Starting phenix.real_space_refine on Wed Jun 18 05:51:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gje_40088/06_2025/8gje_40088.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gje_40088/06_2025/8gje_40088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gje_40088/06_2025/8gje_40088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gje_40088/06_2025/8gje_40088.map" model { file = "/net/cci-nas-00/data/ceres_data/8gje_40088/06_2025/8gje_40088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gje_40088/06_2025/8gje_40088.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20613 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3569 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 1 Chain: "B" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 975 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "H" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "L" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain: "C" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3569 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 1 Chain: "E" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 975 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "G" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "J" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain: "D" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3569 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 1 Chain: "F" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 975 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "I" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "K" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.96, per 1000 atoms: 0.58 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: 6.55 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 3.06 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: 7.53 Time building geometry restraints manager: 7.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6308 1.34 - 1.46: 5422 1.46 - 1.59: 9126 1.59 - 1.71: 3 1.71 - 1.84: 168 Bond restraints: 21027 Sorted by residual: bond pdb=" C1 FUC g 4 " pdb=" C2 FUC g 4 " ideal model delta sigma weight residual 1.528 1.657 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C1 FUC O 4 " pdb=" C2 FUC O 4 " ideal model delta sigma weight residual 1.528 1.657 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C1 FUC X 4 " pdb=" C2 FUC X 4 " ideal model delta sigma weight residual 1.528 1.657 -0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" C1 FUC g 4 " pdb=" O5 FUC g 4 " ideal model delta sigma weight residual 1.400 1.494 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" C1 FUC O 4 " pdb=" O5 FUC O 4 " ideal model delta sigma weight residual 1.400 1.494 -0.094 2.00e-02 2.50e+03 2.21e+01 ... (remaining 21022 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 26927 2.08 - 4.16: 1354 4.16 - 6.23: 243 6.23 - 8.31: 33 8.31 - 10.39: 3 Bond angle restraints: 28560 Sorted by residual: angle pdb=" N ALA D 70 " pdb=" CA ALA D 70 " pdb=" C ALA D 70 " ideal model delta sigma weight residual 108.08 114.78 -6.70 1.69e+00 3.50e-01 1.57e+01 angle pdb=" N ASN C 138 " pdb=" CA ASN C 138 " pdb=" C ASN C 138 " ideal model delta sigma weight residual 107.37 115.55 -8.18 2.07e+00 2.33e-01 1.56e+01 angle pdb=" N ALA C 70 " pdb=" CA ALA C 70 " pdb=" C ALA C 70 " ideal model delta sigma weight residual 108.08 114.75 -6.67 1.69e+00 3.50e-01 1.56e+01 angle pdb=" N ASN D 138 " pdb=" CA ASN D 138 " pdb=" C ASN D 138 " ideal model delta sigma weight residual 107.37 115.52 -8.15 2.07e+00 2.33e-01 1.55e+01 angle pdb=" N ALA A 70 " pdb=" CA ALA A 70 " pdb=" C ALA A 70 " ideal model delta sigma weight residual 108.08 114.73 -6.65 1.69e+00 3.50e-01 1.55e+01 ... (remaining 28555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.21: 13577 21.21 - 42.42: 406 42.42 - 63.62: 168 63.62 - 84.83: 72 84.83 - 106.04: 45 Dihedral angle restraints: 14268 sinusoidal: 7374 harmonic: 6894 Sorted by residual: dihedral pdb=" CA PHE D 376 " pdb=" C PHE D 376 " pdb=" N ASN D 377 " pdb=" CA ASN D 377 " ideal model delta harmonic sigma weight residual 180.00 159.74 20.26 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PHE A 376 " pdb=" C PHE A 376 " pdb=" N ASN A 377 " pdb=" CA ASN A 377 " ideal model delta harmonic sigma weight residual 180.00 159.74 20.26 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PHE C 376 " pdb=" C PHE C 376 " pdb=" N ASN C 377 " pdb=" CA ASN C 377 " ideal model delta harmonic sigma weight residual 180.00 159.75 20.25 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 14265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2873 0.078 - 0.156: 587 0.156 - 0.234: 53 0.234 - 0.311: 24 0.311 - 0.389: 6 Chirality restraints: 3543 Sorted by residual: chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.42e+02 chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.41e+02 chirality pdb=" C1 NAG m 2 " pdb=" O4 NAG m 1 " pdb=" C2 NAG m 2 " pdb=" O5 NAG m 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.39e+02 ... (remaining 3540 not shown) Planarity restraints: 3534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 1 " 0.039 2.00e-02 2.50e+03 3.19e-02 1.28e+01 pdb=" C7 NAG d 1 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG d 1 " 0.030 2.00e-02 2.50e+03 pdb=" N2 NAG d 1 " -0.050 2.00e-02 2.50e+03 pdb=" O7 NAG d 1 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG U 1 " 0.039 2.00e-02 2.50e+03 3.19e-02 1.28e+01 pdb=" C7 NAG U 1 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG U 1 " 0.030 2.00e-02 2.50e+03 pdb=" N2 NAG U 1 " -0.050 2.00e-02 2.50e+03 pdb=" O7 NAG U 1 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG m 1 " 0.039 2.00e-02 2.50e+03 3.19e-02 1.28e+01 pdb=" C7 NAG m 1 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG m 1 " 0.030 2.00e-02 2.50e+03 pdb=" N2 NAG m 1 " -0.050 2.00e-02 2.50e+03 pdb=" O7 NAG m 1 " -0.007 2.00e-02 2.50e+03 ... (remaining 3531 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 9 2.28 - 2.94: 9028 2.94 - 3.59: 26930 3.59 - 4.25: 47408 4.25 - 4.90: 77014 Nonbonded interactions: 160389 Sorted by model distance: nonbonded pdb=" OD1 ASN A 67 " pdb=" CB ASN A 209 " model vdw 1.626 3.440 nonbonded pdb=" OD1 ASN D 67 " pdb=" CB ASN D 209 " model vdw 1.626 3.440 nonbonded pdb=" OD1 ASN C 67 " pdb=" CB ASN C 209 " model vdw 1.626 3.440 nonbonded pdb=" OD1 ASN A 67 " pdb=" CG ASN A 209 " model vdw 2.133 3.270 nonbonded pdb=" OD1 ASN D 67 " pdb=" CG ASN D 209 " model vdw 2.133 3.270 ... (remaining 160384 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' } ncs_group { reference = chain 'O' selection = chain 'X' selection = chain 'g' } ncs_group { reference = chain 'R' selection = chain 'a' selection = chain 'j' } ncs_group { reference = chain 'U' selection = chain 'd' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 47.470 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.130 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.129 21195 Z= 0.349 Angle : 1.126 15.348 29025 Z= 0.572 Chirality : 0.066 0.389 3543 Planarity : 0.007 0.115 3474 Dihedral : 14.032 106.041 9705 Min Nonbonded Distance : 1.626 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.29 % Allowed : 2.00 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.025 0.003 TRP I 50 HIS 0.007 0.002 HIS C 130 PHE 0.035 0.003 PHE A 233 TYR 0.029 0.003 TYR K 71 ARG 0.009 0.001 ARG A 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 60) link_NAG-ASN : angle 2.50702 ( 180) link_ALPHA1-6 : bond 0.01929 ( 12) link_ALPHA1-6 : angle 5.73661 ( 36) link_BETA1-4 : bond 0.01013 ( 36) link_BETA1-4 : angle 3.20007 ( 108) link_ALPHA1-2 : bond 0.00259 ( 6) link_ALPHA1-2 : angle 1.54179 ( 18) link_ALPHA1-3 : bond 0.00539 ( 12) link_ALPHA1-3 : angle 1.76908 ( 36) hydrogen bonds : bond 0.14664 ( 672) hydrogen bonds : angle 7.76708 ( 1809) link_BETA1-6 : bond 0.04877 ( 3) link_BETA1-6 : angle 10.21223 ( 9) SS BOND : bond 0.00590 ( 39) SS BOND : angle 1.87473 ( 78) covalent geometry : bond 0.00726 (21027) covalent geometry : angle 1.05825 (28560) *********************** 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 : 2.136 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: 0.6447 (m-10) REVERT: A 150 MET cc_start: 0.8296 (mmm) cc_final: 0.8030 (tpp) REVERT: A 376 PHE cc_start: 0.7755 (m-80) cc_final: 0.7069 (m-80) REVERT: B 584 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8150 (mt-10) REVERT: B 589 ASP cc_start: 0.8391 (m-30) cc_final: 0.8118 (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: 0.8462 (t0) REVERT: B 652 GLN cc_start: 0.8391 (tp40) cc_final: 0.7949 (tp40) REVERT: H 83 ARG cc_start: 0.8094 (mtm180) cc_final: 0.7783 (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: L 73 LEU cc_start: 0.6773 (tp) cc_final: 0.6261 (tp) REVERT: C 42 VAL cc_start: 0.8322 (t) cc_final: 0.7975 (p) REVERT: C 53 PHE cc_start: 0.7583 (m-80) cc_final: 0.6812 (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: 0.7806 (m110) REVERT: C 432 ARG cc_start: 0.8518 (mtt90) cc_final: 0.8300 (mtm-85) REVERT: E 584 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8317 (mt-10) REVERT: E 652 GLN cc_start: 0.8413 (tp40) cc_final: 0.7920 (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: 0.5819 (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: 0.5851 (m-30) REVERT: D 53 PHE cc_start: 0.7677 (m-80) cc_final: 0.6891 (m-10) REVERT: D 111 LEU cc_start: 0.8905 (mt) cc_final: 0.8595 (mt) REVERT: D 150 MET cc_start: 0.8068 (mmm) cc_final: 0.7763 (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: 0.8376 (mtm-85) REVERT: F 584 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8100 (mt-10) REVERT: F 589 ASP cc_start: 0.8636 (m-30) cc_final: 0.8358 (m-30) REVERT: F 625 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7655 (t0) REVERT: F 639 THR cc_start: 0.8850 (m) cc_final: 0.8618 (p) REVERT: K 61 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.7156 (ptp90) REVERT: K 70 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8083 (pt0) REVERT: K 104 LEU cc_start: 0.7746 (tt) cc_final: 0.7403 (tp) outliers start: 6 outliers final: 3 residues processed: 654 average time/residue: 0.3964 time to fit residues: 370.1998 Evaluate side-chains 346 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 341 time to evaluate : 2.266 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 136 optimal weight: 0.0010 chunk 212 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 GLN L 24 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN J 24 GLN D 138 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 ASN F 543 GLN F 577 GLN I 62 GLN K 77 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.103624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.082499 restraints weight = 48108.456| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.62 r_work: 0.3191 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21195 Z= 0.193 Angle : 0.749 10.423 29025 Z= 0.363 Chirality : 0.049 0.291 3543 Planarity : 0.004 0.033 3474 Dihedral : 10.687 71.828 5197 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.04 % Allowed : 9.18 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.17), residues: 2343 helix: 1.61 (0.26), residues: 390 sheet: 0.60 (0.18), residues: 738 loop : 0.41 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 571 HIS 0.005 0.001 HIS D 374 PHE 0.018 0.002 PHE J 62 TYR 0.028 0.002 TYR L 49 ARG 0.006 0.001 ARG C 480 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 60) link_NAG-ASN : angle 2.38784 ( 180) link_ALPHA1-6 : bond 0.00596 ( 12) link_ALPHA1-6 : angle 2.64565 ( 36) link_BETA1-4 : bond 0.00741 ( 36) link_BETA1-4 : angle 2.04160 ( 108) link_ALPHA1-2 : bond 0.00082 ( 6) link_ALPHA1-2 : angle 1.77342 ( 18) link_ALPHA1-3 : bond 0.00502 ( 12) link_ALPHA1-3 : angle 1.86593 ( 36) hydrogen bonds : bond 0.04610 ( 672) hydrogen bonds : angle 6.35678 ( 1809) link_BETA1-6 : bond 0.04033 ( 3) link_BETA1-6 : angle 4.77387 ( 9) SS BOND : bond 0.00239 ( 39) SS BOND : angle 1.12839 ( 78) covalent geometry : bond 0.00440 (21027) covalent geometry : angle 0.70148 (28560) *********************** 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: 64 poor density : 352 time to evaluate : 2.277 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: 0.8654 (ptm) cc_final: 0.8343 (ptm) REVERT: A 150 MET cc_start: 0.8208 (mmm) cc_final: 0.7882 (tpp) REVERT: A 277 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8651 (tt) REVERT: A 376 PHE cc_start: 0.7923 (m-80) cc_final: 0.7085 (m-80) REVERT: B 584 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8459 (mt-10) REVERT: B 588 LYS cc_start: 0.8718 (mttt) cc_final: 0.8319 (mttm) REVERT: B 589 ASP cc_start: 0.8644 (m-30) cc_final: 0.8242 (m-30) REVERT: B 625 ASN cc_start: 0.8149 (OUTLIER) cc_final: 0.7805 (t0) REVERT: B 648 ASP cc_start: 0.8849 (m-30) cc_final: 0.8425 (t0) REVERT: H 23 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8004 (mp0) REVERT: H 28 ASN cc_start: 0.7867 (t0) cc_final: 0.7566 (t0) REVERT: H 84 SER cc_start: 0.9140 (p) cc_final: 0.8684 (t) REVERT: L 11 LEU cc_start: 0.8448 (mt) cc_final: 0.8203 (mt) REVERT: L 50 ASP cc_start: 0.7270 (t0) cc_final: 0.6135 (t0) REVERT: L 70 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7715 (pt0) REVERT: C 98 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8426 (t0) REVERT: C 152 LYS cc_start: 0.9213 (mttt) cc_final: 0.8861 (mtmm) REVERT: C 185 LYS cc_start: 0.8735 (mttt) cc_final: 0.8164 (tptp) REVERT: C 302 ASN cc_start: 0.8104 (m110) cc_final: 0.7626 (m110) REVERT: C 482 GLU cc_start: 0.8315 (mp0) cc_final: 0.7786 (mp0) REVERT: C 486 TYR cc_start: 0.7675 (p90) cc_final: 0.7065 (p90) REVERT: E 652 GLN cc_start: 0.8693 (tp40) cc_final: 0.8314 (tp40) REVERT: E 657 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8359 (mm-30) REVERT: G 28 ASN cc_start: 0.7981 (t0) cc_final: 0.7629 (t0) REVERT: G 84 SER cc_start: 0.8835 (p) cc_final: 0.8371 (t) REVERT: J 50 ASP cc_start: 0.6952 (t0) cc_final: 0.6716 (t0) REVERT: J 70 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7801 (pt0) REVERT: J 82 ASP cc_start: 0.7140 (m-30) cc_final: 0.6879 (m-30) REVERT: D 53 PHE cc_start: 0.7632 (m-80) cc_final: 0.7254 (m-10) REVERT: D 95 MET cc_start: 0.8527 (ptm) cc_final: 0.8292 (ptm) REVERT: D 150 MET cc_start: 0.8099 (mmm) cc_final: 0.7804 (tpp) REVERT: D 486 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7409 (p90) REVERT: F 576 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8681 (mm) REVERT: F 584 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8610 (mt-10) REVERT: F 589 ASP cc_start: 0.8856 (m-30) cc_final: 0.8644 (m-30) REVERT: F 625 ASN cc_start: 0.8364 (OUTLIER) cc_final: 0.8049 (t0) REVERT: K 24 GLN cc_start: 0.7684 (tt0) cc_final: 0.7460 (tt0) REVERT: K 50 ASP cc_start: 0.7159 (t0) cc_final: 0.5946 (t0) REVERT: K 62 PHE cc_start: 0.7349 (m-80) cc_final: 0.7147 (m-80) REVERT: K 70 GLU cc_start: 0.8530 (mt-10) cc_final: 0.7904 (pt0) REVERT: K 82 ASP cc_start: 0.7296 (m-30) cc_final: 0.6929 (m-30) outliers start: 64 outliers final: 36 residues processed: 401 average time/residue: 0.3535 time to fit residues: 210.9892 Evaluate side-chains 336 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 294 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 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 C residue 46 THR Chi-restraints excluded: chain C residue 51 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 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 482 GLU Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 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 191 optimal weight: 0.8980 chunk 100 optimal weight: 0.4980 chunk 12 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 157 optimal weight: 0.1980 chunk 201 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS A 302 ASN B 575 GLN L 24 GLN C 130 HIS C 425 ASN E 577 GLN J 24 GLN D 130 HIS ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 ASN F 543 GLN I 28 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.101610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.083154 restraints weight = 43772.429| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.01 r_work: 0.3175 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21195 Z= 0.131 Angle : 0.664 9.224 29025 Z= 0.317 Chirality : 0.047 0.290 3543 Planarity : 0.004 0.043 3474 Dihedral : 9.186 65.999 5197 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.76 % Allowed : 10.98 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.17), residues: 2343 helix: 1.68 (0.26), residues: 390 sheet: 0.52 (0.18), residues: 738 loop : 0.38 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 571 HIS 0.004 0.001 HIS D 105 PHE 0.018 0.001 PHE D 376 TYR 0.026 0.001 TYR L 49 ARG 0.005 0.001 ARG C 480 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 60) link_NAG-ASN : angle 2.21243 ( 180) link_ALPHA1-6 : bond 0.00692 ( 12) link_ALPHA1-6 : angle 2.53353 ( 36) link_BETA1-4 : bond 0.00661 ( 36) link_BETA1-4 : angle 1.73672 ( 108) link_ALPHA1-2 : bond 0.00193 ( 6) link_ALPHA1-2 : angle 1.73076 ( 18) link_ALPHA1-3 : bond 0.00789 ( 12) link_ALPHA1-3 : angle 1.43276 ( 36) hydrogen bonds : bond 0.03905 ( 672) hydrogen bonds : angle 5.90740 ( 1809) link_BETA1-6 : bond 0.03918 ( 3) link_BETA1-6 : angle 4.76466 ( 9) SS BOND : bond 0.00221 ( 39) SS BOND : angle 1.01591 ( 78) covalent geometry : bond 0.00283 (21027) covalent geometry : angle 0.61901 (28560) *********************** 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: 58 poor density : 319 time to evaluate : 2.400 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: 0.8529 (ptm) cc_final: 0.8290 (ptm) REVERT: A 150 MET cc_start: 0.8341 (mmm) cc_final: 0.8086 (tpp) REVERT: A 376 PHE cc_start: 0.7864 (m-80) cc_final: 0.7281 (m-80) REVERT: A 486 TYR cc_start: 0.7702 (p90) cc_final: 0.6781 (p90) REVERT: B 589 ASP cc_start: 0.8330 (m-30) cc_final: 0.8016 (m-30) REVERT: B 625 ASN cc_start: 0.7921 (OUTLIER) cc_final: 0.7587 (t0) REVERT: B 630 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7383 (mp0) REVERT: B 648 ASP cc_start: 0.8512 (m-30) cc_final: 0.8179 (t0) REVERT: B 653 GLN cc_start: 0.7670 (tt0) cc_final: 0.7275 (tt0) REVERT: H 28 ASN cc_start: 0.8008 (t0) cc_final: 0.7688 (t0) REVERT: H 84 SER cc_start: 0.9156 (p) cc_final: 0.8722 (t) REVERT: L 3 GLN cc_start: 0.8238 (pp30) cc_final: 0.7931 (pp30) REVERT: L 11 LEU cc_start: 0.8555 (mt) cc_final: 0.8330 (mt) REVERT: L 24 GLN cc_start: 0.7842 (tt0) cc_final: 0.7512 (tt0) REVERT: L 50 ASP cc_start: 0.7885 (t0) cc_final: 0.7270 (t0) REVERT: L 70 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7823 (pt0) REVERT: L 77 ASN cc_start: 0.7607 (t0) cc_final: 0.7364 (t0) REVERT: C 98 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8565 (t0) REVERT: C 185 LYS cc_start: 0.8552 (mttt) cc_final: 0.8307 (tptp) REVERT: C 434 MET cc_start: 0.8901 (ttp) cc_final: 0.8617 (ttp) REVERT: E 579 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8391 (mpp80) REVERT: G 31 ASP cc_start: 0.8848 (m-30) cc_final: 0.8647 (m-30) REVERT: G 84 SER cc_start: 0.8727 (p) cc_final: 0.8338 (t) REVERT: J 50 ASP cc_start: 0.7459 (t0) cc_final: 0.7167 (t0) REVERT: J 70 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7930 (pt0) REVERT: D 53 PHE cc_start: 0.7755 (m-80) cc_final: 0.7438 (m-10) REVERT: D 150 MET cc_start: 0.8341 (mmm) cc_final: 0.8094 (tpp) REVERT: D 320 THR cc_start: 0.9212 (m) cc_final: 0.8986 (p) REVERT: D 425 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.7798 (p0) REVERT: D 486 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.7337 (p90) REVERT: F 577 GLN cc_start: 0.8622 (tp-100) cc_final: 0.8074 (mm-40) REVERT: F 589 ASP cc_start: 0.8555 (m-30) cc_final: 0.8337 (m-30) REVERT: F 625 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7714 (t0) REVERT: F 630 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7450 (mp0) REVERT: K 50 ASP cc_start: 0.7817 (t0) cc_final: 0.7572 (t0) REVERT: K 70 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8066 (pt0) outliers start: 58 outliers final: 35 residues processed: 356 average time/residue: 0.3610 time to fit residues: 193.4845 Evaluate side-chains 320 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 279 time to evaluate : 2.222 ------------------------------------------------------------------------------- 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 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 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 424 ILE Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 579 ARG Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 588 LYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain G residue 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 425 ASN 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 647 GLU Chi-restraints excluded: chain I residue 68 SER 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 123 optimal weight: 7.9990 chunk 176 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 218 optimal weight: 0.0470 chunk 167 optimal weight: 0.0270 overall best weight: 1.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN C 425 ASN ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 ASN ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN I 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 = 0.3568 r_free = 0.3568 target = 0.097416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.078982 restraints weight = 44234.868| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.97 r_work: 0.3109 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 21195 Z= 0.210 Angle : 0.693 9.307 29025 Z= 0.331 Chirality : 0.048 0.294 3543 Planarity : 0.004 0.044 3474 Dihedral : 8.091 52.690 5197 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.38 % Allowed : 11.51 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.17), residues: 2343 helix: 1.55 (0.26), residues: 393 sheet: 0.35 (0.18), residues: 744 loop : 0.22 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 71D HIS 0.004 0.001 HIS C 105 PHE 0.025 0.002 PHE D 53 TYR 0.026 0.002 TYR F 638 ARG 0.004 0.001 ARG C 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 60) link_NAG-ASN : angle 2.20996 ( 180) link_ALPHA1-6 : bond 0.00627 ( 12) link_ALPHA1-6 : angle 2.31615 ( 36) link_BETA1-4 : bond 0.00628 ( 36) link_BETA1-4 : angle 1.77499 ( 108) link_ALPHA1-2 : bond 0.00162 ( 6) link_ALPHA1-2 : angle 1.81079 ( 18) link_ALPHA1-3 : bond 0.00628 ( 12) link_ALPHA1-3 : angle 1.90009 ( 36) hydrogen bonds : bond 0.04067 ( 672) hydrogen bonds : angle 5.69989 ( 1809) link_BETA1-6 : bond 0.03372 ( 3) link_BETA1-6 : angle 4.11726 ( 9) SS BOND : bond 0.00219 ( 39) SS BOND : angle 1.05197 ( 78) covalent geometry : bond 0.00488 (21027) covalent geometry : angle 0.65082 (28560) *********************** 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 366 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 295 time to evaluate : 2.251 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 277 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8194 (tt) REVERT: A 376 PHE cc_start: 0.8118 (m-80) cc_final: 0.7433 (m-80) REVERT: B 589 ASP cc_start: 0.8375 (m-30) cc_final: 0.8150 (m-30) REVERT: B 625 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7586 (t0) REVERT: B 648 ASP cc_start: 0.8460 (m-30) cc_final: 0.8073 (t0) REVERT: H 84 SER cc_start: 0.9120 (p) cc_final: 0.8703 (t) REVERT: L 3 GLN cc_start: 0.8291 (pp30) cc_final: 0.7957 (pp30) REVERT: L 11 LEU cc_start: 0.8741 (mt) cc_final: 0.8512 (mt) REVERT: L 24 GLN cc_start: 0.7894 (tt0) cc_final: 0.7656 (tt0) REVERT: L 50 ASP cc_start: 0.8551 (t0) cc_final: 0.8120 (t0) REVERT: L 70 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7897 (pt0) REVERT: E 579 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8587 (mpp80) REVERT: E 625 ASN cc_start: 0.7944 (OUTLIER) cc_final: 0.7712 (t0) REVERT: G 84 SER cc_start: 0.8701 (p) cc_final: 0.8324 (t) REVERT: J 70 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7905 (pt0) REVERT: D 150 MET cc_start: 0.8457 (mmm) cc_final: 0.8209 (tpp) REVERT: D 320 THR cc_start: 0.9236 (m) cc_final: 0.9035 (p) REVERT: D 486 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.7510 (p90) REVERT: F 577 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8200 (mm-40) REVERT: F 584 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8039 (mt-10) REVERT: F 589 ASP cc_start: 0.8543 (m-30) cc_final: 0.8343 (m-30) REVERT: F 625 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7658 (t0) REVERT: F 626 MET cc_start: 0.7887 (ttt) cc_final: 0.7633 (ttt) REVERT: F 630 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7500 (mp0) REVERT: F 651 THR cc_start: 0.7879 (m) cc_final: 0.7594 (p) REVERT: K 70 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8103 (pt0) outliers start: 71 outliers final: 51 residues processed: 343 average time/residue: 0.3483 time to fit residues: 178.6925 Evaluate side-chains 323 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 266 time to evaluate : 2.200 ------------------------------------------------------------------------------- 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 277 LEU 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 625 ASN Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 579 ARG Chi-restraints excluded: chain E residue 588 LYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 621 ASP Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain 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 213 ILE Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 365 SER 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 588 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 54 LEU 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 61 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 chunk 221 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 ASN ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.097173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.078664 restraints weight = 44251.622| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.02 r_work: 0.3104 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21195 Z= 0.166 Angle : 0.660 9.181 29025 Z= 0.314 Chirality : 0.046 0.292 3543 Planarity : 0.004 0.044 3474 Dihedral : 7.292 53.033 5197 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.33 % Allowed : 13.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2343 helix: 1.64 (0.27), residues: 393 sheet: 0.28 (0.18), residues: 744 loop : 0.12 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP H 71D HIS 0.005 0.001 HIS D 374 PHE 0.012 0.001 PHE D 376 TYR 0.021 0.001 TYR L 49 ARG 0.007 0.000 ARG I 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 60) link_NAG-ASN : angle 2.12662 ( 180) link_ALPHA1-6 : bond 0.00642 ( 12) link_ALPHA1-6 : angle 2.44707 ( 36) link_BETA1-4 : bond 0.00601 ( 36) link_BETA1-4 : angle 1.67968 ( 108) link_ALPHA1-2 : bond 0.00132 ( 6) link_ALPHA1-2 : angle 1.75971 ( 18) link_ALPHA1-3 : bond 0.00662 ( 12) link_ALPHA1-3 : angle 1.79755 ( 36) hydrogen bonds : bond 0.03831 ( 672) hydrogen bonds : angle 5.57648 ( 1809) link_BETA1-6 : bond 0.03596 ( 3) link_BETA1-6 : angle 4.26773 ( 9) SS BOND : bond 0.00214 ( 39) SS BOND : angle 1.01985 ( 78) covalent geometry : bond 0.00378 (21027) covalent geometry : angle 0.61705 (28560) *********************** 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 356 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 286 time to evaluate : 2.304 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 95 MET cc_start: 0.8693 (ptm) cc_final: 0.8472 (ptm) REVERT: A 277 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7975 (tt) REVERT: A 303 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8339 (p) REVERT: A 376 PHE cc_start: 0.8090 (m-80) cc_final: 0.7358 (m-80) REVERT: A 425 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.8282 (p0) REVERT: B 589 ASP cc_start: 0.8379 (m-30) cc_final: 0.8142 (m-30) REVERT: B 625 ASN cc_start: 0.7980 (OUTLIER) cc_final: 0.7628 (t0) REVERT: B 648 ASP cc_start: 0.8341 (m-30) cc_final: 0.8003 (t0) REVERT: H 3 GLN cc_start: 0.8765 (tt0) cc_final: 0.7996 (mt0) REVERT: H 43 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8369 (mp10) REVERT: H 84 SER cc_start: 0.9106 (p) cc_final: 0.8676 (t) REVERT: L 3 GLN cc_start: 0.8153 (pp30) cc_final: 0.7872 (pp30) REVERT: L 50 ASP cc_start: 0.8647 (t0) cc_final: 0.8154 (t0) REVERT: L 70 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7848 (pt0) REVERT: E 579 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8246 (mpp80) REVERT: G 84 SER cc_start: 0.8669 (p) cc_final: 0.8272 (t) REVERT: J 50 ASP cc_start: 0.8470 (t0) cc_final: 0.8201 (t0) REVERT: J 70 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7906 (pt0) REVERT: D 150 MET cc_start: 0.8381 (mmm) cc_final: 0.8106 (tpt) REVERT: D 209 ASN cc_start: 0.8847 (t0) cc_final: 0.8620 (t0) REVERT: D 482 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8089 (mm-30) REVERT: D 486 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.7548 (p90) REVERT: F 577 GLN cc_start: 0.8788 (tp-100) cc_final: 0.8373 (mm-40) REVERT: F 584 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8013 (mt-10) REVERT: F 589 ASP cc_start: 0.8571 (m-30) cc_final: 0.8363 (m-30) REVERT: I 38 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7165 (ttp80) REVERT: K 70 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8015 (pt0) outliers start: 70 outliers final: 43 residues processed: 333 average time/residue: 0.3489 time to fit residues: 175.0850 Evaluate side-chains 312 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 260 time to evaluate : 2.300 ------------------------------------------------------------------------------- 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 276 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 THR 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 625 ASN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain 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 11 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain 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 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 620 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 0.0670 chunk 60 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 145 optimal weight: 0.7980 chunk 115 optimal weight: 0.0970 chunk 211 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 overall best weight: 1.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN 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 = 0.3542 r_free = 0.3542 target = 0.095831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.077374 restraints weight = 44323.082| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.98 r_work: 0.3072 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21195 Z= 0.205 Angle : 0.686 9.816 29025 Z= 0.326 Chirality : 0.047 0.292 3543 Planarity : 0.004 0.043 3474 Dihedral : 7.001 53.162 5195 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.38 % Allowed : 13.74 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2343 helix: 1.64 (0.27), residues: 393 sheet: 0.16 (0.18), residues: 750 loop : -0.06 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP I 71D HIS 0.006 0.001 HIS D 374 PHE 0.014 0.001 PHE A 53 TYR 0.021 0.002 TYR J 49 ARG 0.006 0.001 ARG I 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 60) link_NAG-ASN : angle 2.25245 ( 180) link_ALPHA1-6 : bond 0.00548 ( 12) link_ALPHA1-6 : angle 2.34657 ( 36) link_BETA1-4 : bond 0.00567 ( 36) link_BETA1-4 : angle 1.72655 ( 108) link_ALPHA1-2 : bond 0.00231 ( 6) link_ALPHA1-2 : angle 1.82383 ( 18) link_ALPHA1-3 : bond 0.00605 ( 12) link_ALPHA1-3 : angle 1.88766 ( 36) hydrogen bonds : bond 0.03909 ( 672) hydrogen bonds : angle 5.50435 ( 1809) link_BETA1-6 : bond 0.03459 ( 3) link_BETA1-6 : angle 4.05439 ( 9) SS BOND : bond 0.00233 ( 39) SS BOND : angle 0.99596 ( 78) covalent geometry : bond 0.00471 (21027) covalent geometry : angle 0.64336 (28560) *********************** 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 354 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 283 time to evaluate : 2.160 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 303 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8313 (p) REVERT: B 589 ASP cc_start: 0.8361 (m-30) cc_final: 0.8141 (m-30) REVERT: B 625 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7568 (t0) REVERT: B 630 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7538 (mp0) REVERT: B 648 ASP cc_start: 0.8192 (m-30) cc_final: 0.7886 (t0) REVERT: H 43 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8319 (mp10) REVERT: H 84 SER cc_start: 0.9097 (p) cc_final: 0.8664 (t) REVERT: L 3 GLN cc_start: 0.8235 (pp30) cc_final: 0.7880 (pp30) REVERT: L 24 GLN cc_start: 0.7757 (tt0) cc_final: 0.7543 (tt0) REVERT: L 49 TYR cc_start: 0.8752 (p90) cc_final: 0.8504 (p90) REVERT: L 50 ASP cc_start: 0.8889 (t0) cc_final: 0.8415 (t0) REVERT: L 70 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7837 (pt0) REVERT: C 66 HIS cc_start: 0.7877 (OUTLIER) cc_final: 0.7472 (t-90) REVERT: C 425 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.7974 (p0) REVERT: E 579 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8380 (mpp80) REVERT: E 625 ASN cc_start: 0.7860 (OUTLIER) cc_final: 0.7555 (t0) REVERT: G 38 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8444 (ttp-170) REVERT: G 84 SER cc_start: 0.8729 (p) cc_final: 0.8332 (t) REVERT: J 50 ASP cc_start: 0.8664 (t0) cc_final: 0.8378 (t0) REVERT: J 70 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7919 (pt0) REVERT: D 150 MET cc_start: 0.8414 (mmm) cc_final: 0.8097 (tpt) REVERT: D 209 ASN cc_start: 0.8884 (t0) cc_final: 0.8662 (t0) REVERT: D 482 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8135 (mm-30) REVERT: D 486 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7527 (p90) REVERT: F 577 GLN cc_start: 0.8792 (tp-100) cc_final: 0.8358 (mm-40) REVERT: F 584 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8043 (mt-10) REVERT: F 630 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7576 (mp0) REVERT: I 38 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.7329 (ttp80) REVERT: K 70 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8063 (pt0) outliers start: 71 outliers final: 47 residues processed: 333 average time/residue: 0.3521 time to fit residues: 177.0477 Evaluate side-chains 322 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 264 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 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 584 GLU 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 38 ARG Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 482 GLU Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 588 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 647 GLU Chi-restraints excluded: chain F residue 654 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 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 121 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 213 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN B 653 GLN J 24 GLN ** 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 = 0.3534 r_free = 0.3534 target = 0.095390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.077039 restraints weight = 44228.294| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.97 r_work: 0.3063 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21195 Z= 0.191 Angle : 0.682 14.124 29025 Z= 0.324 Chirality : 0.047 0.387 3543 Planarity : 0.004 0.042 3474 Dihedral : 6.791 53.221 5195 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.38 % Allowed : 14.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2343 helix: 1.72 (0.27), residues: 390 sheet: 0.05 (0.18), residues: 750 loop : -0.18 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP I 71D HIS 0.006 0.001 HIS D 374 PHE 0.013 0.001 PHE D 53 TYR 0.020 0.001 TYR K 49 ARG 0.006 0.001 ARG E 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00314 ( 60) link_NAG-ASN : angle 2.35708 ( 180) link_ALPHA1-6 : bond 0.00477 ( 12) link_ALPHA1-6 : angle 2.34361 ( 36) link_BETA1-4 : bond 0.00579 ( 36) link_BETA1-4 : angle 1.67066 ( 108) link_ALPHA1-2 : bond 0.00185 ( 6) link_ALPHA1-2 : angle 1.77854 ( 18) link_ALPHA1-3 : bond 0.00619 ( 12) link_ALPHA1-3 : angle 1.78341 ( 36) hydrogen bonds : bond 0.03898 ( 672) hydrogen bonds : angle 5.45420 ( 1809) link_BETA1-6 : bond 0.03438 ( 3) link_BETA1-6 : angle 4.04765 ( 9) SS BOND : bond 0.00234 ( 39) SS BOND : angle 0.97406 ( 78) covalent geometry : bond 0.00438 (21027) covalent geometry : angle 0.63712 (28560) *********************** 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 354 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 283 time to evaluate : 2.290 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 303 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8415 (p) REVERT: B 589 ASP cc_start: 0.8390 (m-30) cc_final: 0.8162 (m-30) REVERT: B 625 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7599 (t0) REVERT: B 630 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7494 (mp0) REVERT: B 648 ASP cc_start: 0.8218 (m-30) cc_final: 0.7907 (t0) REVERT: H 43 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8261 (mp10) REVERT: H 84 SER cc_start: 0.9086 (p) cc_final: 0.8632 (t) REVERT: L 3 GLN cc_start: 0.8229 (pp30) cc_final: 0.7938 (pp30) REVERT: L 50 ASP cc_start: 0.8919 (t0) cc_final: 0.8521 (t0) REVERT: L 70 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7685 (pt0) REVERT: C 66 HIS cc_start: 0.7319 (OUTLIER) cc_final: 0.7025 (t-90) REVERT: C 425 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8229 (p0) REVERT: E 579 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8413 (mpp80) REVERT: E 625 ASN cc_start: 0.7756 (OUTLIER) cc_final: 0.7507 (t0) REVERT: G 38 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8453 (ttp-170) REVERT: G 84 SER cc_start: 0.8767 (p) cc_final: 0.8489 (t) REVERT: J 50 ASP cc_start: 0.8728 (t0) cc_final: 0.8478 (t0) REVERT: J 70 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7862 (pt0) REVERT: D 150 MET cc_start: 0.8338 (mmm) cc_final: 0.8020 (tpt) REVERT: D 209 ASN cc_start: 0.9051 (t0) cc_final: 0.8839 (t0) REVERT: D 482 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8177 (mm-30) REVERT: D 486 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.7479 (p90) REVERT: F 577 GLN cc_start: 0.8804 (tp-100) cc_final: 0.8357 (mm-40) REVERT: F 584 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8046 (mt-10) REVERT: F 630 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7536 (mp0) REVERT: I 38 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7308 (ttp80) REVERT: K 50 ASP cc_start: 0.8753 (t0) cc_final: 0.8050 (t0) REVERT: K 70 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8029 (pt0) outliers start: 71 outliers final: 51 residues processed: 332 average time/residue: 0.3519 time to fit residues: 176.5415 Evaluate side-chains 327 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 265 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 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 584 GLU 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 38 ARG Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 99 TYR 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 482 GLU Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 606 THR 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 38 ARG Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 6 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 206 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.096032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.077641 restraints weight = 44316.068| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.98 r_work: 0.3068 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21195 Z= 0.154 Angle : 0.652 10.563 29025 Z= 0.312 Chirality : 0.046 0.324 3543 Planarity : 0.004 0.038 3474 Dihedral : 6.462 52.816 5195 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.23 % Allowed : 15.31 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.17), residues: 2343 helix: 1.72 (0.27), residues: 396 sheet: 0.06 (0.18), residues: 750 loop : -0.19 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP I 71D HIS 0.004 0.001 HIS D 216 PHE 0.013 0.001 PHE D 53 TYR 0.021 0.001 TYR K 49 ARG 0.007 0.001 ARG J 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 60) link_NAG-ASN : angle 2.11187 ( 180) link_ALPHA1-6 : bond 0.00470 ( 12) link_ALPHA1-6 : angle 2.27219 ( 36) link_BETA1-4 : bond 0.00588 ( 36) link_BETA1-4 : angle 1.62704 ( 108) link_ALPHA1-2 : bond 0.00157 ( 6) link_ALPHA1-2 : angle 1.72655 ( 18) link_ALPHA1-3 : bond 0.00645 ( 12) link_ALPHA1-3 : angle 1.67748 ( 36) hydrogen bonds : bond 0.03694 ( 672) hydrogen bonds : angle 5.37674 ( 1809) link_BETA1-6 : bond 0.03589 ( 3) link_BETA1-6 : angle 4.21189 ( 9) SS BOND : bond 0.00206 ( 39) SS BOND : angle 0.89852 ( 78) covalent geometry : bond 0.00347 (21027) covalent geometry : angle 0.61212 (28560) *********************** 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 347 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 279 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 589 ASP cc_start: 0.8372 (m-30) cc_final: 0.8147 (m-30) REVERT: B 625 ASN cc_start: 0.7934 (OUTLIER) cc_final: 0.7627 (t0) REVERT: B 630 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7427 (mp0) REVERT: B 648 ASP cc_start: 0.8181 (m-30) cc_final: 0.7919 (t0) REVERT: H 28 ASN cc_start: 0.8182 (p0) cc_final: 0.7918 (p0) REVERT: H 84 SER cc_start: 0.9061 (p) cc_final: 0.8594 (t) REVERT: L 3 GLN cc_start: 0.8209 (pp30) cc_final: 0.7923 (pp30) REVERT: L 6 GLN cc_start: 0.8111 (tp40) cc_final: 0.7597 (tp40) REVERT: L 50 ASP cc_start: 0.8884 (t0) cc_final: 0.8560 (t0) REVERT: L 70 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7712 (pt0) REVERT: C 66 HIS cc_start: 0.7413 (OUTLIER) cc_final: 0.7072 (t-90) REVERT: C 425 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8262 (p0) REVERT: E 579 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8452 (mpp80) REVERT: E 625 ASN cc_start: 0.7695 (OUTLIER) cc_final: 0.7454 (t0) REVERT: G 84 SER cc_start: 0.8784 (p) cc_final: 0.8481 (t) REVERT: J 50 ASP cc_start: 0.8678 (t0) cc_final: 0.8410 (t0) REVERT: J 70 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7849 (pt0) REVERT: D 150 MET cc_start: 0.8321 (mmm) cc_final: 0.8030 (tpt) REVERT: D 482 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8171 (mm-30) REVERT: D 486 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.7477 (p90) REVERT: F 577 GLN cc_start: 0.8821 (tp-100) cc_final: 0.8338 (mm-40) REVERT: F 584 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8040 (mt-10) REVERT: F 630 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7632 (mp0) REVERT: F 655 LYS cc_start: 0.7375 (ptpt) cc_final: 0.7166 (ptpt) REVERT: I 38 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7282 (ttp80) REVERT: K 50 ASP cc_start: 0.8716 (t0) cc_final: 0.8030 (t0) REVERT: K 70 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8001 (pt0) outliers start: 68 outliers final: 53 residues processed: 325 average time/residue: 0.3597 time to fit residues: 176.3119 Evaluate side-chains 324 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 263 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 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 70 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 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 584 GLU 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 G residue 99 TYR 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 213 ILE Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 482 GLU Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 588 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 38 ARG Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 169 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 141 optimal weight: 0.0980 chunk 91 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 158 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.097882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.080252 restraints weight = 44411.079| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.93 r_work: 0.3114 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21195 Z= 0.128 Angle : 0.639 11.334 29025 Z= 0.306 Chirality : 0.046 0.290 3543 Planarity : 0.004 0.037 3474 Dihedral : 6.120 52.423 5195 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.90 % Allowed : 15.83 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.17), residues: 2343 helix: 1.79 (0.27), residues: 393 sheet: 0.08 (0.18), residues: 750 loop : -0.20 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP I 71D HIS 0.004 0.001 HIS C 374 PHE 0.013 0.001 PHE A 376 TYR 0.022 0.001 TYR K 49 ARG 0.008 0.000 ARG E 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 60) link_NAG-ASN : angle 2.00542 ( 180) link_ALPHA1-6 : bond 0.00472 ( 12) link_ALPHA1-6 : angle 2.19260 ( 36) link_BETA1-4 : bond 0.00588 ( 36) link_BETA1-4 : angle 1.60288 ( 108) link_ALPHA1-2 : bond 0.00156 ( 6) link_ALPHA1-2 : angle 1.66888 ( 18) link_ALPHA1-3 : bond 0.00679 ( 12) link_ALPHA1-3 : angle 1.58901 ( 36) hydrogen bonds : bond 0.03500 ( 672) hydrogen bonds : angle 5.29437 ( 1809) link_BETA1-6 : bond 0.03629 ( 3) link_BETA1-6 : angle 4.35983 ( 9) SS BOND : bond 0.00204 ( 39) SS BOND : angle 0.89452 ( 78) covalent geometry : bond 0.00281 (21027) covalent geometry : angle 0.60061 (28560) *********************** 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 342 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 281 time to evaluate : 2.338 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: B 589 ASP cc_start: 0.8304 (m-30) cc_final: 0.8029 (m-30) REVERT: B 625 ASN cc_start: 0.7899 (OUTLIER) cc_final: 0.7592 (t0) REVERT: B 630 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7411 (mp0) REVERT: B 648 ASP cc_start: 0.8078 (m-30) cc_final: 0.7818 (t0) REVERT: H 28 ASN cc_start: 0.8010 (p0) cc_final: 0.7444 (p0) REVERT: H 31 ASP cc_start: 0.8727 (m-30) cc_final: 0.8463 (m-30) REVERT: H 84 SER cc_start: 0.9091 (p) cc_final: 0.8649 (t) REVERT: L 3 GLN cc_start: 0.8228 (pp30) cc_final: 0.7945 (pp30) REVERT: L 6 GLN cc_start: 0.8091 (tp40) cc_final: 0.7557 (tp40) REVERT: L 50 ASP cc_start: 0.8858 (t0) cc_final: 0.8610 (t0) REVERT: L 70 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7776 (pt0) REVERT: C 66 HIS cc_start: 0.7355 (OUTLIER) cc_final: 0.7071 (t-90) REVERT: E 579 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8443 (mpp80) REVERT: E 625 ASN cc_start: 0.7700 (OUTLIER) cc_final: 0.7480 (t0) REVERT: G 84 SER cc_start: 0.8686 (p) cc_final: 0.8385 (t) REVERT: J 50 ASP cc_start: 0.8644 (t0) cc_final: 0.8385 (t0) REVERT: J 70 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7867 (pt0) REVERT: D 150 MET cc_start: 0.8161 (mmm) cc_final: 0.7863 (tpt) REVERT: D 482 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8147 (mm-30) REVERT: D 486 TYR cc_start: 0.8194 (OUTLIER) cc_final: 0.7357 (p90) REVERT: F 577 GLN cc_start: 0.8771 (tp-100) cc_final: 0.8301 (mm-40) REVERT: F 584 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8010 (mt-10) REVERT: F 626 MET cc_start: 0.7855 (ttt) cc_final: 0.7595 (ttt) REVERT: F 630 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7490 (mp0) REVERT: K 50 ASP cc_start: 0.8645 (t0) cc_final: 0.7965 (t0) REVERT: K 70 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8028 (pt0) outliers start: 61 outliers final: 46 residues processed: 324 average time/residue: 0.3469 time to fit residues: 169.5064 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 : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 579 ARG Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain 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 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 213 ILE Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 365 SER 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 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 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 93 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 145 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 188 optimal weight: 0.3980 chunk 228 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN J 24 GLN ** 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 = 0.3552 r_free = 0.3552 target = 0.096859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.078928 restraints weight = 44543.279| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.94 r_work: 0.3087 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21195 Z= 0.156 Angle : 0.657 11.798 29025 Z= 0.316 Chirality : 0.046 0.292 3543 Planarity : 0.004 0.039 3474 Dihedral : 6.046 52.436 5195 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.95 % Allowed : 16.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.17), residues: 2343 helix: 1.83 (0.27), residues: 393 sheet: 0.12 (0.19), residues: 744 loop : -0.25 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP G 71D HIS 0.006 0.001 HIS C 374 PHE 0.013 0.001 PHE A 376 TYR 0.041 0.001 TYR F 638 ARG 0.009 0.001 ARG J 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 60) link_NAG-ASN : angle 2.03059 ( 180) link_ALPHA1-6 : bond 0.00425 ( 12) link_ALPHA1-6 : angle 2.14854 ( 36) link_BETA1-4 : bond 0.00576 ( 36) link_BETA1-4 : angle 1.62044 ( 108) link_ALPHA1-2 : bond 0.00144 ( 6) link_ALPHA1-2 : angle 1.70742 ( 18) link_ALPHA1-3 : bond 0.00605 ( 12) link_ALPHA1-3 : angle 1.63524 ( 36) hydrogen bonds : bond 0.03624 ( 672) hydrogen bonds : angle 5.26886 ( 1809) link_BETA1-6 : bond 0.03511 ( 3) link_BETA1-6 : angle 4.19891 ( 9) SS BOND : bond 0.00224 ( 39) SS BOND : angle 0.91415 ( 78) covalent geometry : bond 0.00355 (21027) covalent geometry : angle 0.61995 (28560) ********************** 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 338 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 276 time to evaluate : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8407 (p) REVERT: A 486 TYR cc_start: 0.8107 (OUTLIER) cc_final: 0.6576 (p90) REVERT: B 589 ASP cc_start: 0.8289 (m-30) cc_final: 0.8026 (m-30) REVERT: B 625 ASN cc_start: 0.7939 (OUTLIER) cc_final: 0.7628 (t0) REVERT: B 630 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7390 (mp0) REVERT: B 648 ASP cc_start: 0.8030 (m-30) cc_final: 0.7790 (t0) REVERT: H 28 ASN cc_start: 0.8050 (p0) cc_final: 0.7636 (p0) REVERT: H 31 ASP cc_start: 0.8911 (m-30) cc_final: 0.8628 (m-30) REVERT: H 43 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8281 (mp10) REVERT: H 84 SER cc_start: 0.9074 (p) cc_final: 0.8629 (t) REVERT: L 3 GLN cc_start: 0.8171 (pp30) cc_final: 0.7914 (pp30) REVERT: L 50 ASP cc_start: 0.8857 (t0) cc_final: 0.8555 (t0) REVERT: L 70 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7722 (pt0) REVERT: C 66 HIS cc_start: 0.7434 (OUTLIER) cc_final: 0.7154 (t-90) REVERT: E 579 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8430 (mpp80) REVERT: E 625 ASN cc_start: 0.7617 (OUTLIER) cc_final: 0.7412 (t0) REVERT: G 84 SER cc_start: 0.8719 (p) cc_final: 0.8424 (t) REVERT: J 50 ASP cc_start: 0.8668 (t0) cc_final: 0.8452 (t0) REVERT: J 70 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7935 (pt0) REVERT: D 150 MET cc_start: 0.8182 (mmm) cc_final: 0.7875 (tpt) REVERT: D 482 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8143 (mm-30) REVERT: D 486 TYR cc_start: 0.8222 (OUTLIER) cc_final: 0.7365 (p90) REVERT: F 577 GLN cc_start: 0.8798 (tp-100) cc_final: 0.8302 (mm-40) REVERT: F 584 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8029 (mt-10) REVERT: F 655 LYS cc_start: 0.6944 (ptpt) cc_final: 0.6700 (pttm) REVERT: K 50 ASP cc_start: 0.8641 (t0) cc_final: 0.8176 (t0) REVERT: K 70 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8027 (pt0) outliers start: 62 outliers final: 49 residues processed: 320 average time/residue: 0.3785 time to fit residues: 184.5294 Evaluate side-chains 324 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 266 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 486 TYR 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 43 GLN Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 165 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 E residue 545 LEU Chi-restraints excluded: chain E residue 579 ARG Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain 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 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 213 ILE Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 365 SER 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 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 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 64 optimal weight: 0.7980 chunk 159 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 196 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN E 577 GLN ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 24 GLN ** 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 = 0.3561 r_free = 0.3561 target = 0.097223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.079124 restraints weight = 44666.194| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.01 r_work: 0.3091 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21195 Z= 0.149 Angle : 0.651 11.677 29025 Z= 0.312 Chirality : 0.046 0.293 3543 Planarity : 0.004 0.038 3474 Dihedral : 5.980 52.444 5195 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.81 % Allowed : 16.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2343 helix: 1.80 (0.27), residues: 393 sheet: 0.11 (0.19), residues: 744 loop : -0.27 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP G 71D HIS 0.006 0.001 HIS A 374 PHE 0.016 0.001 PHE A 376 TYR 0.024 0.001 TYR F 638 ARG 0.008 0.000 ARG E 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 60) link_NAG-ASN : angle 1.97418 ( 180) link_ALPHA1-6 : bond 0.00418 ( 12) link_ALPHA1-6 : angle 2.11306 ( 36) link_BETA1-4 : bond 0.00577 ( 36) link_BETA1-4 : angle 1.60589 ( 108) link_ALPHA1-2 : bond 0.00149 ( 6) link_ALPHA1-2 : angle 1.67698 ( 18) link_ALPHA1-3 : bond 0.00617 ( 12) link_ALPHA1-3 : angle 1.58423 ( 36) hydrogen bonds : bond 0.03574 ( 672) hydrogen bonds : angle 5.23157 ( 1809) link_BETA1-6 : bond 0.03543 ( 3) link_BETA1-6 : angle 4.21723 ( 9) SS BOND : bond 0.00238 ( 39) SS BOND : angle 0.92555 ( 78) covalent geometry : bond 0.00337 (21027) covalent geometry : angle 0.61433 (28560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8589.87 seconds wall clock time: 149 minutes 14.07 seconds (8954.07 seconds total)