Starting phenix.real_space_refine on Wed May 21 02:44:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gje_40088/05_2025/8gje_40088.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gje_40088/05_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_40088/05_2025/8gje_40088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gje_40088/05_2025/8gje_40088.map" model { file = "/net/cci-nas-00/data/ceres_data/8gje_40088/05_2025/8gje_40088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gje_40088/05_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-5687/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: 12.55, per 1000 atoms: 0.61 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: 6.08 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: 2.88 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: 8.85 Time building geometry restraints manager: 6.92 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: 0.11 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: 1.650 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: 0.030 Extract box with map and model: 0.760 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 48.360 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.180 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.600 ------------------------------------------------------------------------------- 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 : 2.408 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: 0.4000 time to fit residues: 372.6033 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 : 2.265 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.082503 restraints weight = 48108.386| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.62 r_work: 0.3190 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- 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 2.38783 ( 180) link_ALPHA1-6 : bond 0.00596 ( 12) link_ALPHA1-6 : angle 2.64574 ( 36) link_BETA1-4 : bond 0.00741 ( 36) link_BETA1-4 : angle 2.04149 ( 108) link_ALPHA1-2 : bond 0.00082 ( 6) link_ALPHA1-2 : angle 1.77341 ( 18) link_ALPHA1-3 : bond 0.00502 ( 12) link_ALPHA1-3 : angle 1.86596 ( 36) hydrogen bonds : bond 0.04610 ( 672) hydrogen bonds : angle 6.35677 ( 1809) link_BETA1-6 : bond 0.04033 ( 3) link_BETA1-6 : angle 4.77385 ( 9) SS BOND : bond 0.00239 ( 39) SS BOND : angle 1.12838 ( 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 : 2.437 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: 0.8655 (ptm) cc_final: 0.8344 (ptm) REVERT: A 150 MET cc_start: 0.8206 (mmm) cc_final: 0.7880 (tpp) REVERT: A 277 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8650 (tt) REVERT: A 376 PHE cc_start: 0.7922 (m-80) cc_final: 0.7084 (m-80) REVERT: B 584 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8458 (mt-10) REVERT: B 588 LYS cc_start: 0.8717 (mttt) cc_final: 0.8318 (mttm) REVERT: B 589 ASP cc_start: 0.8643 (m-30) cc_final: 0.8241 (m-30) REVERT: B 625 ASN cc_start: 0.8153 (OUTLIER) cc_final: 0.7809 (t0) REVERT: B 648 ASP cc_start: 0.8848 (m-30) cc_final: 0.8425 (t0) REVERT: H 23 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8005 (mp0) REVERT: H 28 ASN cc_start: 0.7867 (t0) cc_final: 0.7566 (t0) REVERT: H 84 SER cc_start: 0.9138 (p) cc_final: 0.8680 (t) REVERT: L 11 LEU cc_start: 0.8446 (mt) cc_final: 0.8201 (mt) REVERT: L 50 ASP cc_start: 0.7270 (t0) cc_final: 0.6134 (t0) REVERT: L 70 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7714 (pt0) REVERT: C 98 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8425 (t0) REVERT: C 152 LYS cc_start: 0.9213 (mttt) cc_final: 0.8860 (mtmm) REVERT: C 185 LYS cc_start: 0.8735 (mttt) cc_final: 0.8163 (tptp) REVERT: C 302 ASN cc_start: 0.8106 (m110) cc_final: 0.7628 (m110) REVERT: C 482 GLU cc_start: 0.8314 (mp0) cc_final: 0.7784 (mp0) REVERT: C 486 TYR cc_start: 0.7675 (p90) cc_final: 0.7064 (p90) REVERT: E 652 GLN cc_start: 0.8691 (tp40) cc_final: 0.8313 (tp40) REVERT: E 657 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8357 (mm-30) REVERT: G 28 ASN cc_start: 0.7982 (t0) cc_final: 0.7631 (t0) REVERT: G 84 SER cc_start: 0.8835 (p) cc_final: 0.8371 (t) REVERT: J 50 ASP cc_start: 0.6951 (t0) cc_final: 0.6715 (t0) REVERT: J 70 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7800 (pt0) REVERT: J 82 ASP cc_start: 0.7138 (m-30) cc_final: 0.6876 (m-30) REVERT: D 53 PHE cc_start: 0.7632 (m-80) cc_final: 0.7253 (m-10) REVERT: D 95 MET cc_start: 0.8525 (ptm) cc_final: 0.8290 (ptm) REVERT: D 150 MET cc_start: 0.8098 (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: 0.8965 (OUTLIER) cc_final: 0.8681 (mm) REVERT: F 584 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8611 (mt-10) REVERT: F 589 ASP cc_start: 0.8855 (m-30) cc_final: 0.8643 (m-30) REVERT: F 625 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.8054 (t0) REVERT: K 24 GLN cc_start: 0.7683 (tt0) cc_final: 0.7459 (tt0) REVERT: K 50 ASP cc_start: 0.7157 (t0) cc_final: 0.5945 (t0) REVERT: K 62 PHE cc_start: 0.7350 (m-80) cc_final: 0.7143 (m-80) REVERT: K 70 GLU cc_start: 0.8531 (mt-10) cc_final: 0.7903 (pt0) REVERT: K 82 ASP cc_start: 0.7300 (m-30) cc_final: 0.6932 (m-30) outliers start: 64 outliers final: 36 residues processed: 401 average time/residue: 0.3516 time to fit residues: 209.0275 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 : 2.346 ------------------------------------------------------------------------------- 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: 1.9990 chunk 12 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 157 optimal weight: 0.4980 chunk 201 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3606 r_free = 0.3606 target = 0.099477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.081047 restraints weight = 43668.095| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.97 r_work: 0.3133 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21195 Z= 0.168 Angle : 0.684 9.284 29025 Z= 0.328 Chirality : 0.047 0.291 3543 Planarity : 0.004 0.036 3474 Dihedral : 9.290 66.792 5197 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.95 % Allowed : 10.84 % Favored : 86.21 % 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: 0.81 (0.17), residues: 2343 helix: 1.66 (0.26), residues: 390 sheet: 0.45 (0.18), residues: 738 loop : 0.35 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 571 HIS 0.004 0.001 HIS C 105 PHE 0.018 0.001 PHE D 376 TYR 0.027 0.002 TYR L 49 ARG 0.005 0.001 ARG K 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 60) link_NAG-ASN : angle 2.27115 ( 180) link_ALPHA1-6 : bond 0.00672 ( 12) link_ALPHA1-6 : angle 2.54606 ( 36) link_BETA1-4 : bond 0.00650 ( 36) link_BETA1-4 : angle 1.75722 ( 108) link_ALPHA1-2 : bond 0.00090 ( 6) link_ALPHA1-2 : angle 1.75243 ( 18) link_ALPHA1-3 : bond 0.00714 ( 12) link_ALPHA1-3 : angle 1.55031 ( 36) hydrogen bonds : bond 0.04107 ( 672) hydrogen bonds : angle 5.92139 ( 1809) link_BETA1-6 : bond 0.03762 ( 3) link_BETA1-6 : angle 4.42564 ( 9) SS BOND : bond 0.00215 ( 39) SS BOND : angle 1.02972 ( 78) covalent geometry : bond 0.00379 (21027) covalent geometry : angle 0.63952 (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 372 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 310 time to evaluate : 2.218 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 150 MET cc_start: 0.8379 (mmm) cc_final: 0.8140 (tpp) REVERT: A 376 PHE cc_start: 0.8122 (m-80) cc_final: 0.7455 (m-80) REVERT: B 589 ASP cc_start: 0.8314 (m-30) cc_final: 0.8012 (m-30) REVERT: B 625 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7610 (t0) REVERT: B 630 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7449 (mp0) REVERT: B 648 ASP cc_start: 0.8520 (m-30) cc_final: 0.8185 (t0) REVERT: B 653 GLN cc_start: 0.7637 (tt0) cc_final: 0.7246 (tt0) REVERT: H 84 SER cc_start: 0.9150 (p) cc_final: 0.8721 (t) REVERT: L 3 GLN cc_start: 0.8255 (pp30) cc_final: 0.7957 (pp30) REVERT: L 11 LEU cc_start: 0.8584 (mt) cc_final: 0.8364 (mt) REVERT: L 24 GLN cc_start: 0.7859 (tt0) cc_final: 0.7617 (tt0) REVERT: L 50 ASP cc_start: 0.8043 (t0) cc_final: 0.7454 (t0) REVERT: L 70 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7843 (pt0) REVERT: L 77 ASN cc_start: 0.7682 (t0) cc_final: 0.7454 (t0) REVERT: C 98 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8592 (t0) REVERT: C 185 LYS cc_start: 0.8563 (mttt) cc_final: 0.8336 (tptp) REVERT: E 575 GLN cc_start: 0.8918 (mt0) cc_final: 0.8420 (mm110) REVERT: E 579 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8390 (mpp80) REVERT: E 657 GLU cc_start: 0.8231 (mm-30) cc_final: 0.8010 (mm-30) REVERT: G 84 SER cc_start: 0.8720 (p) cc_final: 0.8339 (t) REVERT: J 50 ASP cc_start: 0.7693 (t0) cc_final: 0.7433 (t0) REVERT: J 70 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7908 (pt0) REVERT: D 53 PHE cc_start: 0.7720 (m-80) cc_final: 0.7389 (m-10) REVERT: D 150 MET cc_start: 0.8369 (mmm) cc_final: 0.8130 (tpp) REVERT: D 320 THR cc_start: 0.9212 (m) cc_final: 0.8997 (p) REVERT: D 425 ASN cc_start: 0.8379 (OUTLIER) cc_final: 0.7909 (p0) REVERT: D 486 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.7432 (p90) REVERT: F 577 GLN cc_start: 0.8704 (tp-100) cc_final: 0.8195 (mm-40) REVERT: F 589 ASP cc_start: 0.8536 (m-30) cc_final: 0.8328 (m-30) REVERT: F 625 ASN cc_start: 0.8010 (OUTLIER) cc_final: 0.7722 (t0) REVERT: F 630 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7470 (mp0) REVERT: K 50 ASP cc_start: 0.7965 (t0) cc_final: 0.7621 (t0) REVERT: K 70 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8089 (pt0) outliers start: 62 outliers final: 42 residues processed: 351 average time/residue: 0.3513 time to fit residues: 184.4122 Evaluate side-chains 321 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 273 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 579 ARG Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 588 LYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 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 277 LEU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 425 ASN Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain I residue 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: 6.9990 chunk 176 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 chunk 222 optimal weight: 0.9990 chunk 175 optimal weight: 0.7980 chunk 221 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 226 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 167 optimal weight: 0.0060 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 170 GLN C 425 ASN ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 ASN F 575 GLN I 3 GLN K 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.100122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.081731 restraints weight = 43774.776| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.98 r_work: 0.3162 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21195 Z= 0.123 Angle : 0.640 9.051 29025 Z= 0.303 Chirality : 0.046 0.291 3543 Planarity : 0.004 0.043 3474 Dihedral : 8.100 55.357 5197 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.00 % Allowed : 12.17 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.76 (0.17), residues: 2343 helix: 1.65 (0.27), residues: 393 sheet: 0.45 (0.18), residues: 738 loop : 0.28 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP I 71D HIS 0.003 0.001 HIS A 105 PHE 0.026 0.001 PHE D 53 TYR 0.029 0.001 TYR F 638 ARG 0.006 0.000 ARG E 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 60) link_NAG-ASN : angle 2.15903 ( 180) link_ALPHA1-6 : bond 0.00660 ( 12) link_ALPHA1-6 : angle 2.33269 ( 36) link_BETA1-4 : bond 0.00620 ( 36) link_BETA1-4 : angle 1.69943 ( 108) link_ALPHA1-2 : bond 0.00153 ( 6) link_ALPHA1-2 : angle 1.70928 ( 18) link_ALPHA1-3 : bond 0.00762 ( 12) link_ALPHA1-3 : angle 1.65979 ( 36) hydrogen bonds : bond 0.03682 ( 672) hydrogen bonds : angle 5.65969 ( 1809) link_BETA1-6 : bond 0.03670 ( 3) link_BETA1-6 : angle 4.72944 ( 9) SS BOND : bond 0.00198 ( 39) SS BOND : angle 0.95363 ( 78) covalent geometry : bond 0.00265 (21027) covalent geometry : angle 0.59558 (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 372 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 309 time to evaluate : 2.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7868 (tt) REVERT: A 376 PHE cc_start: 0.8061 (m-80) cc_final: 0.7453 (m-80) REVERT: B 589 ASP cc_start: 0.8264 (m-30) cc_final: 0.8048 (m-30) REVERT: B 625 ASN cc_start: 0.7895 (OUTLIER) cc_final: 0.7566 (t0) REVERT: B 648 ASP cc_start: 0.8315 (m-30) cc_final: 0.7974 (t0) REVERT: H 72 ASP cc_start: 0.7870 (m-30) cc_final: 0.5087 (m-30) REVERT: H 84 SER cc_start: 0.9119 (p) cc_final: 0.8695 (t) REVERT: L 3 GLN cc_start: 0.8268 (pp30) cc_final: 0.7936 (pp30) REVERT: L 11 LEU cc_start: 0.8701 (mt) cc_final: 0.8457 (mt) REVERT: L 24 GLN cc_start: 0.7817 (tt0) cc_final: 0.7491 (tt0) REVERT: L 49 TYR cc_start: 0.8627 (p90) cc_final: 0.8396 (p90) REVERT: L 50 ASP cc_start: 0.8318 (t0) cc_final: 0.7794 (t0) REVERT: L 70 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7825 (pt0) REVERT: C 185 LYS cc_start: 0.8575 (mttt) cc_final: 0.8366 (tptp) REVERT: C 302 ASN cc_start: 0.7857 (m110) cc_final: 0.7657 (m110) REVERT: E 579 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8448 (mpp80) REVERT: G 84 SER cc_start: 0.8687 (p) cc_final: 0.8297 (t) REVERT: J 70 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7917 (pt0) REVERT: D 150 MET cc_start: 0.8407 (mmm) cc_final: 0.8154 (tpp) REVERT: D 320 THR cc_start: 0.9237 (m) cc_final: 0.9004 (p) REVERT: D 482 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7966 (mm-30) REVERT: D 486 TYR cc_start: 0.8047 (OUTLIER) cc_final: 0.7481 (p90) REVERT: F 577 GLN cc_start: 0.8566 (tp-100) cc_final: 0.7989 (mm-40) REVERT: F 584 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8015 (mt-10) REVERT: F 625 ASN cc_start: 0.8030 (OUTLIER) cc_final: 0.7822 (t0) REVERT: I 28 ASN cc_start: 0.7942 (t0) cc_final: 0.7672 (t0) REVERT: K 70 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8087 (pt0) outliers start: 63 outliers final: 39 residues processed: 351 average time/residue: 0.3376 time to fit residues: 176.5907 Evaluate side-chains 327 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 282 time to evaluate : 2.109 ------------------------------------------------------------------------------- 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 B residue 581 LEU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain E residue 538 THR 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 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 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 625 ASN Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain K residue 63 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 61 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 8 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 221 optimal weight: 0.7980 chunk 163 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN H 43 GLN C 425 ASN ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 GLN ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.097813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.079334 restraints weight = 44258.496| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.99 r_work: 0.3098 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3763 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= 0.176 Angle : 0.665 9.640 29025 Z= 0.315 Chirality : 0.047 0.291 3543 Planarity : 0.004 0.047 3474 Dihedral : 7.197 52.526 5197 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.09 % Allowed : 13.31 % Favored : 83.59 % 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: 0.62 (0.17), residues: 2343 helix: 1.66 (0.27), residues: 393 sheet: 0.35 (0.18), residues: 741 loop : 0.14 (0.18), residues: 1209 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 0.015 0.001 PHE D 376 TYR 0.020 0.001 TYR L 49 ARG 0.006 0.001 ARG E 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 60) link_NAG-ASN : angle 2.16986 ( 180) link_ALPHA1-6 : bond 0.00669 ( 12) link_ALPHA1-6 : angle 2.41287 ( 36) link_BETA1-4 : bond 0.00586 ( 36) link_BETA1-4 : angle 1.71385 ( 108) link_ALPHA1-2 : bond 0.00126 ( 6) link_ALPHA1-2 : angle 1.76156 ( 18) link_ALPHA1-3 : bond 0.00649 ( 12) link_ALPHA1-3 : angle 1.85173 ( 36) hydrogen bonds : bond 0.03850 ( 672) hydrogen bonds : angle 5.53674 ( 1809) link_BETA1-6 : bond 0.03640 ( 3) link_BETA1-6 : angle 4.18415 ( 9) SS BOND : bond 0.00236 ( 39) SS BOND : angle 1.06605 ( 78) covalent geometry : bond 0.00401 (21027) covalent geometry : angle 0.62185 (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 354 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 289 time to evaluate : 2.170 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: 0.8361 (OUTLIER) cc_final: 0.7945 (tt) REVERT: A 376 PHE cc_start: 0.8046 (m-80) cc_final: 0.7341 (m-80) REVERT: B 589 ASP cc_start: 0.8278 (m-30) cc_final: 0.8065 (m-30) REVERT: B 625 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7559 (t0) REVERT: B 630 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7414 (mp0) REVERT: B 648 ASP cc_start: 0.8420 (m-30) cc_final: 0.8059 (t0) REVERT: H 28 ASN cc_start: 0.7843 (t0) cc_final: 0.7594 (t0) REVERT: H 43 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8383 (mp10) REVERT: H 84 SER cc_start: 0.9103 (p) cc_final: 0.8690 (t) REVERT: L 3 GLN cc_start: 0.8231 (pp30) cc_final: 0.7926 (pp30) REVERT: L 50 ASP cc_start: 0.8707 (t0) cc_final: 0.8228 (t0) REVERT: L 70 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7872 (pt0) REVERT: E 579 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8515 (mpp80) REVERT: E 625 ASN cc_start: 0.7942 (OUTLIER) cc_final: 0.7665 (t0) REVERT: G 84 SER cc_start: 0.8669 (p) cc_final: 0.8221 (t) REVERT: J 50 ASP cc_start: 0.8479 (t0) cc_final: 0.8134 (t0) REVERT: J 70 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7908 (pt0) REVERT: D 150 MET cc_start: 0.8386 (mmm) cc_final: 0.8166 (tpp) REVERT: D 209 ASN cc_start: 0.8841 (t0) cc_final: 0.8615 (t0) REVERT: D 320 THR cc_start: 0.9249 (m) cc_final: 0.9040 (p) REVERT: D 482 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8122 (mm-30) REVERT: D 486 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.7520 (p90) REVERT: F 577 GLN cc_start: 0.8616 (tp-100) cc_final: 0.8046 (mm-40) REVERT: F 584 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8018 (mt-10) REVERT: F 630 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7604 (mp0) REVERT: K 70 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8050 (pt0) outliers start: 65 outliers final: 48 residues processed: 334 average time/residue: 0.3341 time to fit residues: 168.4409 Evaluate side-chains 325 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 270 time to evaluate : 2.199 ------------------------------------------------------------------------------- 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 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 51 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 579 ARG Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 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 595 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain K residue 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: 3.9990 chunk 60 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 211 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 653 GLN J 24 GLN ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.096490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.078065 restraints weight = 44255.337| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.97 r_work: 0.3085 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21195 Z= 0.194 Angle : 0.676 10.103 29025 Z= 0.322 Chirality : 0.047 0.292 3543 Planarity : 0.004 0.042 3474 Dihedral : 6.930 53.266 5195 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.42 % Allowed : 13.93 % Favored : 82.64 % 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: 0.47 (0.17), residues: 2343 helix: 1.74 (0.27), residues: 393 sheet: 0.20 (0.18), residues: 741 loop : 0.01 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP I 71D HIS 0.006 0.001 HIS D 374 PHE 0.016 0.001 PHE D 376 TYR 0.024 0.002 TYR L 49 ARG 0.007 0.001 ARG I 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 60) link_NAG-ASN : angle 2.21516 ( 180) link_ALPHA1-6 : bond 0.00546 ( 12) link_ALPHA1-6 : angle 2.33534 ( 36) link_BETA1-4 : bond 0.00568 ( 36) link_BETA1-4 : angle 1.72114 ( 108) link_ALPHA1-2 : bond 0.00175 ( 6) link_ALPHA1-2 : angle 1.78301 ( 18) link_ALPHA1-3 : bond 0.00622 ( 12) link_ALPHA1-3 : angle 1.84462 ( 36) hydrogen bonds : bond 0.03880 ( 672) hydrogen bonds : angle 5.48126 ( 1809) link_BETA1-6 : bond 0.03397 ( 3) link_BETA1-6 : angle 4.11639 ( 9) SS BOND : bond 0.00228 ( 39) SS BOND : angle 1.01448 ( 78) covalent geometry : bond 0.00447 (21027) covalent geometry : angle 0.63373 (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 362 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 290 time to evaluate : 2.130 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: 0.8581 (OUTLIER) cc_final: 0.8290 (p) REVERT: A 376 PHE cc_start: 0.8147 (m-80) cc_final: 0.7436 (m-80) REVERT: B 589 ASP cc_start: 0.8302 (m-30) cc_final: 0.8078 (m-30) REVERT: B 625 ASN cc_start: 0.7878 (OUTLIER) cc_final: 0.7551 (t0) REVERT: B 630 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7440 (mp0) REVERT: B 648 ASP cc_start: 0.8330 (m-30) cc_final: 0.7951 (t0) REVERT: H 28 ASN cc_start: 0.7770 (t0) cc_final: 0.7516 (t0) REVERT: H 43 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8181 (mp10) REVERT: H 84 SER cc_start: 0.9096 (p) cc_final: 0.8664 (t) REVERT: L 3 GLN cc_start: 0.8229 (pp30) cc_final: 0.7865 (pp30) REVERT: L 24 GLN cc_start: 0.7730 (tt0) cc_final: 0.7520 (tt0) REVERT: L 50 ASP cc_start: 0.8815 (t0) cc_final: 0.8370 (t0) REVERT: L 70 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7881 (pt0) REVERT: E 625 ASN cc_start: 0.7731 (OUTLIER) cc_final: 0.7513 (t0) REVERT: G 84 SER cc_start: 0.8746 (p) cc_final: 0.8456 (t) REVERT: J 50 ASP cc_start: 0.8615 (t0) cc_final: 0.8310 (t0) REVERT: J 70 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7925 (pt0) REVERT: D 150 MET cc_start: 0.8404 (mmm) cc_final: 0.8095 (tpt) REVERT: D 482 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8158 (mm-30) REVERT: D 486 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.7487 (p90) REVERT: F 584 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8009 (mt-10) REVERT: F 630 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7515 (mp0) REVERT: I 38 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7302 (ttp80) REVERT: K 70 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8072 (pt0) outliers start: 72 outliers final: 53 residues processed: 339 average time/residue: 0.3346 time to fit residues: 170.6526 Evaluate side-chains 325 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 265 time to evaluate : 2.097 ------------------------------------------------------------------------------- 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 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 46 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 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 647 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain K residue 7 SER 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: 0.9990 chunk 37 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 213 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN D 302 ASN ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN K 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.096908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.078491 restraints weight = 44038.300| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.98 r_work: 0.3106 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21195 Z= 0.144 Angle : 0.650 13.878 29025 Z= 0.308 Chirality : 0.046 0.385 3543 Planarity : 0.004 0.040 3474 Dihedral : 6.561 52.783 5195 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.33 % Allowed : 14.74 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.42 (0.17), residues: 2343 helix: 1.88 (0.27), residues: 390 sheet: 0.19 (0.18), residues: 750 loop : -0.11 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP I 71D HIS 0.004 0.001 HIS D 374 PHE 0.015 0.001 PHE D 376 TYR 0.022 0.001 TYR J 49 ARG 0.006 0.000 ARG I 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 60) link_NAG-ASN : angle 2.28291 ( 180) link_ALPHA1-6 : bond 0.00515 ( 12) link_ALPHA1-6 : angle 2.30622 ( 36) link_BETA1-4 : bond 0.00578 ( 36) link_BETA1-4 : angle 1.64374 ( 108) link_ALPHA1-2 : bond 0.00148 ( 6) link_ALPHA1-2 : angle 1.70880 ( 18) link_ALPHA1-3 : bond 0.00675 ( 12) link_ALPHA1-3 : angle 1.69796 ( 36) hydrogen bonds : bond 0.03616 ( 672) hydrogen bonds : angle 5.37791 ( 1809) link_BETA1-6 : bond 0.03665 ( 3) link_BETA1-6 : angle 4.30893 ( 9) SS BOND : bond 0.00209 ( 39) SS BOND : angle 0.91448 ( 78) covalent geometry : bond 0.00323 (21027) covalent geometry : angle 0.60525 (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 361 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 291 time to evaluate : 2.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8450 (p) REVERT: A 376 PHE cc_start: 0.8082 (m-80) cc_final: 0.7353 (m-80) REVERT: B 589 ASP cc_start: 0.8325 (m-30) cc_final: 0.8097 (m-30) REVERT: B 625 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7552 (t0) REVERT: B 630 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7372 (mp0) REVERT: B 648 ASP cc_start: 0.8184 (m-30) cc_final: 0.7887 (t0) REVERT: H 84 SER cc_start: 0.9077 (p) cc_final: 0.8611 (t) REVERT: L 3 GLN cc_start: 0.8208 (pp30) cc_final: 0.7923 (pp30) REVERT: L 50 ASP cc_start: 0.8882 (t0) cc_final: 0.8509 (t0) REVERT: L 70 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7833 (pt0) REVERT: C 66 HIS cc_start: 0.7269 (OUTLIER) cc_final: 0.7043 (t-90) REVERT: E 579 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8290 (mpp80) REVERT: E 625 ASN cc_start: 0.7854 (OUTLIER) cc_final: 0.7606 (t0) REVERT: G 84 SER cc_start: 0.8722 (p) cc_final: 0.8437 (t) REVERT: J 50 ASP cc_start: 0.8612 (t0) cc_final: 0.8344 (t0) REVERT: J 70 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7936 (pt0) REVERT: D 150 MET cc_start: 0.8324 (mmm) cc_final: 0.8120 (tpp) REVERT: D 217 TYR cc_start: 0.9212 (m-80) cc_final: 0.8820 (m-80) REVERT: D 482 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8144 (mm-30) REVERT: D 486 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7499 (p90) REVERT: F 577 GLN cc_start: 0.8572 (tp-100) cc_final: 0.8083 (mm-40) REVERT: F 584 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7997 (mt-10) REVERT: F 630 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7660 (mp0) REVERT: I 38 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7200 (ttp80) REVERT: K 62 PHE cc_start: 0.7260 (m-80) cc_final: 0.7029 (m-80) REVERT: K 70 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8032 (pt0) outliers start: 70 outliers final: 47 residues processed: 336 average time/residue: 0.3492 time to fit residues: 176.4502 Evaluate side-chains 322 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 267 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 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 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 E residue 625 ASN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 320 THR 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 647 GLU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain 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: 3.9990 chunk 90 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 206 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 575 GLN H 43 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 = 0.3553 r_free = 0.3553 target = 0.096506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.078009 restraints weight = 44329.217| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.03 r_work: 0.3092 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21195 Z= 0.150 Angle : 0.647 10.626 29025 Z= 0.308 Chirality : 0.046 0.354 3543 Planarity : 0.004 0.042 3474 Dihedral : 6.275 52.600 5195 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.14 % Allowed : 15.41 % 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: 0.38 (0.17), residues: 2343 helix: 1.88 (0.27), residues: 390 sheet: 0.18 (0.18), residues: 750 loop : -0.15 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP I 71D HIS 0.004 0.001 HIS D 374 PHE 0.012 0.001 PHE D 376 TYR 0.021 0.001 TYR L 49 ARG 0.008 0.001 ARG J 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 60) link_NAG-ASN : angle 2.10062 ( 180) link_ALPHA1-6 : bond 0.00478 ( 12) link_ALPHA1-6 : angle 2.23698 ( 36) link_BETA1-4 : bond 0.00583 ( 36) link_BETA1-4 : angle 1.63781 ( 108) link_ALPHA1-2 : bond 0.00145 ( 6) link_ALPHA1-2 : angle 1.71019 ( 18) link_ALPHA1-3 : bond 0.00641 ( 12) link_ALPHA1-3 : angle 1.69433 ( 36) hydrogen bonds : bond 0.03655 ( 672) hydrogen bonds : angle 5.32556 ( 1809) link_BETA1-6 : bond 0.03599 ( 3) link_BETA1-6 : angle 4.28162 ( 9) SS BOND : bond 0.00204 ( 39) SS BOND : angle 0.91082 ( 78) covalent geometry : bond 0.00338 (21027) covalent geometry : angle 0.60633 (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 355 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 289 time to evaluate : 2.396 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: 0.8786 (OUTLIER) cc_final: 0.8432 (p) REVERT: A 376 PHE cc_start: 0.8096 (m-80) cc_final: 0.7339 (m-80) REVERT: B 589 ASP cc_start: 0.8347 (m-30) cc_final: 0.8105 (m-30) REVERT: B 625 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7575 (t0) REVERT: B 630 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7421 (mp0) REVERT: B 648 ASP cc_start: 0.8188 (m-30) cc_final: 0.7919 (t0) REVERT: H 84 SER cc_start: 0.9136 (p) cc_final: 0.8712 (t) REVERT: L 3 GLN cc_start: 0.8168 (pp30) cc_final: 0.7878 (pp30) REVERT: L 6 GLN cc_start: 0.8155 (tp40) cc_final: 0.7724 (tp40) REVERT: L 50 ASP cc_start: 0.8861 (t0) cc_final: 0.8541 (t0) REVERT: L 70 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7839 (pt0) REVERT: C 66 HIS cc_start: 0.7251 (OUTLIER) cc_final: 0.7019 (t-90) REVERT: E 625 ASN cc_start: 0.7824 (OUTLIER) cc_final: 0.7558 (t0) REVERT: G 84 SER cc_start: 0.8782 (p) cc_final: 0.8487 (t) REVERT: J 50 ASP cc_start: 0.8664 (t0) cc_final: 0.8436 (t0) REVERT: J 70 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7910 (pt0) REVERT: D 150 MET cc_start: 0.8329 (mmm) cc_final: 0.8024 (tpt) REVERT: D 425 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8231 (p0) REVERT: D 486 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7403 (p90) REVERT: F 577 GLN cc_start: 0.8575 (tp-100) cc_final: 0.8031 (mm-40) REVERT: F 584 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8012 (mt-10) REVERT: F 634 GLU cc_start: 0.8725 (tp30) cc_final: 0.8507 (tt0) REVERT: I 38 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7279 (ttp80) REVERT: K 50 ASP cc_start: 0.8621 (t0) cc_final: 0.7922 (t0) REVERT: K 70 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8041 (pt0) outliers start: 66 outliers final: 50 residues processed: 333 average time/residue: 0.3460 time to fit residues: 173.5163 Evaluate side-chains 330 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 273 time to evaluate : 2.365 ------------------------------------------------------------------------------- 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 426 MET Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain 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 425 ASN 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 636 SER Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 169 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 575 GLN E 577 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 = 0.3554 r_free = 0.3554 target = 0.096631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.078378 restraints weight = 44151.377| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.97 r_work: 0.3101 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4401 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= 0.150 Angle : 0.652 11.489 29025 Z= 0.312 Chirality : 0.046 0.290 3543 Planarity : 0.004 0.041 3474 Dihedral : 6.119 52.546 5195 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.04 % Allowed : 15.88 % Favored : 81.07 % 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: 0.34 (0.17), residues: 2343 helix: 1.88 (0.27), residues: 390 sheet: 0.16 (0.18), residues: 750 loop : -0.20 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP I 71D HIS 0.004 0.001 HIS D 374 PHE 0.012 0.001 PHE D 376 TYR 0.022 0.001 TYR K 49 ARG 0.007 0.000 ARG E 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 60) link_NAG-ASN : angle 2.03991 ( 180) link_ALPHA1-6 : bond 0.00444 ( 12) link_ALPHA1-6 : angle 2.19502 ( 36) link_BETA1-4 : bond 0.00575 ( 36) link_BETA1-4 : angle 1.62520 ( 108) link_ALPHA1-2 : bond 0.00147 ( 6) link_ALPHA1-2 : angle 1.69541 ( 18) link_ALPHA1-3 : bond 0.00627 ( 12) link_ALPHA1-3 : angle 1.65259 ( 36) hydrogen bonds : bond 0.03642 ( 672) hydrogen bonds : angle 5.30931 ( 1809) link_BETA1-6 : bond 0.03588 ( 3) link_BETA1-6 : angle 4.24720 ( 9) SS BOND : bond 0.00192 ( 39) SS BOND : angle 0.94059 ( 78) covalent geometry : bond 0.00341 (21027) covalent geometry : angle 0.61325 (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 348 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 284 time to evaluate : 2.185 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: 0.8729 (OUTLIER) cc_final: 0.8373 (p) REVERT: A 376 PHE cc_start: 0.8067 (m-80) cc_final: 0.7310 (m-80) REVERT: B 589 ASP cc_start: 0.8285 (m-30) cc_final: 0.8062 (m-30) REVERT: B 625 ASN cc_start: 0.7831 (OUTLIER) cc_final: 0.7485 (t0) REVERT: B 648 ASP cc_start: 0.8140 (m-30) cc_final: 0.7863 (t0) REVERT: H 84 SER cc_start: 0.9114 (p) cc_final: 0.8673 (t) REVERT: L 3 GLN cc_start: 0.8222 (pp30) cc_final: 0.7940 (pp30) REVERT: L 6 GLN cc_start: 0.8156 (tp40) cc_final: 0.7730 (tp40) REVERT: L 50 ASP cc_start: 0.8920 (t0) cc_final: 0.8669 (t0) REVERT: L 70 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7799 (pt0) REVERT: C 66 HIS cc_start: 0.7290 (OUTLIER) cc_final: 0.7013 (t-90) REVERT: E 625 ASN cc_start: 0.7763 (OUTLIER) cc_final: 0.7549 (t0) REVERT: E 655 LYS cc_start: 0.7272 (pttm) cc_final: 0.6832 (pttm) REVERT: G 84 SER cc_start: 0.8734 (p) cc_final: 0.8439 (t) REVERT: J 50 ASP cc_start: 0.8652 (t0) cc_final: 0.8429 (t0) REVERT: J 70 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7886 (pt0) REVERT: D 150 MET cc_start: 0.8307 (mmm) cc_final: 0.7999 (tpt) REVERT: D 425 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8220 (p0) REVERT: D 486 TYR cc_start: 0.8224 (OUTLIER) cc_final: 0.7428 (p90) REVERT: F 577 GLN cc_start: 0.8557 (tp-100) cc_final: 0.8021 (mm-40) REVERT: F 584 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8000 (mt-10) REVERT: F 626 MET cc_start: 0.8341 (ttt) cc_final: 0.7703 (ttt) REVERT: F 630 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7582 (mp0) REVERT: F 634 GLU cc_start: 0.8690 (tp30) cc_final: 0.8472 (tt0) REVERT: F 638 TYR cc_start: 0.8684 (m-10) cc_final: 0.8384 (m-10) REVERT: F 655 LYS cc_start: 0.6937 (ptpt) cc_final: 0.6710 (pttm) REVERT: I 38 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7258 (ttp80) REVERT: K 50 ASP cc_start: 0.8621 (t0) cc_final: 0.7915 (t0) REVERT: K 70 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8072 (pt0) outliers start: 64 outliers final: 50 residues processed: 328 average time/residue: 0.3507 time to fit residues: 172.6878 Evaluate side-chains 325 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 268 time to evaluate : 2.520 ------------------------------------------------------------------------------- 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 426 MET Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 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 425 ASN 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 620 THR Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER 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: 0.0000 chunk 145 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 188 optimal weight: 0.8980 chunk 228 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.096210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.078156 restraints weight = 44550.483| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.94 r_work: 0.3079 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4518 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= 0.185 Angle : 0.672 11.588 29025 Z= 0.322 Chirality : 0.046 0.294 3543 Planarity : 0.004 0.043 3474 Dihedral : 6.174 52.770 5195 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.09 % Allowed : 16.17 % Favored : 80.74 % 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: 1.81 (0.27), residues: 393 sheet: 0.18 (0.19), residues: 744 loop : -0.28 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP G 71D HIS 0.006 0.001 HIS D 374 PHE 0.012 0.001 PHE D 376 TYR 0.021 0.001 TYR K 49 ARG 0.008 0.001 ARG E 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 60) link_NAG-ASN : angle 2.03221 ( 180) link_ALPHA1-6 : bond 0.00414 ( 12) link_ALPHA1-6 : angle 2.17120 ( 36) link_BETA1-4 : bond 0.00576 ( 36) link_BETA1-4 : angle 1.64515 ( 108) link_ALPHA1-2 : bond 0.00191 ( 6) link_ALPHA1-2 : angle 1.75687 ( 18) link_ALPHA1-3 : bond 0.00566 ( 12) link_ALPHA1-3 : angle 1.70536 ( 36) hydrogen bonds : bond 0.03778 ( 672) hydrogen bonds : angle 5.33139 ( 1809) link_BETA1-6 : bond 0.03430 ( 3) link_BETA1-6 : angle 4.05083 ( 9) SS BOND : bond 0.00208 ( 39) SS BOND : angle 0.96558 ( 78) covalent geometry : bond 0.00425 (21027) covalent geometry : angle 0.63479 (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: 65 poor density : 273 time to evaluate : 2.377 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: 0.8595 (OUTLIER) cc_final: 0.8392 (p) REVERT: A 426 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6917 (mtm) REVERT: B 589 ASP cc_start: 0.8290 (m-30) cc_final: 0.8070 (m-30) REVERT: B 625 ASN cc_start: 0.7749 (OUTLIER) cc_final: 0.7411 (t0) REVERT: B 648 ASP cc_start: 0.8120 (m-30) cc_final: 0.7822 (t0) REVERT: H 84 SER cc_start: 0.9088 (p) cc_final: 0.8647 (t) REVERT: L 3 GLN cc_start: 0.8166 (pp30) cc_final: 0.7892 (pp30) REVERT: L 50 ASP cc_start: 0.8893 (t0) cc_final: 0.8584 (t0) REVERT: L 70 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7750 (pt0) REVERT: C 66 HIS cc_start: 0.7298 (OUTLIER) cc_final: 0.7049 (t-90) REVERT: E 625 ASN cc_start: 0.7719 (OUTLIER) cc_final: 0.7473 (t0) REVERT: G 84 SER cc_start: 0.8722 (p) cc_final: 0.8434 (t) REVERT: J 50 ASP cc_start: 0.8683 (t0) cc_final: 0.8476 (t0) REVERT: J 70 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7919 (pt0) REVERT: D 150 MET cc_start: 0.8335 (mmm) cc_final: 0.8053 (tpt) REVERT: D 425 ASN cc_start: 0.8492 (OUTLIER) cc_final: 0.8236 (p0) REVERT: D 486 TYR cc_start: 0.8291 (OUTLIER) cc_final: 0.7409 (p90) REVERT: F 577 GLN cc_start: 0.8562 (tp-100) cc_final: 0.8036 (mm-40) REVERT: F 584 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8020 (mt-10) REVERT: F 630 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7663 (mp0) REVERT: F 655 LYS cc_start: 0.6980 (ptpt) cc_final: 0.6766 (pttm) REVERT: I 38 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7304 (ttp80) REVERT: K 50 ASP cc_start: 0.8691 (t0) cc_final: 0.8021 (t0) REVERT: K 70 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8070 (pt0) outliers start: 65 outliers final: 51 residues processed: 320 average time/residue: 0.3422 time to fit residues: 164.8239 Evaluate side-chains 325 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 266 time to evaluate : 2.339 ------------------------------------------------------------------------------- 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 426 MET Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain 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 426 MET Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 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 425 ASN 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 606 THR Chi-restraints excluded: chain F residue 620 THR Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER 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: 0.4980 chunk 159 optimal weight: 0.2980 chunk 3 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 161 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 196 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 653 GLN E 577 GLN J 24 GLN ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.097634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.079465 restraints weight = 44230.230| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.98 r_work: 0.3111 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4584 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= 0.120 Angle : 0.636 11.619 29025 Z= 0.305 Chirality : 0.045 0.288 3543 Planarity : 0.004 0.037 3474 Dihedral : 5.839 52.440 5195 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.04 % Allowed : 16.41 % Favored : 80.55 % 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: 1.82 (0.27), residues: 393 sheet: 0.15 (0.19), residues: 735 loop : -0.25 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP H 71D HIS 0.004 0.001 HIS D 216 PHE 0.019 0.001 PHE H 73 TYR 0.034 0.001 TYR F 638 ARG 0.008 0.000 ARG E 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 60) link_NAG-ASN : angle 1.97130 ( 180) link_ALPHA1-6 : bond 0.00465 ( 12) link_ALPHA1-6 : angle 2.09626 ( 36) link_BETA1-4 : bond 0.00590 ( 36) link_BETA1-4 : angle 1.57378 ( 108) link_ALPHA1-2 : bond 0.00229 ( 6) link_ALPHA1-2 : angle 1.61200 ( 18) link_ALPHA1-3 : bond 0.00702 ( 12) link_ALPHA1-3 : angle 1.48147 ( 36) hydrogen bonds : bond 0.03403 ( 672) hydrogen bonds : angle 5.22691 ( 1809) link_BETA1-6 : bond 0.03732 ( 3) link_BETA1-6 : angle 4.45087 ( 9) SS BOND : bond 0.00194 ( 39) SS BOND : angle 0.92640 ( 78) covalent geometry : bond 0.00261 (21027) covalent geometry : angle 0.59865 (28560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8417.50 seconds wall clock time: 147 minutes 25.53 seconds (8845.53 seconds total)