (mt0) cc_final: 0.8501 (mm-40) REVERT: F 577 GLN cc_start: 0.8720 (tp-100) cc_final: 0.8380 (mm-40) REVERT: F 584 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7950 (mt-10) REVERT: I 38 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7093 (ttp80) REVERT: K 62 PHE cc_start: 0.7225 (m-80) cc_final: 0.6989 (m-80) REVERT: K 70 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8029 (pt0) outliers start: 60 outliers final: 39 residues processed: 341 average time/residue: 0.1646 time to fit residues: 84.9565 Evaluate side-chains 317 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 271 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 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 72 ASP Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 425 ASN 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 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 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 320 THR 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 620 THR Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain I residue 11 VAL 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: 1.9990 chunk 207 optimal weight: 0.0270 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.0050 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 0.0970 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 158 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 overall best weight: 0.3050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 139 ASN J 24 GLN D 302 ASN ** 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 = 0.3607 r_free = 0.3607 target = 0.100137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.081942 restraints weight = 44066.328| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.98 r_work: 0.3156 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21195 Z= 0.103 Angle : 0.604 13.343 29025 Z= 0.289 Chirality : 0.044 0.378 3543 Planarity : 0.003 0.044 3474 Dihedral : 4.500 52.059 2576 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.66 % Allowed : 15.45 % Favored : 81.88 % 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 are not related in a simple way. whole: 0.55 (0.17), residues: 2343 helix: 1.63 (0.26), residues: 396 sheet: 0.33 (0.18), residues: 741 loop : 0.08 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 542 TYR 0.024 0.001 TYR L 49 PHE 0.014 0.001 PHE D 376 TRP 0.034 0.001 TRP I 71D HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (21027) covalent geometry : angle 0.56858 / 0.28 (28560) SS BOND : bond 0.00203 / 0.13 ( 39) SS BOND : angle 0.86957 / 0.69 ( 78) hydrogen bonds : bond 0.03307 / 2.23 ( 672) hydrogen bonds : angle 5.23967 / 3.71 ( 1809) link_ALPHA1-2 : bond 0.00173 / 0.08 ( 6) link_ALPHA1-2 : angle 1.53989 / 1.00 ( 18) link_ALPHA1-3 : bond 0.00457 / 0.27 ( 12) link_ALPHA1-3 : angle 1.37161 / 0.95 ( 36) link_ALPHA1-6 : bond 0.00741 / 0.43 ( 12) link_ALPHA1-6 : angle 1.95755 / 1.47 ( 36) link_BETA1-4 : bond 0.00529 / 0.33 ( 36) link_BETA1-4 : angle 1.37060 / 0.92 ( 108) link_BETA1-6 : bond 0.01785 / 0.89 ( 3) link_BETA1-6 : angle 2.46722 / 1.69 ( 9) link_NAG-ASN : bond 0.00329 / 0.18 ( 60) link_NAG-ASN : angle 2.07772 / 1.57 ( 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 350 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 294 time to evaluate : 0.810 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 150 MET cc_start: 0.8186 (mmm) cc_final: 0.7973 (tpp) REVERT: A 376 PHE cc_start: 0.8030 (m-80) cc_final: 0.7350 (m-80) REVERT: B 589 ASP cc_start: 0.8266 (m-30) cc_final: 0.7932 (m-30) REVERT: B 625 ASN cc_start: 0.7828 (OUTLIER) cc_final: 0.7464 (t0) REVERT: B 630 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7314 (mp0) REVERT: B 648 ASP cc_start: 0.8198 (m-30) cc_final: 0.7935 (t0) REVERT: H 3 GLN cc_start: 0.8675 (tt0) cc_final: 0.7955 (mt0) REVERT: H 84 SER cc_start: 0.9068 (p) cc_final: 0.8625 (t) REVERT: L 3 GLN cc_start: 0.8249 (pp30) cc_final: 0.7987 (pp30) REVERT: L 50 ASP cc_start: 0.8713 (t0) cc_final: 0.8290 (t0) REVERT: L 53 LYS cc_start: 0.8110 (mttm) cc_final: 0.7860 (mttm) REVERT: L 70 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7844 (pt0) REVERT: C 259 LEU cc_start: 0.8318 (mt) cc_final: 0.8107 (mt) REVERT: C 425 ASN cc_start: 0.8291 (OUTLIER) cc_final: 0.7707 (p0) REVERT: E 543 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8336 (tm-30) REVERT: E 625 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7358 (t0) REVERT: E 629 MET cc_start: 0.8874 (tpp) cc_final: 0.8624 (tpp) REVERT: G 84 SER cc_start: 0.8762 (p) cc_final: 0.8482 (t) REVERT: J 50 ASP cc_start: 0.8495 (t0) cc_final: 0.8168 (t0) REVERT: J 70 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7903 (pt0) REVERT: J 77 ASN cc_start: 0.7783 (t0) cc_final: 0.7572 (t0) REVERT: D 53 PHE cc_start: 0.7453 (m-80) cc_final: 0.6959 (m-10) REVERT: D 209 ASN cc_start: 0.8890 (t0) cc_final: 0.8592 (t0) REVERT: D 217 TYR cc_start: 0.9109 (m-80) cc_final: 0.8744 (m-80) REVERT: D 486 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.7518 (p90) REVERT: F 575 GLN cc_start: 0.8882 (mt0) cc_final: 0.8518 (mm-40) REVERT: F 577 GLN cc_start: 0.8757 (tp-100) cc_final: 0.8339 (mm-40) REVERT: F 584 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7963 (mt-10) REVERT: F 626 MET cc_start: 0.7772 (ttt) cc_final: 0.7430 (ttt) REVERT: F 630 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7245 (mp0) REVERT: F 638 TYR cc_start: 0.8687 (m-10) cc_final: 0.8475 (m-10) REVERT: K 70 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8069 (pt0) outliers start: 56 outliers final: 40 residues processed: 329 average time/residue: 0.1658 time to fit residues: 82.2257 Evaluate side-chains 316 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 272 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 595 ILE 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 L residue 63 SER 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 165 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 425 ASN Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 545 LEU 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 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 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 68 SER Chi-restraints excluded: chain I residue 99 TYR 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: 1.9990 chunk 81 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS C 139 ASN E 619 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.098190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.079871 restraints weight = 43924.973| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.99 r_work: 0.3134 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21195 Z= 0.126 Angle : 0.605 11.106 29025 Z= 0.292 Chirality : 0.044 0.330 3543 Planarity : 0.003 0.041 3474 Dihedral : 4.511 51.998 2576 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.81 % Allowed : 15.50 % Favored : 81.69 % 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 are not related in a simple way. whole: 0.58 (0.17), residues: 2343 helix: 1.78 (0.27), residues: 393 sheet: 0.34 (0.19), residues: 735 loop : 0.04 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 542 TYR 0.020 0.001 TYR K 49 PHE 0.016 0.001 PHE C 376 TRP 0.034 0.001 TRP G 71D HIS 0.006 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (21027) covalent geometry : angle 0.57381 / 0.29 (28560) SS BOND : bond 0.00341 / 0.26 ( 39) SS BOND : angle 0.87255 / 0.68 ( 78) hydrogen bonds : bond 0.03445 / 2.33 ( 672) hydrogen bonds : angle 5.19076 / 3.68 ( 1809) link_ALPHA1-2 : bond 0.00153 / 0.07 ( 6) link_ALPHA1-2 : angle 1.60033 / 1.05 ( 18) link_ALPHA1-3 : bond 0.00404 / 0.24 ( 12) link_ALPHA1-3 : angle 1.42286 / 0.98 ( 36) link_ALPHA1-6 : bond 0.00674 / 0.39 ( 12) link_ALPHA1-6 : angle 1.93223 / 1.44 ( 36) link_BETA1-4 : bond 0.00500 / 0.31 ( 36) link_BETA1-4 : angle 1.37837 / 0.93 ( 108) link_BETA1-6 : bond 0.01666 / 0.84 ( 3) link_BETA1-6 : angle 2.35687 / 1.60 ( 9) link_NAG-ASN : bond 0.00310 / 0.18 ( 60) link_NAG-ASN : angle 1.89477 / 1.41 ( 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 345 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 286 time to evaluate : 0.863 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 34 MET cc_start: 0.8034 (mmp) cc_final: 0.7598 (mmp) REVERT: A 95 MET cc_start: 0.8502 (ptm) cc_final: 0.8296 (ptm) REVERT: A 150 MET cc_start: 0.8175 (mmm) cc_final: 0.7966 (tpp) REVERT: B 589 ASP cc_start: 0.8271 (m-30) cc_final: 0.7888 (m-30) REVERT: B 625 ASN cc_start: 0.7839 (OUTLIER) cc_final: 0.7497 (t0) REVERT: B 648 ASP cc_start: 0.7969 (m-30) cc_final: 0.7738 (t0) REVERT: H 3 GLN cc_start: 0.8672 (tt0) cc_final: 0.7938 (mt0) REVERT: H 84 SER cc_start: 0.9049 (p) cc_final: 0.8628 (t) REVERT: L 3 GLN cc_start: 0.8185 (pp30) cc_final: 0.7922 (pp30) REVERT: L 50 ASP cc_start: 0.8770 (t0) cc_final: 0.8349 (t0) REVERT: L 53 LYS cc_start: 0.8215 (mttm) cc_final: 0.7956 (mttm) REVERT: L 70 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7822 (pt0) REVERT: C 302 ASN cc_start: 0.7843 (m110) cc_final: 0.7396 (m-40) REVERT: C 425 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.7851 (p0) REVERT: E 625 ASN cc_start: 0.7656 (OUTLIER) cc_final: 0.7379 (t0) REVERT: E 629 MET cc_start: 0.8915 (tpp) cc_final: 0.8709 (tpp) REVERT: G 84 SER cc_start: 0.8766 (p) cc_final: 0.8475 (t) REVERT: J 50 ASP cc_start: 0.8548 (t0) cc_final: 0.8277 (t0) REVERT: J 70 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7917 (pt0) REVERT: J 77 ASN cc_start: 0.7950 (t0) cc_final: 0.7725 (t0) REVERT: D 53 PHE cc_start: 0.7498 (m-80) cc_final: 0.6958 (m-10) REVERT: D 209 ASN cc_start: 0.8897 (t0) cc_final: 0.8607 (t0) REVERT: D 217 TYR cc_start: 0.9172 (m-80) cc_final: 0.8840 (m-80) REVERT: D 486 TYR cc_start: 0.8135 (OUTLIER) cc_final: 0.7551 (p90) REVERT: F 575 GLN cc_start: 0.8847 (mt0) cc_final: 0.8550 (mm-40) REVERT: F 577 GLN cc_start: 0.8798 (tp-100) cc_final: 0.8319 (mm-40) REVERT: F 584 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7998 (mt-10) REVERT: F 626 MET cc_start: 0.7898 (ttt) cc_final: 0.7662 (ttt) REVERT: F 630 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7361 (mp0) REVERT: F 652 GLN cc_start: 0.8663 (tt0) cc_final: 0.8416 (tt0) REVERT: K 50 ASP cc_start: 0.8569 (t0) cc_final: 0.7896 (t0) REVERT: K 70 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8013 (pt0) outliers start: 59 outliers final: 46 residues processed: 322 average time/residue: 0.1677 time to fit residues: 81.4817 Evaluate side-chains 323 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 273 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 A residue 426 MET Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 620 THR 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 L residue 63 SER 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 165 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 425 ASN 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 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 72 ASP Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 80 MET 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 595 ILE Chi-restraints excluded: chain F residue 620 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 640 ASP 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 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.4980 chunk 142 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 185 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 GLN B 653 GLN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3543 r_free = 0.3543 target = 0.096289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.078167 restraints weight = 44469.431| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.97 r_work: 0.3069 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21195 Z= 0.206 Angle : 0.673 11.749 29025 Z= 0.326 Chirality : 0.046 0.274 3543 Planarity : 0.004 0.045 3474 Dihedral : 4.736 51.086 2576 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.85 % Allowed : 16.21 % 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 are not related in a simple way. whole: 0.38 (0.17), residues: 2343 helix: 1.68 (0.27), residues: 393 sheet: 0.21 (0.19), residues: 750 loop : -0.11 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 542 TYR 0.026 0.002 TYR L 49 PHE 0.014 0.002 PHE C 376 TRP 0.037 0.002 TRP G 71D HIS 0.012 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 (21027) covalent geometry : angle 0.64165 / 0.32 (28560) SS BOND : bond 0.00252 / 0.18 ( 39) SS BOND : angle 0.91185 / 0.69 ( 78) hydrogen bonds : bond 0.03880 / 2.62 ( 672) hydrogen bonds : angle 5.30598 / 3.77 ( 1809) link_ALPHA1-2 : bond 0.00274 / 0.16 ( 6) link_ALPHA1-2 : angle 1.79987 / 1.19 ( 18) link_ALPHA1-3 : bond 0.00344 / 0.21 ( 12) link_ALPHA1-3 : angle 1.56580 / 1.07 ( 36) link_ALPHA1-6 : bond 0.00603 / 0.34 ( 12) link_ALPHA1-6 : angle 1.99544 / 1.48 ( 36) link_BETA1-4 : bond 0.00483 / 0.30 ( 36) link_BETA1-4 : angle 1.45980 / 0.99 ( 108) link_BETA1-6 : bond 0.01567 / 0.79 ( 3) link_BETA1-6 : angle 2.32176 / 1.56 ( 9) link_NAG-ASN : bond 0.00292 / 0.18 ( 60) link_NAG-ASN : angle 2.04321 / 1.51 ( 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 341 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 281 time to evaluate : 0.744 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 95 MET cc_start: 0.8616 (ptm) cc_final: 0.8414 (ptm) REVERT: A 150 MET cc_start: 0.8272 (mmm) cc_final: 0.8059 (tpp) REVERT: A 303 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8505 (p) REVERT: B 589 ASP cc_start: 0.8382 (m-30) cc_final: 0.8054 (m-30) REVERT: B 625 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7541 (t0) REVERT: B 630 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7464 (mp0) REVERT: B 648 ASP cc_start: 0.8138 (m-30) cc_final: 0.7872 (t0) REVERT: H 3 GLN cc_start: 0.8698 (tt0) cc_final: 0.7951 (mt0) REVERT: H 84 SER cc_start: 0.9060 (p) cc_final: 0.8630 (t) REVERT: L 3 GLN cc_start: 0.8236 (pp30) cc_final: 0.7969 (pp30) REVERT: L 50 ASP cc_start: 0.8764 (t0) cc_final: 0.8451 (t0) REVERT: L 53 LYS cc_start: 0.8206 (mttm) cc_final: 0.7966 (mttm) REVERT: L 70 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7778 (pt0) REVERT: C 98 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8542 (m-40) REVERT: C 302 ASN cc_start: 0.8125 (m110) cc_final: 0.7757 (m110) REVERT: C 425 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.7940 (p0) REVERT: E 625 ASN cc_start: 0.7637 (OUTLIER) cc_final: 0.7336 (t0) REVERT: G 84 SER cc_start: 0.8773 (p) cc_final: 0.8480 (t) REVERT: J 50 ASP cc_start: 0.8717 (t0) cc_final: 0.8499 (t0) REVERT: J 70 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7885 (pt0) REVERT: D 53 PHE cc_start: 0.7721 (m-80) cc_final: 0.7383 (m-10) REVERT: D 209 ASN cc_start: 0.8998 (t0) cc_final: 0.8786 (t0) REVERT: D 486 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.7529 (p90) REVERT: F 575 GLN cc_start: 0.8876 (mt0) cc_final: 0.8564 (mm-40) REVERT: F 577 GLN cc_start: 0.8852 (tp-100) cc_final: 0.8376 (mm-40) REVERT: F 584 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8051 (mt-10) REVERT: F 626 MET cc_start: 0.8105 (ttt) cc_final: 0.7746 (ttt) REVERT: F 630 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7365 (mp0) REVERT: I 38 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7376 (ttp80) REVERT: K 50 ASP cc_start: 0.8723 (t0) cc_final: 0.8062 (t0) REVERT: K 70 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8033 (pt0) outliers start: 60 outliers final: 45 residues processed: 324 average time/residue: 0.1706 time to fit residues: 82.8434 Evaluate side-chains 319 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 267 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 303 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 619 GLN Chi-restraints excluded: chain B residue 620 THR 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 L residue 63 SER 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 C residue 425 ASN Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 545 LEU 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 74 ASP 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 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 620 THR 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 38 ARG Chi-restraints excluded: chain I residue 68 SER 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: 4.9990 chunk 75 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 191 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 619 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.097138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.079074 restraints weight = 44225.099| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.95 r_work: 0.3113 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21195 Z= 0.130 Angle : 0.632 12.101 29025 Z= 0.307 Chirality : 0.045 0.270 3543 Planarity : 0.004 0.040 3474 Dihedral : 4.649 50.736 2576 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.71 % Allowed : 16.60 % Favored : 80.69 % 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 are not related in a simple way. whole: 0.42 (0.17), residues: 2343 helix: 1.74 (0.27), residues: 396 sheet: 0.23 (0.19), residues: 750 loop : -0.10 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 542 TYR 0.022 0.001 TYR K 49 PHE 0.018 0.001 PHE C 376 TRP 0.042 0.001 TRP H 71D HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (21027) covalent geometry : angle 0.60308 / 0.30 (28560) SS BOND : bond 0.00185 / 0.12 ( 39) SS BOND : angle 0.87922 / 0.68 ( 78) hydrogen bonds : bond 0.03551 / 2.40 ( 672) hydrogen bonds : angle 5.24910 / 3.73 ( 1809) link_ALPHA1-2 : bond 0.00154 / 0.07 ( 6) link_ALPHA1-2 : angle 1.63272 / 1.07 ( 18) link_ALPHA1-3 : bond 0.00418 / 0.25 ( 12) link_ALPHA1-3 : angle 1.41749 / 0.97 ( 36) link_ALPHA1-6 : bond 0.00642 / 0.37 ( 12) link_ALPHA1-6 : angle 1.91543 / 1.43 ( 36) link_BETA1-4 : bond 0.00491 / 0.31 ( 36) link_BETA1-4 : angle 1.35593 / 0.92 ( 108) link_BETA1-6 : bond 0.01687 / 0.85 ( 3) link_BETA1-6 : angle 2.38119 / 1.63 ( 9) link_NAG-ASN : bond 0.00292 / 0.16 ( 60) link_NAG-ASN : angle 1.91198 / 1.42 ( 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 333 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 276 time to evaluate : 0.795 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 95 MET cc_start: 0.8522 (ptm) cc_final: 0.8308 (ptm) REVERT: A 150 MET cc_start: 0.8167 (mmm) cc_final: 0.7966 (tpp) REVERT: A 303 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8487 (p) REVERT: B 589 ASP cc_start: 0.8322 (m-30) cc_final: 0.8009 (m-30) REVERT: B 625 ASN cc_start: 0.7792 (OUTLIER) cc_final: 0.7492 (t0) REVERT: B 630 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7446 (mp0) REVERT: H 3 GLN cc_start: 0.8648 (tt0) cc_final: 0.7940 (mt0) REVERT: H 84 SER cc_start: 0.9089 (p) cc_final: 0.8635 (t) REVERT: L 3 GLN cc_start: 0.8207 (pp30) cc_final: 0.7967 (pp30) REVERT: L 50 ASP cc_start: 0.8719 (t0) cc_final: 0.8399 (t0) REVERT: L 53 LYS cc_start: 0.8145 (mttm) cc_final: 0.7901 (mttm) REVERT: L 70 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7787 (pt0) REVERT: C 302 ASN cc_start: 0.8087 (m110) cc_final: 0.7733 (m110) REVERT: C 425 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.7799 (p0) REVERT: E 625 ASN cc_start: 0.7648 (OUTLIER) cc_final: 0.7344 (t0) REVERT: G 84 SER cc_start: 0.8729 (p) cc_final: 0.8443 (t) REVERT: J 50 ASP cc_start: 0.8639 (t0) cc_final: 0.8411 (t0) REVERT: J 70 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7897 (pt0) REVERT: D 53 PHE cc_start: 0.7632 (m-80) cc_final: 0.7317 (m-10) REVERT: D 486 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.7357 (p90) REVERT: F 575 GLN cc_start: 0.8946 (mt0) cc_final: 0.8559 (mm-40) REVERT: F 577 GLN cc_start: 0.8761 (tp-100) cc_final: 0.8286 (mm-40) REVERT: F 584 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8002 (mt-10) REVERT: F 626 MET cc_start: 0.7944 (ttt) cc_final: 0.7485 (ttt) REVERT: I 38 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7235 (ttp80) REVERT: K 50 ASP cc_start: 0.8589 (t0) cc_final: 0.8122 (t0) REVERT: K 70 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8084 (pt0) outliers start: 57 outliers final: 44 residues processed: 316 average time/residue: 0.1656 time to fit residues: 79.1698 Evaluate side-chains 318 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 268 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 303 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 620 THR 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 L residue 63 SER Chi-restraints excluded: chain C residue 69 TRP 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 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 425 ASN 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 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 110 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 595 ILE Chi-restraints excluded: chain F residue 620 THR Chi-restraints excluded: chain F residue 636 SER 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 17 ASP Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 25 optimal weight: 0.7980 chunk 72 optimal weight: 0.0970 chunk 196 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 209 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 173 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** K 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.098055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.080702 restraints weight = 44504.452| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.87 r_work: 0.3092 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 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 0.038 21195 Z= 0.150 Angle : 0.640 12.043 29025 Z= 0.312 Chirality : 0.045 0.268 3543 Planarity : 0.004 0.042 3474 Dihedral : 4.634 50.259 2576 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.52 % Allowed : 17.02 % Favored : 80.46 % 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 are not related in a simple way. whole: 0.38 (0.18), residues: 2343 helix: 1.67 (0.27), residues: 396 sheet: 0.20 (0.19), residues: 750 loop : -0.10 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 542 TYR 0.022 0.001 TYR L 49 PHE 0.018 0.001 PHE C 376 TRP 0.036 0.001 TRP G 71D HIS 0.008 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (21027) covalent geometry : angle 0.61123 / 0.31 (28560) SS BOND : bond 0.00200 / 0.13 ( 39) SS BOND : angle 0.86977 / 0.67 ( 78) hydrogen bonds : bond 0.03616 / 2.43 ( 672) hydrogen bonds : angle 5.20752 / 3.71 ( 1809) link_ALPHA1-2 : bond 0.00164 / 0.08 ( 6) link_ALPHA1-2 : angle 1.65291 / 1.08 ( 18) link_ALPHA1-3 : bond 0.00391 / 0.23 ( 12) link_ALPHA1-3 : angle 1.44362 / 0.99 ( 36) link_ALPHA1-6 : bond 0.00618 / 0.35 ( 12) link_ALPHA1-6 : angle 1.88318 / 1.39 ( 36) link_BETA1-4 : bond 0.00477 / 0.30 ( 36) link_BETA1-4 : angle 1.36919 / 0.93 ( 108) link_BETA1-6 : bond 0.01578 / 0.79 ( 3) link_BETA1-6 : angle 2.31470 / 1.57 ( 9) link_NAG-ASN : bond 0.00276 / 0.16 ( 60) link_NAG-ASN : angle 1.89045 / 1.41 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4186.89 seconds wall clock time: 73 minutes 8.94 seconds (4388.94 seconds total)