Starting phenix.real_space_refine on Mon Oct 13 10:13:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p3i_71241/10_2025/9p3i_71241.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p3i_71241/10_2025/9p3i_71241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p3i_71241/10_2025/9p3i_71241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p3i_71241/10_2025/9p3i_71241.map" model { file = "/net/cci-nas-00/data/ceres_data/9p3i_71241/10_2025/9p3i_71241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p3i_71241/10_2025/9p3i_71241.cif" } resolution = 2.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 292 5.16 5 C 19740 2.51 5 N 5044 2.21 5 O 6532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31608 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 3956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3956 Classifications: {'peptide': 516} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 491} Chain breaks: 1 Chain: "B" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3644 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 23, 'TRANS': 451} Chain: "C" Number of atoms: 3956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3956 Classifications: {'peptide': 516} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 491} Chain breaks: 1 Chain: "D" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3644 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 23, 'TRANS': 451} Chain: "E" Number of atoms: 3956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3956 Classifications: {'peptide': 516} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 491} Chain breaks: 1 Chain: "F" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3644 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 23, 'TRANS': 451} Chain: "G" Number of atoms: 3956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3956 Classifications: {'peptide': 516} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 491} Chain breaks: 1 Chain: "H" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3644 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 23, 'TRANS': 451} Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "E" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "F" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "G" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "H" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Time building chain proxies: 7.63, per 1000 atoms: 0.24 Number of scatterers: 31608 At special positions: 0 Unit cell: (155.584, 155.584, 137.28, 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 292 16.00 O 6532 8.00 N 5044 7.00 C 19740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=96, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 132 " distance=2.03 Simple disulfide: pdb=" SG CYS A 137 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 250 " distance=2.03 Simple disulfide: pdb=" SG CYS A 239 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 438 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 408 " - pdb=" SG CYS A 427 " distance=2.03 Simple disulfide: pdb=" SG CYS A 455 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 742 " - pdb=" SG CYS B 780 " distance=2.03 Simple disulfide: pdb=" SG CYS B 754 " - pdb=" SG CYS B 887 " distance=2.03 Simple disulfide: pdb=" SG CYS B 768 " - pdb=" SG CYS B 898 " distance=2.03 Simple disulfide: pdb=" SG CYS B 783 " - pdb=" SG CYS B 906 " distance=2.03 Simple disulfide: pdb=" SG CYS B 809 " - pdb=" SG CYS B 818 " distance=2.03 Simple disulfide: pdb=" SG CYS B 826 " - pdb=" SG CYS B 835 " distance=2.03 Simple disulfide: pdb=" SG CYS B 866 " - pdb=" SG CYS B 870 " distance=2.03 Simple disulfide: pdb=" SG CYS B 972 " - pdb=" SG CYS B1002 " distance=2.03 Simple disulfide: pdb=" SG CYS B 995 " - pdb=" SG CYS B1047 " distance=2.03 Simple disulfide: pdb=" SG CYS B1012 " - pdb=" SG CYS B1017 " distance=2.03 Simple disulfide: pdb=" SG CYS B1048 " - pdb=" SG CYS B1053 " distance=2.03 Simple disulfide: pdb=" SG CYS B1087 " - pdb=" SG CYS B1091 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 132 " distance=2.03 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 189 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 250 " distance=2.03 Simple disulfide: pdb=" SG CYS C 239 " - pdb=" SG CYS C 354 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 438 " distance=2.03 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 408 " - pdb=" SG CYS C 427 " distance=2.03 Simple disulfide: pdb=" SG CYS C 455 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 742 " - pdb=" SG CYS D 780 " distance=2.03 Simple disulfide: pdb=" SG CYS D 754 " - pdb=" SG CYS D 887 " distance=2.03 Simple disulfide: pdb=" SG CYS D 768 " - pdb=" SG CYS D 898 " distance=2.03 Simple disulfide: pdb=" SG CYS D 783 " - pdb=" SG CYS D 906 " distance=2.03 Simple disulfide: pdb=" SG CYS D 809 " - pdb=" SG CYS D 818 " distance=2.03 Simple disulfide: pdb=" SG CYS D 826 " - pdb=" SG CYS D 835 " distance=2.03 Simple disulfide: pdb=" SG CYS D 866 " - pdb=" SG CYS D 870 " distance=2.03 Simple disulfide: pdb=" SG CYS D 972 " - pdb=" SG CYS D1002 " distance=2.03 Simple disulfide: pdb=" SG CYS D 995 " - pdb=" SG CYS D1047 " distance=2.03 Simple disulfide: pdb=" SG CYS D1012 " - pdb=" SG CYS D1017 " distance=2.03 Simple disulfide: pdb=" SG CYS D1048 " - pdb=" SG CYS D1053 " distance=2.03 Simple disulfide: pdb=" SG CYS D1087 " - pdb=" SG CYS D1091 " distance=2.03 Simple disulfide: pdb=" SG CYS E 30 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 161 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 132 " distance=2.03 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 179 " - pdb=" SG CYS E 189 " distance=2.03 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 250 " distance=2.03 Simple disulfide: pdb=" SG CYS E 239 " - pdb=" SG CYS E 354 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 438 " distance=2.03 Simple disulfide: pdb=" SG CYS E 383 " - pdb=" SG CYS E 392 " distance=2.03 Simple disulfide: pdb=" SG CYS E 408 " - pdb=" SG CYS E 427 " distance=2.03 Simple disulfide: pdb=" SG CYS E 455 " - pdb=" SG CYS E 478 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 773 " distance=2.03 Simple disulfide: pdb=" SG CYS F 742 " - pdb=" SG CYS F 780 " distance=2.03 Simple disulfide: pdb=" SG CYS F 754 " - pdb=" SG CYS F 887 " distance=2.03 Simple disulfide: pdb=" SG CYS F 768 " - pdb=" SG CYS F 898 " distance=2.03 Simple disulfide: pdb=" SG CYS F 783 " - pdb=" SG CYS F 906 " distance=2.03 Simple disulfide: pdb=" SG CYS F 809 " - pdb=" SG CYS F 818 " distance=2.03 Simple disulfide: pdb=" SG CYS F 826 " - pdb=" SG CYS F 835 " distance=2.03 Simple disulfide: pdb=" SG CYS F 866 " - pdb=" SG CYS F 870 " distance=2.03 Simple disulfide: pdb=" SG CYS F 972 " - pdb=" SG CYS F1002 " distance=2.03 Simple disulfide: pdb=" SG CYS F 995 " - pdb=" SG CYS F1047 " distance=2.03 Simple disulfide: pdb=" SG CYS F1012 " - pdb=" SG CYS F1017 " distance=2.03 Simple disulfide: pdb=" SG CYS F1048 " - pdb=" SG CYS F1053 " distance=2.03 Simple disulfide: pdb=" SG CYS F1087 " - pdb=" SG CYS F1091 " distance=2.03 Simple disulfide: pdb=" SG CYS G 30 " - pdb=" SG CYS G 155 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 161 " distance=2.03 Simple disulfide: pdb=" SG CYS G 113 " - pdb=" SG CYS G 132 " distance=2.03 Simple disulfide: pdb=" SG CYS G 137 " - pdb=" SG CYS G 142 " distance=2.03 Simple disulfide: pdb=" SG CYS G 179 " - pdb=" SG CYS G 189 " distance=2.03 Simple disulfide: pdb=" SG CYS G 214 " - pdb=" SG CYS G 250 " distance=2.03 Simple disulfide: pdb=" SG CYS G 239 " - pdb=" SG CYS G 354 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 438 " distance=2.03 Simple disulfide: pdb=" SG CYS G 383 " - pdb=" SG CYS G 392 " distance=2.03 Simple disulfide: pdb=" SG CYS G 408 " - pdb=" SG CYS G 427 " distance=2.03 Simple disulfide: pdb=" SG CYS G 455 " - pdb=" SG CYS G 478 " distance=2.03 Simple disulfide: pdb=" SG CYS H 738 " - pdb=" SG CYS H 773 " distance=2.03 Simple disulfide: pdb=" SG CYS H 742 " - pdb=" SG CYS H 780 " distance=2.03 Simple disulfide: pdb=" SG CYS H 754 " - pdb=" SG CYS H 887 " distance=2.03 Simple disulfide: pdb=" SG CYS H 768 " - pdb=" SG CYS H 898 " distance=2.03 Simple disulfide: pdb=" SG CYS H 783 " - pdb=" SG CYS H 906 " distance=2.03 Simple disulfide: pdb=" SG CYS H 809 " - pdb=" SG CYS H 818 " distance=2.03 Simple disulfide: pdb=" SG CYS H 826 " - pdb=" SG CYS H 835 " distance=2.03 Simple disulfide: pdb=" SG CYS H 866 " - pdb=" SG CYS H 870 " distance=2.03 Simple disulfide: pdb=" SG CYS H 972 " - pdb=" SG CYS H1002 " distance=2.03 Simple disulfide: pdb=" SG CYS H 995 " - pdb=" SG CYS H1047 " distance=2.03 Simple disulfide: pdb=" SG CYS H1012 " - pdb=" SG CYS H1017 " distance=2.03 Simple disulfide: pdb=" SG CYS H1048 " - pdb=" SG CYS H1053 " distance=2.03 Simple disulfide: pdb=" SG CYS H1087 " - pdb=" SG CYS H1091 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 5 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 5 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 5 " " BMA W 3 " - " MAN W 4 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG I 1 " - " ASN A 138 " " NAG J 1 " - " ASN A 350 " " NAG K 1 " - " ASN A 402 " " NAG L 1 " - " ASN B 930 " " NAG M 1 " - " ASN C 138 " " NAG N 1 " - " ASN C 350 " " NAG O 1 " - " ASN C 402 " " NAG P 1 " - " ASN D 930 " " NAG Q 1 " - " ASN E 138 " " NAG R 1 " - " ASN E 350 " " NAG S 1 " - " ASN E 402 " " NAG T 1 " - " ASN F 930 " " NAG U 1 " - " ASN G 138 " " NAG V 1 " - " ASN G 350 " " NAG W 1 " - " ASN G 402 " " NAG X 1 " - " ASN H 930 " Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds 7880 Ramachandran restraints generated. 3940 Oldfield, 0 Emsley, 3940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7344 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 44 sheets defined 19.9% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.719A pdb=" N ILE A 58 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 221 through 224 Processing helix chain 'A' and resid 225 through 234 Processing helix chain 'A' and resid 266 through 279 Processing helix chain 'A' and resid 446 through 463 Processing helix chain 'A' and resid 469 through 479 Processing helix chain 'A' and resid 481 through 512 removed outlier: 6.807A pdb=" N TRP A 498 " --> pdb=" O PHE A 494 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 499 " --> pdb=" O CYS A 495 " (cutoff:3.500A) Proline residue: A 502 - end of helix Processing helix chain 'A' and resid 629 through 650 removed outlier: 3.680A pdb=" N VAL A 645 " --> pdb=" O THR A 641 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE A 646 " --> pdb=" O CYS A 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 752 removed outlier: 3.777A pdb=" N SER B 752 " --> pdb=" O TRP B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 858 removed outlier: 3.706A pdb=" N GLY B 858 " --> pdb=" O LEU B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 922 Processing helix chain 'B' and resid 923 through 926 Processing helix chain 'B' and resid 963 through 968 removed outlier: 3.598A pdb=" N LEU B 967 " --> pdb=" O SER B 963 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 968 " --> pdb=" O PHE B 964 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 963 through 968' Processing helix chain 'B' and resid 1089 through 1106 removed outlier: 3.738A pdb=" N PHE B1093 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY B1106 " --> pdb=" O GLY B1102 " (cutoff:3.500A) Processing helix chain 'B' and resid 1108 through 1127 removed outlier: 3.526A pdb=" N VAL B1112 " --> pdb=" O TRP B1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 58 removed outlier: 3.719A pdb=" N ILE C 58 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 157 Processing helix chain 'C' and resid 195 through 200 Processing helix chain 'C' and resid 221 through 224 Processing helix chain 'C' and resid 225 through 234 Processing helix chain 'C' and resid 266 through 279 Processing helix chain 'C' and resid 446 through 463 Processing helix chain 'C' and resid 469 through 479 Processing helix chain 'C' and resid 481 through 512 removed outlier: 6.808A pdb=" N TRP C 498 " --> pdb=" O PHE C 494 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL C 499 " --> pdb=" O CYS C 495 " (cutoff:3.500A) Proline residue: C 502 - end of helix Processing helix chain 'C' and resid 629 through 650 removed outlier: 3.680A pdb=" N VAL C 645 " --> pdb=" O THR C 641 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE C 646 " --> pdb=" O CYS C 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 752 removed outlier: 3.777A pdb=" N SER D 752 " --> pdb=" O TRP D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 858 removed outlier: 3.707A pdb=" N GLY D 858 " --> pdb=" O LEU D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 922 Processing helix chain 'D' and resid 923 through 926 Processing helix chain 'D' and resid 963 through 968 removed outlier: 3.598A pdb=" N LEU D 967 " --> pdb=" O SER D 963 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER D 968 " --> pdb=" O PHE D 964 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 963 through 968' Processing helix chain 'D' and resid 1089 through 1106 removed outlier: 3.738A pdb=" N PHE D1093 " --> pdb=" O PHE D1089 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY D1106 " --> pdb=" O GLY D1102 " (cutoff:3.500A) Processing helix chain 'D' and resid 1108 through 1127 removed outlier: 3.526A pdb=" N VAL D1112 " --> pdb=" O TRP D1108 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 58 removed outlier: 3.719A pdb=" N ILE E 58 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 157 Processing helix chain 'E' and resid 195 through 200 Processing helix chain 'E' and resid 221 through 224 Processing helix chain 'E' and resid 225 through 234 Processing helix chain 'E' and resid 266 through 279 Processing helix chain 'E' and resid 446 through 463 Processing helix chain 'E' and resid 469 through 479 Processing helix chain 'E' and resid 481 through 512 removed outlier: 6.808A pdb=" N TRP E 498 " --> pdb=" O PHE E 494 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL E 499 " --> pdb=" O CYS E 495 " (cutoff:3.500A) Proline residue: E 502 - end of helix Processing helix chain 'E' and resid 629 through 650 removed outlier: 3.680A pdb=" N VAL E 645 " --> pdb=" O THR E 641 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE E 646 " --> pdb=" O CYS E 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 752 removed outlier: 3.777A pdb=" N SER F 752 " --> pdb=" O TRP F 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 854 through 858 removed outlier: 3.706A pdb=" N GLY F 858 " --> pdb=" O LEU F 855 " (cutoff:3.500A) Processing helix chain 'F' and resid 914 through 922 Processing helix chain 'F' and resid 923 through 926 Processing helix chain 'F' and resid 963 through 968 removed outlier: 3.598A pdb=" N LEU F 967 " --> pdb=" O SER F 963 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER F 968 " --> pdb=" O PHE F 964 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 963 through 968' Processing helix chain 'F' and resid 1089 through 1106 removed outlier: 3.737A pdb=" N PHE F1093 " --> pdb=" O PHE F1089 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY F1106 " --> pdb=" O GLY F1102 " (cutoff:3.500A) Processing helix chain 'F' and resid 1108 through 1127 removed outlier: 3.526A pdb=" N VAL F1112 " --> pdb=" O TRP F1108 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 58 removed outlier: 3.719A pdb=" N ILE G 58 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 157 Processing helix chain 'G' and resid 195 through 200 Processing helix chain 'G' and resid 221 through 224 Processing helix chain 'G' and resid 225 through 234 Processing helix chain 'G' and resid 266 through 279 Processing helix chain 'G' and resid 446 through 463 Processing helix chain 'G' and resid 469 through 479 Processing helix chain 'G' and resid 481 through 512 removed outlier: 6.808A pdb=" N TRP G 498 " --> pdb=" O PHE G 494 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL G 499 " --> pdb=" O CYS G 495 " (cutoff:3.500A) Proline residue: G 502 - end of helix Processing helix chain 'G' and resid 629 through 650 removed outlier: 3.680A pdb=" N VAL G 645 " --> pdb=" O THR G 641 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE G 646 " --> pdb=" O CYS G 642 " (cutoff:3.500A) Processing helix chain 'H' and resid 747 through 752 removed outlier: 3.778A pdb=" N SER H 752 " --> pdb=" O TRP H 749 " (cutoff:3.500A) Processing helix chain 'H' and resid 854 through 858 removed outlier: 3.706A pdb=" N GLY H 858 " --> pdb=" O LEU H 855 " (cutoff:3.500A) Processing helix chain 'H' and resid 914 through 922 Processing helix chain 'H' and resid 923 through 926 Processing helix chain 'H' and resid 963 through 968 removed outlier: 3.598A pdb=" N LEU H 967 " --> pdb=" O SER H 963 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER H 968 " --> pdb=" O PHE H 964 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 963 through 968' Processing helix chain 'H' and resid 1089 through 1106 removed outlier: 3.738A pdb=" N PHE H1093 " --> pdb=" O PHE H1089 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY H1106 " --> pdb=" O GLY H1102 " (cutoff:3.500A) Processing helix chain 'H' and resid 1108 through 1127 removed outlier: 3.525A pdb=" N VAL H1112 " --> pdb=" O TRP H1108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 30 removed outlier: 6.396A pdb=" N TYR A 24 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE A 173 " --> pdb=" O TYR A 24 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A 26 " --> pdb=" O ILE A 173 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLU A 175 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET A 28 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 130 through 137 Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 110 removed outlier: 10.830A pdb=" N PHE A 339 " --> pdb=" O GLN A 75 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N SER A 77 " --> pdb=" O PHE A 339 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE A 341 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N THR A 79 " --> pdb=" O PHE A 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 184 Processing sheet with id=AA5, first strand: chain 'A' and resid 293 through 295 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 293 through 295 current: chain 'B' and resid 687 through 695 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 703 through 735 current: chain 'B' and resid 781 through 812 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 815 through 821 current: chain 'B' and resid 859 through 862 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 859 through 862 current: chain 'B' and resid 884 through 886 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 884 through 886 current: chain 'B' and resid 941 through 944 Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 303 Processing sheet with id=AA7, first strand: chain 'A' and resid 379 through 386 removed outlier: 4.567A pdb=" N GLN A 421 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AA9, first strand: chain 'B' and resid 663 through 664 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 663 through 664 current: chain 'B' and resid 990 through 1012 removed outlier: 8.315A pdb=" N GLU B1001 " --> pdb=" O ALA B1026 " (cutoff:3.500A) removed outlier: 11.214A pdb=" N ALA B1026 " --> pdb=" O GLU B1001 " (cutoff:3.500A) removed outlier: 9.798A pdb=" N ASN B1024 " --> pdb=" O PRO B1003 " (cutoff:3.500A) removed outlier: 11.148A pdb=" N PHE B1005 " --> pdb=" O VAL B1022 " (cutoff:3.500A) removed outlier: 9.774A pdb=" N VAL B1022 " --> pdb=" O PHE B1005 " (cutoff:3.500A) removed outlier: 11.334A pdb=" N THR B1007 " --> pdb=" O SER B1020 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N SER B1020 " --> pdb=" O THR B1007 " (cutoff:3.500A) removed outlier: 11.452A pdb=" N ILE B1009 " --> pdb=" O TYR B1018 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N TYR B1018 " --> pdb=" O ILE B1009 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA B1011 " --> pdb=" O MET B1016 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N MET B1016 " --> pdb=" O ALA B1011 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1016 through 1036 current: chain 'B' and resid 1052 through 1053 Processing sheet with id=AB1, first strand: chain 'B' and resid 676 through 683 removed outlier: 3.616A pdb=" N GLY B 838 " --> pdb=" O HIS B 953 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN B 955 " --> pdb=" O ILE B 836 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ILE B 836 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL B 957 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL B 834 " --> pdb=" O VAL B 957 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 893 through 898 Processing sheet with id=AB3, first strand: chain 'C' and resid 23 through 30 removed outlier: 6.397A pdb=" N TYR C 24 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ILE C 173 " --> pdb=" O TYR C 24 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU C 26 " --> pdb=" O ILE C 173 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU C 175 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N MET C 28 " --> pdb=" O GLU C 175 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 130 through 137 Processing sheet with id=AB5, first strand: chain 'C' and resid 100 through 110 removed outlier: 10.830A pdb=" N PHE C 339 " --> pdb=" O GLN C 75 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N SER C 77 " --> pdb=" O PHE C 339 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE C 341 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N THR C 79 " --> pdb=" O PHE C 341 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 183 through 184 Processing sheet with id=AB7, first strand: chain 'C' and resid 293 through 295 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 293 through 295 current: chain 'D' and resid 687 through 695 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 703 through 735 current: chain 'D' and resid 781 through 812 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 815 through 821 current: chain 'D' and resid 859 through 862 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 859 through 862 current: chain 'D' and resid 884 through 886 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 884 through 886 current: chain 'D' and resid 941 through 944 Processing sheet with id=AB8, first strand: chain 'C' and resid 299 through 303 Processing sheet with id=AB9, first strand: chain 'C' and resid 379 through 386 removed outlier: 4.567A pdb=" N GLN C 421 " --> pdb=" O SER C 396 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AC2, first strand: chain 'D' and resid 663 through 664 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 663 through 664 current: chain 'D' and resid 990 through 1012 removed outlier: 8.315A pdb=" N GLU D1001 " --> pdb=" O ALA D1026 " (cutoff:3.500A) removed outlier: 11.213A pdb=" N ALA D1026 " --> pdb=" O GLU D1001 " (cutoff:3.500A) removed outlier: 9.798A pdb=" N ASN D1024 " --> pdb=" O PRO D1003 " (cutoff:3.500A) removed outlier: 11.148A pdb=" N PHE D1005 " --> pdb=" O VAL D1022 " (cutoff:3.500A) removed outlier: 9.774A pdb=" N VAL D1022 " --> pdb=" O PHE D1005 " (cutoff:3.500A) removed outlier: 11.335A pdb=" N THR D1007 " --> pdb=" O SER D1020 " (cutoff:3.500A) removed outlier: 9.943A pdb=" N SER D1020 " --> pdb=" O THR D1007 " (cutoff:3.500A) removed outlier: 11.452A pdb=" N ILE D1009 " --> pdb=" O TYR D1018 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N TYR D1018 " --> pdb=" O ILE D1009 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA D1011 " --> pdb=" O MET D1016 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N MET D1016 " --> pdb=" O ALA D1011 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 1016 through 1036 current: chain 'D' and resid 1052 through 1053 Processing sheet with id=AC3, first strand: chain 'D' and resid 676 through 683 removed outlier: 3.617A pdb=" N GLY D 838 " --> pdb=" O HIS D 953 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN D 955 " --> pdb=" O ILE D 836 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE D 836 " --> pdb=" O ASN D 955 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL D 957 " --> pdb=" O VAL D 834 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL D 834 " --> pdb=" O VAL D 957 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 893 through 898 Processing sheet with id=AC5, first strand: chain 'E' and resid 23 through 30 removed outlier: 6.396A pdb=" N TYR E 24 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE E 173 " --> pdb=" O TYR E 24 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU E 26 " --> pdb=" O ILE E 173 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLU E 175 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET E 28 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 130 through 137 Processing sheet with id=AC7, first strand: chain 'E' and resid 100 through 110 removed outlier: 10.830A pdb=" N PHE E 339 " --> pdb=" O GLN E 75 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N SER E 77 " --> pdb=" O PHE E 339 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE E 341 " --> pdb=" O SER E 77 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N THR E 79 " --> pdb=" O PHE E 341 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 183 through 184 Processing sheet with id=AC9, first strand: chain 'E' and resid 293 through 295 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 293 through 295 current: chain 'F' and resid 687 through 695 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 703 through 735 current: chain 'F' and resid 781 through 812 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 815 through 821 current: chain 'F' and resid 859 through 862 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 859 through 862 current: chain 'F' and resid 884 through 886 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 884 through 886 current: chain 'F' and resid 941 through 944 Processing sheet with id=AD1, first strand: chain 'E' and resid 299 through 303 Processing sheet with id=AD2, first strand: chain 'E' and resid 379 through 386 removed outlier: 4.567A pdb=" N GLN E 421 " --> pdb=" O SER E 396 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AD4, first strand: chain 'F' and resid 663 through 664 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 663 through 664 current: chain 'F' and resid 990 through 1012 removed outlier: 8.315A pdb=" N GLU F1001 " --> pdb=" O ALA F1026 " (cutoff:3.500A) removed outlier: 11.214A pdb=" N ALA F1026 " --> pdb=" O GLU F1001 " (cutoff:3.500A) removed outlier: 9.798A pdb=" N ASN F1024 " --> pdb=" O PRO F1003 " (cutoff:3.500A) removed outlier: 11.148A pdb=" N PHE F1005 " --> pdb=" O VAL F1022 " (cutoff:3.500A) removed outlier: 9.774A pdb=" N VAL F1022 " --> pdb=" O PHE F1005 " (cutoff:3.500A) removed outlier: 11.335A pdb=" N THR F1007 " --> pdb=" O SER F1020 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N SER F1020 " --> pdb=" O THR F1007 " (cutoff:3.500A) removed outlier: 11.452A pdb=" N ILE F1009 " --> pdb=" O TYR F1018 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N TYR F1018 " --> pdb=" O ILE F1009 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA F1011 " --> pdb=" O MET F1016 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N MET F1016 " --> pdb=" O ALA F1011 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 1016 through 1036 current: chain 'F' and resid 1052 through 1053 Processing sheet with id=AD5, first strand: chain 'F' and resid 676 through 683 removed outlier: 3.616A pdb=" N GLY F 838 " --> pdb=" O HIS F 953 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN F 955 " --> pdb=" O ILE F 836 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE F 836 " --> pdb=" O ASN F 955 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL F 957 " --> pdb=" O VAL F 834 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL F 834 " --> pdb=" O VAL F 957 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 893 through 898 Processing sheet with id=AD7, first strand: chain 'G' and resid 23 through 30 removed outlier: 6.396A pdb=" N TYR G 24 " --> pdb=" O GLN G 171 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE G 173 " --> pdb=" O TYR G 24 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU G 26 " --> pdb=" O ILE G 173 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU G 175 " --> pdb=" O LEU G 26 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET G 28 " --> pdb=" O GLU G 175 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 130 through 137 Processing sheet with id=AD9, first strand: chain 'G' and resid 100 through 110 removed outlier: 10.830A pdb=" N PHE G 339 " --> pdb=" O GLN G 75 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N SER G 77 " --> pdb=" O PHE G 339 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE G 341 " --> pdb=" O SER G 77 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N THR G 79 " --> pdb=" O PHE G 341 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 183 through 184 Processing sheet with id=AE2, first strand: chain 'G' and resid 293 through 295 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 293 through 295 current: chain 'H' and resid 687 through 695 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 703 through 735 current: chain 'H' and resid 781 through 812 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 815 through 821 current: chain 'H' and resid 859 through 862 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 859 through 862 current: chain 'H' and resid 884 through 886 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 884 through 886 current: chain 'H' and resid 941 through 944 Processing sheet with id=AE3, first strand: chain 'G' and resid 299 through 303 Processing sheet with id=AE4, first strand: chain 'G' and resid 379 through 386 removed outlier: 4.567A pdb=" N GLN G 421 " --> pdb=" O SER G 396 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AE6, first strand: chain 'H' and resid 663 through 664 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 663 through 664 current: chain 'H' and resid 990 through 1012 removed outlier: 8.315A pdb=" N GLU H1001 " --> pdb=" O ALA H1026 " (cutoff:3.500A) removed outlier: 11.213A pdb=" N ALA H1026 " --> pdb=" O GLU H1001 " (cutoff:3.500A) removed outlier: 9.798A pdb=" N ASN H1024 " --> pdb=" O PRO H1003 " (cutoff:3.500A) removed outlier: 11.148A pdb=" N PHE H1005 " --> pdb=" O VAL H1022 " (cutoff:3.500A) removed outlier: 9.774A pdb=" N VAL H1022 " --> pdb=" O PHE H1005 " (cutoff:3.500A) removed outlier: 11.335A pdb=" N THR H1007 " --> pdb=" O SER H1020 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N SER H1020 " --> pdb=" O THR H1007 " (cutoff:3.500A) removed outlier: 11.452A pdb=" N ILE H1009 " --> pdb=" O TYR H1018 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N TYR H1018 " --> pdb=" O ILE H1009 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA H1011 " --> pdb=" O MET H1016 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N MET H1016 " --> pdb=" O ALA H1011 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 1016 through 1036 current: chain 'H' and resid 1052 through 1053 Processing sheet with id=AE7, first strand: chain 'H' and resid 676 through 683 removed outlier: 3.616A pdb=" N GLY H 838 " --> pdb=" O HIS H 953 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN H 955 " --> pdb=" O ILE H 836 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ILE H 836 " --> pdb=" O ASN H 955 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL H 957 " --> pdb=" O VAL H 834 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL H 834 " --> pdb=" O VAL H 957 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 893 through 898 1040 hydrogen bonds defined for protein. 2796 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.03 Time building geometry restraints manager: 3.70 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: 9646 1.34 - 1.46: 6241 1.46 - 1.58: 15589 1.58 - 1.70: 0 1.70 - 1.82: 372 Bond restraints: 31848 Sorted by residual: bond pdb=" N ILE F 670 " pdb=" CA ILE F 670 " ideal model delta sigma weight residual 1.456 1.488 -0.032 8.70e-03 1.32e+04 1.32e+01 bond pdb=" N ILE H 670 " pdb=" CA ILE H 670 " ideal model delta sigma weight residual 1.456 1.488 -0.032 8.70e-03 1.32e+04 1.32e+01 bond pdb=" N ILE D 670 " pdb=" CA ILE D 670 " ideal model delta sigma weight residual 1.456 1.488 -0.032 8.70e-03 1.32e+04 1.32e+01 bond pdb=" N ILE B 670 " pdb=" CA ILE B 670 " ideal model delta sigma weight residual 1.456 1.487 -0.031 8.70e-03 1.32e+04 1.24e+01 bond pdb=" CA TYR D 690 " pdb=" C TYR D 690 " ideal model delta sigma weight residual 1.522 1.485 0.037 1.20e-02 6.94e+03 9.63e+00 ... (remaining 31843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 42036 1.88 - 3.77: 1108 3.77 - 5.65: 120 5.65 - 7.53: 30 7.53 - 9.42: 10 Bond angle restraints: 43304 Sorted by residual: angle pdb=" CA GLU H 701 " pdb=" CB GLU H 701 " pdb=" CG GLU H 701 " ideal model delta sigma weight residual 114.10 121.76 -7.66 2.00e+00 2.50e-01 1.47e+01 angle pdb=" CA GLU F 701 " pdb=" CB GLU F 701 " pdb=" CG GLU F 701 " ideal model delta sigma weight residual 114.10 121.76 -7.66 2.00e+00 2.50e-01 1.47e+01 angle pdb=" CA GLU D 701 " pdb=" CB GLU D 701 " pdb=" CG GLU D 701 " ideal model delta sigma weight residual 114.10 121.75 -7.65 2.00e+00 2.50e-01 1.46e+01 angle pdb=" CA GLU B 701 " pdb=" CB GLU B 701 " pdb=" CG GLU B 701 " ideal model delta sigma weight residual 114.10 121.73 -7.63 2.00e+00 2.50e-01 1.46e+01 angle pdb=" CG ARG D 960 " pdb=" CD ARG D 960 " pdb=" NE ARG D 960 " ideal model delta sigma weight residual 112.00 119.56 -7.56 2.20e+00 2.07e-01 1.18e+01 ... (remaining 43299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.23: 18158 21.23 - 42.46: 1400 42.46 - 63.68: 266 63.68 - 84.91: 104 84.91 - 106.14: 56 Dihedral angle restraints: 19984 sinusoidal: 8572 harmonic: 11412 Sorted by residual: dihedral pdb=" CB CYS B 742 " pdb=" SG CYS B 742 " pdb=" SG CYS B 780 " pdb=" CB CYS B 780 " ideal model delta sinusoidal sigma weight residual 93.00 148.93 -55.93 1 1.00e+01 1.00e-02 4.22e+01 dihedral pdb=" CB CYS F 742 " pdb=" SG CYS F 742 " pdb=" SG CYS F 780 " pdb=" CB CYS F 780 " ideal model delta sinusoidal sigma weight residual 93.00 148.92 -55.92 1 1.00e+01 1.00e-02 4.22e+01 dihedral pdb=" CB CYS D 742 " pdb=" SG CYS D 742 " pdb=" SG CYS D 780 " pdb=" CB CYS D 780 " ideal model delta sinusoidal sigma weight residual 93.00 148.92 -55.92 1 1.00e+01 1.00e-02 4.22e+01 ... (remaining 19981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 4743 0.093 - 0.185: 436 0.185 - 0.278: 49 0.278 - 0.370: 8 0.370 - 0.463: 8 Chirality restraints: 5244 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-02 2.50e+03 5.36e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-02 2.50e+03 5.33e+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 -1.94 -0.46 2.00e-02 2.50e+03 5.29e+02 ... (remaining 5241 not shown) Planarity restraints: 5352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 1 " -0.174 2.00e-02 2.50e+03 1.48e-01 2.76e+02 pdb=" C7 NAG W 1 " 0.032 2.00e-02 2.50e+03 pdb=" C8 NAG W 1 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG W 1 " 0.244 2.00e-02 2.50e+03 pdb=" O7 NAG W 1 " -0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 1 " 0.174 2.00e-02 2.50e+03 1.48e-01 2.75e+02 pdb=" C7 NAG O 1 " -0.032 2.00e-02 2.50e+03 pdb=" C8 NAG O 1 " -0.034 2.00e-02 2.50e+03 pdb=" N2 NAG O 1 " -0.243 2.00e-02 2.50e+03 pdb=" O7 NAG O 1 " 0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 1 " 0.174 2.00e-02 2.50e+03 1.48e-01 2.75e+02 pdb=" C7 NAG S 1 " -0.032 2.00e-02 2.50e+03 pdb=" C8 NAG S 1 " -0.034 2.00e-02 2.50e+03 pdb=" N2 NAG S 1 " -0.243 2.00e-02 2.50e+03 pdb=" O7 NAG S 1 " 0.135 2.00e-02 2.50e+03 ... (remaining 5349 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 236 2.63 - 3.19: 27067 3.19 - 3.76: 46901 3.76 - 4.33: 69038 4.33 - 4.90: 112830 Nonbonded interactions: 256072 Sorted by model distance: nonbonded pdb=" O ASN D1107 " pdb=" OD1 ASN D1107 " model vdw 2.057 3.040 nonbonded pdb=" O ASN B1107 " pdb=" OD1 ASN B1107 " model vdw 2.059 3.040 nonbonded pdb=" OD1 ASP B 945 " pdb=" O HOH B1201 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASP H 945 " pdb=" O HOH H1201 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASP F 945 " pdb=" O HOH F1201 " model vdw 2.223 3.040 ... (remaining 256067 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'L' selection = chain 'P' selection = chain 'T' selection = chain 'X' } 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: 6.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.240 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.100 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:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 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 : 0.006 0.048 32004 Z= 0.302 Angle : 0.762 15.452 43676 Z= 0.394 Chirality : 0.057 0.463 5244 Planarity : 0.010 0.216 5336 Dihedral : 16.897 106.138 12352 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.10 % Favored : 96.80 % Rotamer: Outliers : 0.77 % Allowed : 19.29 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.14), residues: 3940 helix: 0.68 (0.23), residues: 604 sheet: 0.31 (0.15), residues: 1384 loop : -0.78 (0.13), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.002 ARG G 629 TYR 0.016 0.001 TYR H 690 PHE 0.029 0.001 PHE H1093 TRP 0.023 0.001 TRP H1108 HIS 0.005 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00533 (31848) covalent geometry : angle 0.68287 (43304) SS BOND : bond 0.00243 ( 96) SS BOND : angle 0.70382 ( 192) hydrogen bonds : bond 0.18438 ( 1040) hydrogen bonds : angle 6.90411 ( 2796) link_ALPHA1-3 : bond 0.04401 ( 8) link_ALPHA1-3 : angle 5.80156 ( 24) link_ALPHA1-6 : bond 0.03796 ( 8) link_ALPHA1-6 : angle 3.38471 ( 24) link_BETA1-4 : bond 0.04485 ( 28) link_BETA1-4 : angle 6.27031 ( 84) link_NAG-ASN : bond 0.01081 ( 16) link_NAG-ASN : angle 3.75684 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7880 Ramachandran restraints generated. 3940 Oldfield, 0 Emsley, 3940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7880 Ramachandran restraints generated. 3940 Oldfield, 0 Emsley, 3940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 297 time to evaluate : 1.202 Fit side-chains REVERT: A 46 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8700 (mt-10) REVERT: A 372 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8857 (mt-10) REVERT: A 414 GLN cc_start: 0.8638 (pp30) cc_final: 0.8289 (pp30) REVERT: B 673 LYS cc_start: 0.9514 (mttt) cc_final: 0.9301 (mppt) REVERT: B 886 ARG cc_start: 0.8646 (mtp85) cc_final: 0.8227 (mmt180) REVERT: B 927 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8268 (mm-40) REVERT: B 1066 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7593 (tp30) REVERT: C 46 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8716 (mt-10) REVERT: C 372 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8851 (mt-10) REVERT: C 414 GLN cc_start: 0.8670 (pp30) cc_final: 0.8325 (pp30) REVERT: C 429 ARG cc_start: 0.8916 (mtp85) cc_final: 0.8374 (mtp85) REVERT: C 431 ASP cc_start: 0.8908 (p0) cc_final: 0.8551 (p0) REVERT: D 673 LYS cc_start: 0.9521 (mttt) cc_final: 0.9305 (mppt) REVERT: D 886 ARG cc_start: 0.8632 (mtp85) cc_final: 0.8219 (mmt180) REVERT: D 924 ASP cc_start: 0.9287 (m-30) cc_final: 0.9039 (m-30) REVERT: D 927 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8217 (mm-40) REVERT: E 46 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8710 (mt-10) REVERT: E 372 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8832 (mt-10) REVERT: E 414 GLN cc_start: 0.8654 (pp30) cc_final: 0.8314 (pp30) REVERT: F 673 LYS cc_start: 0.9525 (mttt) cc_final: 0.9306 (mppt) REVERT: F 886 ARG cc_start: 0.8637 (mtp85) cc_final: 0.8228 (mmt180) REVERT: F 924 ASP cc_start: 0.9293 (m-30) cc_final: 0.9040 (m-30) REVERT: F 927 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8247 (mm-40) REVERT: G 46 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8715 (mt-10) REVERT: G 372 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8843 (mt-10) REVERT: G 414 GLN cc_start: 0.8648 (pp30) cc_final: 0.8298 (pp30) REVERT: G 429 ARG cc_start: 0.8913 (mtp85) cc_final: 0.8369 (mtp85) REVERT: G 431 ASP cc_start: 0.8917 (p0) cc_final: 0.8566 (p0) REVERT: H 673 LYS cc_start: 0.9507 (mttt) cc_final: 0.9295 (mppt) REVERT: H 886 ARG cc_start: 0.8629 (mtp85) cc_final: 0.8224 (mmt180) REVERT: H 924 ASP cc_start: 0.9283 (m-30) cc_final: 0.9034 (m-30) REVERT: H 927 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8233 (mm-40) outliers start: 27 outliers final: 13 residues processed: 324 average time/residue: 0.8385 time to fit residues: 312.9971 Evaluate side-chains 270 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 257 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 291 SER Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain H residue 834 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.0030 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 5.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN B1030 ASN B1107 ASN D1030 ASN D1107 ASN E 143 GLN F1030 ASN F1107 ASN H1030 ASN H1107 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.092257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.061911 restraints weight = 54734.449| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 3.01 r_work: 0.2609 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 32004 Z= 0.102 Angle : 0.529 7.310 43676 Z= 0.262 Chirality : 0.042 0.137 5244 Planarity : 0.003 0.041 5336 Dihedral : 10.336 75.680 5384 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.78 % Allowed : 17.59 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.14), residues: 3940 helix: 2.00 (0.22), residues: 588 sheet: 0.58 (0.15), residues: 1304 loop : -0.63 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 960 TYR 0.008 0.001 TYR G 631 PHE 0.007 0.001 PHE E 425 TRP 0.014 0.001 TRP D1108 HIS 0.003 0.000 HIS D 820 Details of bonding type rmsd covalent geometry : bond 0.00215 (31848) covalent geometry : angle 0.51296 (43304) SS BOND : bond 0.00207 ( 96) SS BOND : angle 0.60242 ( 192) hydrogen bonds : bond 0.03827 ( 1040) hydrogen bonds : angle 5.03037 ( 2796) link_ALPHA1-3 : bond 0.01449 ( 8) link_ALPHA1-3 : angle 1.16918 ( 24) link_ALPHA1-6 : bond 0.00408 ( 8) link_ALPHA1-6 : angle 1.78770 ( 24) link_BETA1-4 : bond 0.00682 ( 28) link_BETA1-4 : angle 2.40927 ( 84) link_NAG-ASN : bond 0.00411 ( 16) link_NAG-ASN : angle 1.89292 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7880 Ramachandran restraints generated. 3940 Oldfield, 0 Emsley, 3940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7880 Ramachandran restraints generated. 3940 Oldfield, 0 Emsley, 3940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 284 time to evaluate : 1.335 Fit side-chains REVERT: A 372 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8831 (mt-10) REVERT: A 414 GLN cc_start: 0.8600 (pp30) cc_final: 0.8225 (pp30) REVERT: B 656 MET cc_start: 0.9010 (mmt) cc_final: 0.8674 (OUTLIER) REVERT: B 673 LYS cc_start: 0.9590 (mttt) cc_final: 0.9374 (mttm) REVERT: B 693 LYS cc_start: 0.9061 (ttpt) cc_final: 0.8652 (ttpp) REVERT: B 886 ARG cc_start: 0.8629 (mtp85) cc_final: 0.8268 (mmt180) REVERT: B 927 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8270 (mm-40) REVERT: B 1066 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7590 (tp30) REVERT: C 46 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8624 (mt-10) REVERT: C 372 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8814 (mt-10) REVERT: C 414 GLN cc_start: 0.8607 (pp30) cc_final: 0.8228 (pp30) REVERT: D 656 MET cc_start: 0.8968 (mmt) cc_final: 0.8635 (OUTLIER) REVERT: D 673 LYS cc_start: 0.9599 (mttt) cc_final: 0.9355 (mttm) REVERT: D 693 LYS cc_start: 0.9071 (ttpt) cc_final: 0.8666 (ttpp) REVERT: D 886 ARG cc_start: 0.8615 (mtp85) cc_final: 0.8254 (mmt180) REVERT: D 927 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8301 (mm-40) REVERT: D 1066 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7573 (tp30) REVERT: E 46 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8591 (mt-10) REVERT: E 372 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8838 (mt-10) REVERT: E 414 GLN cc_start: 0.8599 (pp30) cc_final: 0.8225 (pp30) REVERT: E 429 ARG cc_start: 0.8973 (mtp85) cc_final: 0.8612 (mtp85) REVERT: E 431 ASP cc_start: 0.8996 (p0) cc_final: 0.8725 (p0) REVERT: F 656 MET cc_start: 0.8995 (mmt) cc_final: 0.8659 (OUTLIER) REVERT: F 673 LYS cc_start: 0.9593 (mttt) cc_final: 0.9353 (mttm) REVERT: F 693 LYS cc_start: 0.9064 (ttpt) cc_final: 0.8678 (ttpp) REVERT: F 886 ARG cc_start: 0.8614 (mtp85) cc_final: 0.8247 (mmt180) REVERT: F 927 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8311 (mm-40) REVERT: F 1066 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7560 (tp30) REVERT: G 372 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8823 (mt-10) REVERT: G 414 GLN cc_start: 0.8606 (pp30) cc_final: 0.8231 (pp30) REVERT: H 656 MET cc_start: 0.8984 (mmt) cc_final: 0.8654 (OUTLIER) REVERT: H 673 LYS cc_start: 0.9599 (mttt) cc_final: 0.9358 (mttm) REVERT: H 693 LYS cc_start: 0.9070 (ttpt) cc_final: 0.8668 (ttpp) REVERT: H 886 ARG cc_start: 0.8613 (mtp85) cc_final: 0.8248 (mmt180) REVERT: H 927 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8302 (mm-40) REVERT: H 1066 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7589 (tp30) outliers start: 62 outliers final: 25 residues processed: 330 average time/residue: 0.8451 time to fit residues: 319.7258 Evaluate side-chains 294 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 273 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 1006 MET Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 1006 MET Chi-restraints excluded: chain D residue 1014 LEU Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain F residue 1006 MET Chi-restraints excluded: chain F residue 1014 LEU Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 482 LEU Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain H residue 834 VAL Chi-restraints excluded: chain H residue 1006 MET Chi-restraints excluded: chain H residue 1014 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 351 optimal weight: 0.9980 chunk 366 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 217 optimal weight: 7.9990 chunk 202 optimal weight: 7.9990 chunk 179 optimal weight: 9.9990 chunk 360 optimal weight: 3.9990 chunk 326 optimal weight: 0.2980 chunk 342 optimal weight: 2.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1030 ASN B1107 ASN D1030 ASN D1107 ASN F1030 ASN F1107 ASN H1030 ASN H1107 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.087472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.058175 restraints weight = 56402.131| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 2.91 r_work: 0.2571 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2434 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 32004 Z= 0.176 Angle : 0.543 8.680 43676 Z= 0.268 Chirality : 0.043 0.173 5244 Planarity : 0.003 0.039 5336 Dihedral : 8.896 71.162 5371 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.10 % Allowed : 16.82 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.14), residues: 3940 helix: 2.69 (0.22), residues: 584 sheet: 0.51 (0.15), residues: 1348 loop : -0.50 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 960 TYR 0.010 0.001 TYR A 120 PHE 0.014 0.001 PHE A 459 TRP 0.010 0.001 TRP D1108 HIS 0.003 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00415 (31848) covalent geometry : angle 0.52711 (43304) SS BOND : bond 0.00260 ( 96) SS BOND : angle 0.70517 ( 192) hydrogen bonds : bond 0.03815 ( 1040) hydrogen bonds : angle 4.72315 ( 2796) link_ALPHA1-3 : bond 0.01146 ( 8) link_ALPHA1-3 : angle 1.37296 ( 24) link_ALPHA1-6 : bond 0.00290 ( 8) link_ALPHA1-6 : angle 1.84452 ( 24) link_BETA1-4 : bond 0.00599 ( 28) link_BETA1-4 : angle 2.27753 ( 84) link_NAG-ASN : bond 0.00293 ( 16) link_NAG-ASN : angle 1.89658 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7880 Ramachandran restraints generated. 3940 Oldfield, 0 Emsley, 3940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7880 Ramachandran restraints generated. 3940 Oldfield, 0 Emsley, 3940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 283 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8665 (mt-10) REVERT: A 414 GLN cc_start: 0.8649 (pp30) cc_final: 0.8204 (pp30) REVERT: A 420 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8676 (mm-30) REVERT: B 656 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8750 (OUTLIER) REVERT: B 673 LYS cc_start: 0.9562 (mttt) cc_final: 0.9358 (mttp) REVERT: B 693 LYS cc_start: 0.9062 (ttpt) cc_final: 0.8625 (ttpp) REVERT: B 886 ARG cc_start: 0.8766 (mtp85) cc_final: 0.8316 (mmt180) REVERT: B 927 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8233 (mm-40) REVERT: B 1066 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7576 (tp30) REVERT: C 46 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8624 (mt-10) REVERT: C 372 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8834 (mt-10) REVERT: C 414 GLN cc_start: 0.8653 (pp30) cc_final: 0.8223 (pp30) REVERT: C 429 ARG cc_start: 0.8958 (mtp85) cc_final: 0.8601 (mtp85) REVERT: C 431 ASP cc_start: 0.8997 (p0) cc_final: 0.8705 (p0) REVERT: D 656 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8718 (OUTLIER) REVERT: D 673 LYS cc_start: 0.9576 (mttt) cc_final: 0.9374 (mttp) REVERT: D 693 LYS cc_start: 0.9091 (ttpt) cc_final: 0.8649 (ttpp) REVERT: D 886 ARG cc_start: 0.8757 (mtp85) cc_final: 0.8306 (mmt180) REVERT: D 927 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8194 (mm-40) REVERT: D 1066 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7571 (tp30) REVERT: E 46 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8614 (mt-10) REVERT: E 372 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8820 (mt-10) REVERT: E 414 GLN cc_start: 0.8668 (pp30) cc_final: 0.8229 (pp30) REVERT: E 420 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8671 (mm-30) REVERT: E 429 ARG cc_start: 0.8982 (mtp85) cc_final: 0.8604 (mtp85) REVERT: E 431 ASP cc_start: 0.8982 (p0) cc_final: 0.8675 (p0) REVERT: F 656 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8722 (OUTLIER) REVERT: F 673 LYS cc_start: 0.9571 (mttt) cc_final: 0.9366 (mttp) REVERT: F 693 LYS cc_start: 0.9070 (ttpt) cc_final: 0.8636 (ttpp) REVERT: F 886 ARG cc_start: 0.8771 (mtp85) cc_final: 0.8313 (mmt180) REVERT: F 927 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8221 (mm-40) REVERT: F 1066 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7589 (tp30) REVERT: G 46 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8578 (mt-10) REVERT: G 414 GLN cc_start: 0.8653 (pp30) cc_final: 0.8216 (pp30) REVERT: G 429 ARG cc_start: 0.8968 (mtp85) cc_final: 0.8615 (mtp85) REVERT: G 431 ASP cc_start: 0.9000 (p0) cc_final: 0.8708 (p0) REVERT: H 656 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8714 (OUTLIER) REVERT: H 673 LYS cc_start: 0.9569 (mttt) cc_final: 0.9362 (mttp) REVERT: H 693 LYS cc_start: 0.9073 (ttpt) cc_final: 0.8641 (ttpp) REVERT: H 886 ARG cc_start: 0.8765 (mtp85) cc_final: 0.8300 (mmt180) REVERT: H 927 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8213 (mm-40) REVERT: H 1066 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7579 (tp30) outliers start: 73 outliers final: 41 residues processed: 325 average time/residue: 0.8282 time to fit residues: 310.5774 Evaluate side-chains 309 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 268 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 1006 MET Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain D residue 932 THR Chi-restraints excluded: chain D residue 972 CYS Chi-restraints excluded: chain D residue 1006 MET Chi-restraints excluded: chain D residue 1014 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 644 ILE Chi-restraints excluded: chain F residue 656 MET Chi-restraints excluded: chain F residue 932 THR Chi-restraints excluded: chain F residue 1006 MET Chi-restraints excluded: chain F residue 1014 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 482 LEU Chi-restraints excluded: chain G residue 644 ILE Chi-restraints excluded: chain H residue 656 MET Chi-restraints excluded: chain H residue 834 VAL Chi-restraints excluded: chain H residue 932 THR Chi-restraints excluded: chain H residue 972 CYS Chi-restraints excluded: chain H residue 1006 MET Chi-restraints excluded: chain H residue 1014 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 64 optimal weight: 0.6980 chunk 120 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1030 ASN B1107 ASN D1030 ASN D1107 ASN F1030 ASN F1107 ASN H1030 ASN H1107 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.088024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.058739 restraints weight = 56018.934| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 2.92 r_work: 0.2586 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2450 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 32004 Z= 0.130 Angle : 0.519 9.251 43676 Z= 0.255 Chirality : 0.042 0.186 5244 Planarity : 0.003 0.037 5336 Dihedral : 7.440 63.930 5371 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.15 % Allowed : 16.30 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.14), residues: 3940 helix: 2.97 (0.22), residues: 584 sheet: 0.69 (0.15), residues: 1324 loop : -0.59 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 960 TYR 0.009 0.001 TYR B 690 PHE 0.012 0.001 PHE A 459 TRP 0.013 0.001 TRP D1108 HIS 0.002 0.000 HIS G 203 Details of bonding type rmsd covalent geometry : bond 0.00302 (31848) covalent geometry : angle 0.50426 (43304) SS BOND : bond 0.00296 ( 96) SS BOND : angle 0.67816 ( 192) hydrogen bonds : bond 0.03270 ( 1040) hydrogen bonds : angle 4.49101 ( 2796) link_ALPHA1-3 : bond 0.01289 ( 8) link_ALPHA1-3 : angle 1.33344 ( 24) link_ALPHA1-6 : bond 0.00424 ( 8) link_ALPHA1-6 : angle 1.95167 ( 24) link_BETA1-4 : bond 0.00578 ( 28) link_BETA1-4 : angle 2.04821 ( 84) link_NAG-ASN : bond 0.00198 ( 16) link_NAG-ASN : angle 1.86835 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7880 Ramachandran restraints generated. 3940 Oldfield, 0 Emsley, 3940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7880 Ramachandran restraints generated. 3940 Oldfield, 0 Emsley, 3940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 291 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8610 (mm-30) REVERT: A 414 GLN cc_start: 0.8684 (pp30) cc_final: 0.8218 (pp30) REVERT: A 429 ARG cc_start: 0.8964 (mtp85) cc_final: 0.8599 (mtp85) REVERT: A 431 ASP cc_start: 0.9015 (p0) cc_final: 0.8719 (p0) REVERT: B 656 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8702 (mmp) REVERT: B 673 LYS cc_start: 0.9550 (mttt) cc_final: 0.9344 (mttp) REVERT: B 691 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8811 (ptm-80) REVERT: B 693 LYS cc_start: 0.9049 (ttpt) cc_final: 0.8613 (ttpp) REVERT: B 886 ARG cc_start: 0.8845 (mtp85) cc_final: 0.8379 (mmt180) REVERT: B 927 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8248 (mm-40) REVERT: B 1066 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7592 (tp30) REVERT: B 1093 PHE cc_start: 0.9127 (m-80) cc_final: 0.8924 (m-80) REVERT: B 1104 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7843 (mp) REVERT: C 46 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8596 (mt-10) REVERT: C 372 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8833 (mt-10) REVERT: C 414 GLN cc_start: 0.8658 (pp30) cc_final: 0.8203 (pp30) REVERT: C 429 ARG cc_start: 0.8954 (mtp85) cc_final: 0.8635 (mtp85) REVERT: C 431 ASP cc_start: 0.8960 (p0) cc_final: 0.8594 (p0) REVERT: D 656 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8700 (mmp) REVERT: D 673 LYS cc_start: 0.9568 (mttt) cc_final: 0.9358 (mttp) REVERT: D 691 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8761 (ptm-80) REVERT: D 693 LYS cc_start: 0.9075 (ttpt) cc_final: 0.8632 (ttpp) REVERT: D 886 ARG cc_start: 0.8828 (mtp85) cc_final: 0.8371 (mmt180) REVERT: D 927 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8231 (mm-40) REVERT: D 1066 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7556 (tp30) REVERT: D 1093 PHE cc_start: 0.9137 (m-80) cc_final: 0.8917 (m-80) REVERT: E 46 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8593 (mt-10) REVERT: E 414 GLN cc_start: 0.8670 (pp30) cc_final: 0.8207 (pp30) REVERT: E 429 ARG cc_start: 0.8969 (mtp85) cc_final: 0.8620 (mtp85) REVERT: E 431 ASP cc_start: 0.8939 (p0) cc_final: 0.8540 (p0) REVERT: F 656 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8706 (mmp) REVERT: F 673 LYS cc_start: 0.9564 (mttt) cc_final: 0.9356 (mttp) REVERT: F 691 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8794 (ptm-80) REVERT: F 693 LYS cc_start: 0.9076 (ttpt) cc_final: 0.8640 (ttpp) REVERT: F 886 ARG cc_start: 0.8842 (mtp85) cc_final: 0.8377 (mmt180) REVERT: F 927 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8236 (mm-40) REVERT: F 1066 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7596 (tp30) REVERT: F 1093 PHE cc_start: 0.9134 (m-80) cc_final: 0.8932 (m-80) REVERT: G 46 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8552 (mt-10) REVERT: G 372 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8829 (mt-10) REVERT: G 414 GLN cc_start: 0.8657 (pp30) cc_final: 0.8203 (pp30) REVERT: G 429 ARG cc_start: 0.8951 (mtp85) cc_final: 0.8632 (mtp85) REVERT: G 431 ASP cc_start: 0.8963 (p0) cc_final: 0.8598 (p0) REVERT: H 656 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8677 (mmp) REVERT: H 673 LYS cc_start: 0.9556 (mttt) cc_final: 0.9352 (mttp) REVERT: H 691 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8755 (ptm-80) REVERT: H 693 LYS cc_start: 0.9076 (ttpt) cc_final: 0.8640 (ttpp) REVERT: H 886 ARG cc_start: 0.8838 (mtp85) cc_final: 0.8382 (mmt180) REVERT: H 927 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8243 (mm-40) REVERT: H 1066 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7559 (tp30) REVERT: H 1093 PHE cc_start: 0.9139 (m-80) cc_final: 0.8920 (m-80) outliers start: 75 outliers final: 32 residues processed: 340 average time/residue: 0.8666 time to fit residues: 336.6329 Evaluate side-chains 319 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 278 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 972 CYS Chi-restraints excluded: chain B residue 1006 MET Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1104 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain D residue 691 ARG Chi-restraints excluded: chain D residue 972 CYS Chi-restraints excluded: chain D residue 1006 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 644 ILE Chi-restraints excluded: chain F residue 656 MET Chi-restraints excluded: chain F residue 691 ARG Chi-restraints excluded: chain F residue 972 CYS Chi-restraints excluded: chain F residue 1006 MET Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 482 LEU Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain G residue 644 ILE Chi-restraints excluded: chain H residue 656 MET Chi-restraints excluded: chain H residue 691 ARG Chi-restraints excluded: chain H residue 834 VAL Chi-restraints excluded: chain H residue 972 CYS Chi-restraints excluded: chain H residue 1006 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 33 optimal weight: 5.9990 chunk 293 optimal weight: 30.0000 chunk 5 optimal weight: 6.9990 chunk 356 optimal weight: 0.2980 chunk 208 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 373 optimal weight: 0.2980 chunk 53 optimal weight: 10.0000 chunk 229 optimal weight: 4.9990 chunk 236 optimal weight: 4.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1030 ASN B1107 ASN D1030 ASN D1107 ASN F1030 ASN F1107 ASN H1030 ASN H1107 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.086220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.056899 restraints weight = 56589.568| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 2.92 r_work: 0.2545 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2408 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 32004 Z= 0.231 Angle : 0.577 10.290 43676 Z= 0.286 Chirality : 0.044 0.184 5244 Planarity : 0.004 0.040 5336 Dihedral : 7.282 64.099 5371 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.78 % Allowed : 15.13 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.14), residues: 3940 helix: 2.66 (0.22), residues: 608 sheet: 0.64 (0.15), residues: 1300 loop : -0.65 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 960 TYR 0.011 0.001 TYR G 120 PHE 0.018 0.002 PHE C 459 TRP 0.015 0.001 TRP D1108 HIS 0.004 0.001 HIS E 203 Details of bonding type rmsd covalent geometry : bond 0.00549 (31848) covalent geometry : angle 0.56162 (43304) SS BOND : bond 0.00298 ( 96) SS BOND : angle 0.88868 ( 192) hydrogen bonds : bond 0.03769 ( 1040) hydrogen bonds : angle 4.55481 ( 2796) link_ALPHA1-3 : bond 0.01014 ( 8) link_ALPHA1-3 : angle 1.55065 ( 24) link_ALPHA1-6 : bond 0.00308 ( 8) link_ALPHA1-6 : angle 1.91249 ( 24) link_BETA1-4 : bond 0.00478 ( 28) link_BETA1-4 : angle 2.10187 ( 84) link_NAG-ASN : bond 0.00365 ( 16) link_NAG-ASN : angle 2.11050 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7880 Ramachandran restraints generated. 3940 Oldfield, 0 Emsley, 3940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7880 Ramachandran restraints generated. 3940 Oldfield, 0 Emsley, 3940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 277 time to evaluate : 1.314 Fit side-chains revert: symmetry clash REVERT: A 46 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8627 (mm-30) REVERT: A 414 GLN cc_start: 0.8729 (pp30) cc_final: 0.8258 (pp30) REVERT: B 656 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8674 (mmp) REVERT: B 673 LYS cc_start: 0.9559 (mttt) cc_final: 0.9342 (mttp) REVERT: B 691 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.8387 (ptm-80) REVERT: B 693 LYS cc_start: 0.9074 (ttpt) cc_final: 0.8619 (ttpp) REVERT: B 927 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8208 (mm-40) REVERT: B 1066 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7571 (tp30) REVERT: B 1093 PHE cc_start: 0.9113 (m-80) cc_final: 0.8908 (m-80) REVERT: B 1104 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7860 (mp) REVERT: C 46 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8783 (mm-30) REVERT: C 143 GLN cc_start: 0.9378 (OUTLIER) cc_final: 0.8864 (tp40) REVERT: C 372 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8842 (mt-10) REVERT: C 414 GLN cc_start: 0.8744 (pp30) cc_final: 0.8273 (pp30) REVERT: D 656 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8672 (mmp) REVERT: D 673 LYS cc_start: 0.9555 (mttt) cc_final: 0.9340 (mttp) REVERT: D 691 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8798 (ptm-80) REVERT: D 693 LYS cc_start: 0.9085 (ttpt) cc_final: 0.8614 (ttpp) REVERT: D 927 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8186 (mm-40) REVERT: D 1066 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7599 (tp30) REVERT: D 1093 PHE cc_start: 0.9116 (m-80) cc_final: 0.8874 (m-80) REVERT: D 1104 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7830 (mp) REVERT: E 46 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8564 (mt-10) REVERT: E 414 GLN cc_start: 0.8742 (pp30) cc_final: 0.8272 (pp30) REVERT: E 429 ARG cc_start: 0.8970 (mtp85) cc_final: 0.8657 (mtp85) REVERT: F 656 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8676 (mmp) REVERT: F 673 LYS cc_start: 0.9560 (mttt) cc_final: 0.9342 (mttp) REVERT: F 691 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8386 (ptm-80) REVERT: F 693 LYS cc_start: 0.9094 (ttpt) cc_final: 0.8635 (ttpp) REVERT: F 927 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8209 (mm-40) REVERT: F 1066 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7599 (tp30) REVERT: F 1093 PHE cc_start: 0.9121 (m-80) cc_final: 0.8876 (m-80) REVERT: F 1104 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7877 (mp) REVERT: G 46 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8769 (mt-10) REVERT: G 143 GLN cc_start: 0.9387 (OUTLIER) cc_final: 0.8844 (tp40) REVERT: G 414 GLN cc_start: 0.8737 (pp30) cc_final: 0.8265 (pp30) REVERT: H 656 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8672 (mmp) REVERT: H 673 LYS cc_start: 0.9560 (mttt) cc_final: 0.9342 (mttp) REVERT: H 691 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8787 (ptm-80) REVERT: H 693 LYS cc_start: 0.9094 (ttpt) cc_final: 0.8638 (ttpp) REVERT: H 927 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8201 (mm-40) REVERT: H 1066 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7608 (tp30) REVERT: H 1093 PHE cc_start: 0.9124 (m-80) cc_final: 0.8885 (m-80) REVERT: H 1104 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7863 (mp) outliers start: 97 outliers final: 51 residues processed: 337 average time/residue: 0.8846 time to fit residues: 341.1532 Evaluate side-chains 331 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 266 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 972 CYS Chi-restraints excluded: chain B residue 1006 MET Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1104 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain D residue 691 ARG Chi-restraints excluded: chain D residue 932 THR Chi-restraints excluded: chain D residue 1006 MET Chi-restraints excluded: chain D residue 1014 LEU Chi-restraints excluded: chain D residue 1101 LEU Chi-restraints excluded: chain D residue 1104 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 644 ILE Chi-restraints excluded: chain F residue 656 MET Chi-restraints excluded: chain F residue 691 ARG Chi-restraints excluded: chain F residue 932 THR Chi-restraints excluded: chain F residue 1006 MET Chi-restraints excluded: chain F residue 1014 LEU Chi-restraints excluded: chain F residue 1101 LEU Chi-restraints excluded: chain F residue 1104 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 482 LEU Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain G residue 644 ILE Chi-restraints excluded: chain H residue 656 MET Chi-restraints excluded: chain H residue 691 ARG Chi-restraints excluded: chain H residue 834 VAL Chi-restraints excluded: chain H residue 932 THR Chi-restraints excluded: chain H residue 1006 MET Chi-restraints excluded: chain H residue 1014 LEU Chi-restraints excluded: chain H residue 1101 LEU Chi-restraints excluded: chain H residue 1104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 269 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 164 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 350 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 118 optimal weight: 6.9990 chunk 227 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 303 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1030 ASN B1107 ASN D1030 ASN D1107 ASN F1030 ASN F1107 ASN H1030 ASN H1107 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.087026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.057564 restraints weight = 55912.482| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 2.92 r_work: 0.2557 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2419 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 32004 Z= 0.158 Angle : 0.544 11.375 43676 Z= 0.268 Chirality : 0.042 0.189 5244 Planarity : 0.004 0.044 5336 Dihedral : 6.939 61.012 5371 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.67 % Allowed : 15.18 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.14), residues: 3940 helix: 2.72 (0.22), residues: 608 sheet: 0.66 (0.15), residues: 1300 loop : -0.67 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 960 TYR 0.010 0.001 TYR B 690 PHE 0.013 0.001 PHE A 459 TRP 0.016 0.001 TRP F1108 HIS 0.002 0.000 HIS G 203 Details of bonding type rmsd covalent geometry : bond 0.00369 (31848) covalent geometry : angle 0.52953 (43304) SS BOND : bond 0.00232 ( 96) SS BOND : angle 0.81825 ( 192) hydrogen bonds : bond 0.03331 ( 1040) hydrogen bonds : angle 4.43847 ( 2796) link_ALPHA1-3 : bond 0.01247 ( 8) link_ALPHA1-3 : angle 1.49301 ( 24) link_ALPHA1-6 : bond 0.00427 ( 8) link_ALPHA1-6 : angle 1.81614 ( 24) link_BETA1-4 : bond 0.00509 ( 28) link_BETA1-4 : angle 1.96138 ( 84) link_NAG-ASN : bond 0.00205 ( 16) link_NAG-ASN : angle 1.98149 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7880 Ramachandran restraints generated. 3940 Oldfield, 0 Emsley, 3940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7880 Ramachandran restraints generated. 3940 Oldfield, 0 Emsley, 3940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 269 time to evaluate : 1.334 Fit side-chains REVERT: A 46 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8593 (mm-30) REVERT: A 414 GLN cc_start: 0.8706 (pp30) cc_final: 0.8212 (pp30) REVERT: A 429 ARG cc_start: 0.8881 (mtp85) cc_final: 0.8571 (mtp85) REVERT: A 431 ASP cc_start: 0.8955 (p0) cc_final: 0.8526 (p0) REVERT: B 656 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8652 (mmp) REVERT: B 673 LYS cc_start: 0.9555 (mttt) cc_final: 0.9334 (mttp) REVERT: B 691 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.8811 (ptm-80) REVERT: B 693 LYS cc_start: 0.9083 (ttpt) cc_final: 0.8629 (ttpp) REVERT: B 927 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8228 (mm-40) REVERT: B 1066 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7573 (tp30) REVERT: B 1093 PHE cc_start: 0.9121 (m-80) cc_final: 0.8914 (m-80) REVERT: C 46 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8584 (mm-30) REVERT: C 414 GLN cc_start: 0.8706 (pp30) cc_final: 0.8219 (pp30) REVERT: D 656 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8670 (mmp) REVERT: D 691 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8815 (ptm-80) REVERT: D 693 LYS cc_start: 0.9084 (ttpt) cc_final: 0.8602 (ttpp) REVERT: D 927 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8223 (mm-40) REVERT: D 1066 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7582 (tp30) REVERT: D 1093 PHE cc_start: 0.9111 (m-80) cc_final: 0.8878 (m-80) REVERT: E 46 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8571 (mm-30) REVERT: E 414 GLN cc_start: 0.8702 (pp30) cc_final: 0.8226 (pp30) REVERT: F 656 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8652 (mmp) REVERT: F 673 LYS cc_start: 0.9556 (mttt) cc_final: 0.9333 (mttp) REVERT: F 691 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8424 (ptm-80) REVERT: F 693 LYS cc_start: 0.9094 (ttpt) cc_final: 0.8642 (ttpp) REVERT: F 927 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8216 (mm-40) REVERT: F 1066 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7565 (tp30) REVERT: F 1093 PHE cc_start: 0.9132 (m-80) cc_final: 0.8920 (m-80) REVERT: F 1104 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7887 (mp) REVERT: G 46 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8563 (mm-30) REVERT: G 414 GLN cc_start: 0.8697 (pp30) cc_final: 0.8223 (pp30) REVERT: H 656 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8665 (mmp) REVERT: H 673 LYS cc_start: 0.9554 (mttt) cc_final: 0.9330 (mttp) REVERT: H 691 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8802 (ptm-80) REVERT: H 693 LYS cc_start: 0.9099 (ttpt) cc_final: 0.8649 (ttpp) REVERT: H 927 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8234 (mm-40) REVERT: H 1066 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7592 (tp30) REVERT: H 1093 PHE cc_start: 0.9116 (m-80) cc_final: 0.8886 (m-80) REVERT: H 1104 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7885 (mp) outliers start: 93 outliers final: 47 residues processed: 329 average time/residue: 0.8632 time to fit residues: 324.5824 Evaluate side-chains 322 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 265 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 1006 MET Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain D residue 691 ARG Chi-restraints excluded: chain D residue 768 CYS Chi-restraints excluded: chain D residue 932 THR Chi-restraints excluded: chain D residue 1006 MET Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 644 ILE Chi-restraints excluded: chain F residue 656 MET Chi-restraints excluded: chain F residue 691 ARG Chi-restraints excluded: chain F residue 768 CYS Chi-restraints excluded: chain F residue 932 THR Chi-restraints excluded: chain F residue 1006 MET Chi-restraints excluded: chain F residue 1104 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 482 LEU Chi-restraints excluded: chain G residue 490 LEU Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain G residue 644 ILE Chi-restraints excluded: chain H residue 656 MET Chi-restraints excluded: chain H residue 691 ARG Chi-restraints excluded: chain H residue 768 CYS Chi-restraints excluded: chain H residue 834 VAL Chi-restraints excluded: chain H residue 932 THR Chi-restraints excluded: chain H residue 1006 MET Chi-restraints excluded: chain H residue 1104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 364 optimal weight: 0.0020 chunk 325 optimal weight: 1.9990 chunk 388 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 355 optimal weight: 0.9990 chunk 147 optimal weight: 40.0000 chunk 137 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 357 optimal weight: 10.0000 chunk 390 optimal weight: 9.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1030 ASN B1107 ASN D1030 ASN D1107 ASN F1030 ASN F1107 ASN H1030 ASN H1107 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.087676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.058233 restraints weight = 56232.375| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.94 r_work: 0.2577 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2440 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32004 Z= 0.120 Angle : 0.530 11.965 43676 Z= 0.260 Chirality : 0.042 0.193 5244 Planarity : 0.003 0.043 5336 Dihedral : 6.671 58.962 5371 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.24 % Allowed : 15.84 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.14), residues: 3940 helix: 3.06 (0.22), residues: 584 sheet: 0.64 (0.15), residues: 1316 loop : -0.59 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 960 TYR 0.009 0.001 TYR B 690 PHE 0.011 0.001 PHE E 459 TRP 0.016 0.001 TRP D1108 HIS 0.002 0.000 HIS B 935 Details of bonding type rmsd covalent geometry : bond 0.00280 (31848) covalent geometry : angle 0.51701 (43304) SS BOND : bond 0.00196 ( 96) SS BOND : angle 0.68399 ( 192) hydrogen bonds : bond 0.03082 ( 1040) hydrogen bonds : angle 4.32545 ( 2796) link_ALPHA1-3 : bond 0.01200 ( 8) link_ALPHA1-3 : angle 1.53045 ( 24) link_ALPHA1-6 : bond 0.00493 ( 8) link_ALPHA1-6 : angle 1.74412 ( 24) link_BETA1-4 : bond 0.00523 ( 28) link_BETA1-4 : angle 1.85588 ( 84) link_NAG-ASN : bond 0.00195 ( 16) link_NAG-ASN : angle 1.94972 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7880 Ramachandran restraints generated. 3940 Oldfield, 0 Emsley, 3940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7880 Ramachandran restraints generated. 3940 Oldfield, 0 Emsley, 3940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 277 time to evaluate : 1.304 Fit side-chains REVERT: A 46 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8582 (mm-30) REVERT: A 414 GLN cc_start: 0.8686 (pp30) cc_final: 0.8247 (pp30) REVERT: A 429 ARG cc_start: 0.8877 (mtp85) cc_final: 0.8578 (mtp85) REVERT: A 431 ASP cc_start: 0.8894 (p0) cc_final: 0.8489 (p0) REVERT: B 656 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8686 (mmp) REVERT: B 673 LYS cc_start: 0.9555 (mttt) cc_final: 0.9328 (mttp) REVERT: B 691 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8804 (ptm-80) REVERT: B 693 LYS cc_start: 0.9073 (ttpt) cc_final: 0.8623 (ttpp) REVERT: B 927 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8225 (mm-40) REVERT: B 1066 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7571 (tp30) REVERT: B 1093 PHE cc_start: 0.9125 (m-80) cc_final: 0.8879 (m-80) REVERT: C 46 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8754 (mm-30) REVERT: C 143 GLN cc_start: 0.9372 (OUTLIER) cc_final: 0.8863 (tp40) REVERT: C 414 GLN cc_start: 0.8689 (pp30) cc_final: 0.8192 (pp30) REVERT: C 429 ARG cc_start: 0.8881 (mtp85) cc_final: 0.8577 (mtp85) REVERT: C 431 ASP cc_start: 0.8962 (p0) cc_final: 0.8536 (p0) REVERT: D 656 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8728 (mmp) REVERT: D 691 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8828 (ptm-80) REVERT: D 693 LYS cc_start: 0.9064 (ttpt) cc_final: 0.8616 (ttpp) REVERT: D 927 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8228 (mm-40) REVERT: D 1066 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7572 (tp30) REVERT: D 1093 PHE cc_start: 0.9113 (m-80) cc_final: 0.8865 (m-80) REVERT: E 46 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8518 (mm-30) REVERT: E 414 GLN cc_start: 0.8690 (pp30) cc_final: 0.8195 (pp30) REVERT: E 429 ARG cc_start: 0.8876 (mtp85) cc_final: 0.8571 (mtp85) REVERT: E 431 ASP cc_start: 0.8927 (p0) cc_final: 0.8491 (p0) REVERT: F 656 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8730 (mmp) REVERT: F 673 LYS cc_start: 0.9560 (mttt) cc_final: 0.9357 (mttp) REVERT: F 691 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.8771 (ptm-80) REVERT: F 693 LYS cc_start: 0.9082 (ttpt) cc_final: 0.8636 (ttpp) REVERT: F 927 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8234 (mm-40) REVERT: F 1066 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7580 (tp30) REVERT: F 1093 PHE cc_start: 0.9131 (m-80) cc_final: 0.8910 (m-80) REVERT: F 1104 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7870 (mp) REVERT: G 46 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8727 (mm-30) REVERT: G 143 GLN cc_start: 0.9377 (OUTLIER) cc_final: 0.8859 (tp40) REVERT: G 414 GLN cc_start: 0.8679 (pp30) cc_final: 0.8182 (pp30) REVERT: G 429 ARG cc_start: 0.8881 (mtp85) cc_final: 0.8577 (mtp85) REVERT: G 431 ASP cc_start: 0.8969 (p0) cc_final: 0.8546 (p0) REVERT: H 656 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8727 (mmp) REVERT: H 673 LYS cc_start: 0.9550 (mttt) cc_final: 0.9338 (mttp) REVERT: H 691 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.8705 (ptm-80) REVERT: H 693 LYS cc_start: 0.9074 (ttpt) cc_final: 0.8625 (ttpp) REVERT: H 927 GLN cc_start: 0.8725 (mm-40) cc_final: 0.8243 (mm-40) REVERT: H 1066 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7567 (tp30) REVERT: H 1093 PHE cc_start: 0.9120 (m-80) cc_final: 0.8874 (m-80) outliers start: 78 outliers final: 50 residues processed: 324 average time/residue: 0.8837 time to fit residues: 327.8116 Evaluate side-chains 331 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 270 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 1006 MET Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain D residue 691 ARG Chi-restraints excluded: chain D residue 768 CYS Chi-restraints excluded: chain D residue 932 THR Chi-restraints excluded: chain D residue 1006 MET Chi-restraints excluded: chain D residue 1014 LEU Chi-restraints excluded: chain D residue 1101 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 644 ILE Chi-restraints excluded: chain F residue 656 MET Chi-restraints excluded: chain F residue 691 ARG Chi-restraints excluded: chain F residue 768 CYS Chi-restraints excluded: chain F residue 932 THR Chi-restraints excluded: chain F residue 1006 MET Chi-restraints excluded: chain F residue 1101 LEU Chi-restraints excluded: chain F residue 1104 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 482 LEU Chi-restraints excluded: chain G residue 490 LEU Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain G residue 644 ILE Chi-restraints excluded: chain H residue 656 MET Chi-restraints excluded: chain H residue 691 ARG Chi-restraints excluded: chain H residue 768 CYS Chi-restraints excluded: chain H residue 834 VAL Chi-restraints excluded: chain H residue 932 THR Chi-restraints excluded: chain H residue 1006 MET Chi-restraints excluded: chain H residue 1101 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 42 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 306 optimal weight: 7.9990 chunk 225 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 27 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 361 optimal weight: 10.0000 chunk 338 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1030 ASN B1107 ASN D1030 ASN D1107 ASN F1030 ASN F1107 ASN H1030 ASN H1107 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.087274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.058013 restraints weight = 56346.519| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 2.93 r_work: 0.2565 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2427 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32004 Z= 0.148 Angle : 0.548 12.000 43676 Z= 0.269 Chirality : 0.042 0.193 5244 Planarity : 0.004 0.055 5336 Dihedral : 6.668 58.214 5371 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.15 % Allowed : 16.16 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.14), residues: 3940 helix: 2.77 (0.22), residues: 608 sheet: 0.54 (0.15), residues: 1324 loop : -0.58 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 960 TYR 0.010 0.001 TYR B 690 PHE 0.013 0.001 PHE C 459 TRP 0.017 0.001 TRP D1108 HIS 0.002 0.000 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00349 (31848) covalent geometry : angle 0.53595 (43304) SS BOND : bond 0.00225 ( 96) SS BOND : angle 0.70842 ( 192) hydrogen bonds : bond 0.03194 ( 1040) hydrogen bonds : angle 4.32026 ( 2796) link_ALPHA1-3 : bond 0.01078 ( 8) link_ALPHA1-3 : angle 1.53934 ( 24) link_ALPHA1-6 : bond 0.00490 ( 8) link_ALPHA1-6 : angle 1.75991 ( 24) link_BETA1-4 : bond 0.00496 ( 28) link_BETA1-4 : angle 1.84962 ( 84) link_NAG-ASN : bond 0.00213 ( 16) link_NAG-ASN : angle 1.94857 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7880 Ramachandran restraints generated. 3940 Oldfield, 0 Emsley, 3940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7880 Ramachandran restraints generated. 3940 Oldfield, 0 Emsley, 3940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 273 time to evaluate : 1.281 Fit side-chains REVERT: A 46 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8583 (mm-30) REVERT: A 414 GLN cc_start: 0.8660 (pp30) cc_final: 0.8158 (pp30) REVERT: A 429 ARG cc_start: 0.8898 (mtp85) cc_final: 0.8633 (mtp85) REVERT: A 431 ASP cc_start: 0.8900 (p0) cc_final: 0.8515 (p0) REVERT: B 656 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8742 (mmp) REVERT: B 673 LYS cc_start: 0.9540 (mttt) cc_final: 0.9325 (mttp) REVERT: B 691 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8828 (ptm-80) REVERT: B 693 LYS cc_start: 0.9083 (ttpt) cc_final: 0.8597 (ttpp) REVERT: B 927 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8230 (mm-40) REVERT: B 1066 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7567 (tp30) REVERT: B 1093 PHE cc_start: 0.9133 (m-80) cc_final: 0.8914 (m-80) REVERT: C 46 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8758 (mm-30) REVERT: C 143 GLN cc_start: 0.9365 (OUTLIER) cc_final: 0.8843 (tp40) REVERT: C 414 GLN cc_start: 0.8702 (pp30) cc_final: 0.8187 (pp30) REVERT: C 429 ARG cc_start: 0.8915 (mtp85) cc_final: 0.8643 (mtp85) REVERT: C 431 ASP cc_start: 0.8933 (p0) cc_final: 0.8520 (p0) REVERT: D 656 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8750 (mmp) REVERT: D 691 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.8834 (ptm-80) REVERT: D 693 LYS cc_start: 0.9077 (ttpt) cc_final: 0.8633 (ttpp) REVERT: D 927 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8236 (mm-40) REVERT: D 1066 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7565 (tp30) REVERT: D 1093 PHE cc_start: 0.9123 (m-80) cc_final: 0.8881 (m-80) REVERT: E 46 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8537 (mm-30) REVERT: E 414 GLN cc_start: 0.8698 (pp30) cc_final: 0.8192 (pp30) REVERT: E 429 ARG cc_start: 0.8922 (mtp85) cc_final: 0.8647 (mtp85) REVERT: E 431 ASP cc_start: 0.8912 (p0) cc_final: 0.8509 (p0) REVERT: F 656 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8765 (mmp) REVERT: F 691 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8838 (ptm-80) REVERT: F 693 LYS cc_start: 0.9094 (ttpt) cc_final: 0.8686 (ttpp) REVERT: F 927 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8238 (mm-40) REVERT: F 1066 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7575 (tp30) REVERT: F 1093 PHE cc_start: 0.9144 (m-80) cc_final: 0.8927 (m-80) REVERT: F 1104 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7903 (mp) REVERT: G 46 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8749 (mm-30) REVERT: G 143 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.8853 (tp40) REVERT: G 414 GLN cc_start: 0.8694 (pp30) cc_final: 0.8177 (pp30) REVERT: G 429 ARG cc_start: 0.8916 (mtp85) cc_final: 0.8645 (mtp85) REVERT: G 431 ASP cc_start: 0.8939 (p0) cc_final: 0.8527 (p0) REVERT: H 656 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8749 (mmp) REVERT: H 691 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8796 (ptm-80) REVERT: H 693 LYS cc_start: 0.9082 (ttpt) cc_final: 0.8615 (ttpp) REVERT: H 927 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8246 (mm-40) REVERT: H 1066 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7575 (tp30) REVERT: H 1093 PHE cc_start: 0.9142 (m-80) cc_final: 0.8905 (m-80) outliers start: 75 outliers final: 54 residues processed: 319 average time/residue: 0.9100 time to fit residues: 331.8429 Evaluate side-chains 335 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 270 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 1006 MET Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain D residue 691 ARG Chi-restraints excluded: chain D residue 768 CYS Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 932 THR Chi-restraints excluded: chain D residue 1006 MET Chi-restraints excluded: chain D residue 1101 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 644 ILE Chi-restraints excluded: chain F residue 656 MET Chi-restraints excluded: chain F residue 691 ARG Chi-restraints excluded: chain F residue 768 CYS Chi-restraints excluded: chain F residue 834 VAL Chi-restraints excluded: chain F residue 932 THR Chi-restraints excluded: chain F residue 1006 MET Chi-restraints excluded: chain F residue 1101 LEU Chi-restraints excluded: chain F residue 1104 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 482 LEU Chi-restraints excluded: chain G residue 490 LEU Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain G residue 644 ILE Chi-restraints excluded: chain H residue 656 MET Chi-restraints excluded: chain H residue 691 ARG Chi-restraints excluded: chain H residue 768 CYS Chi-restraints excluded: chain H residue 834 VAL Chi-restraints excluded: chain H residue 932 THR Chi-restraints excluded: chain H residue 1006 MET Chi-restraints excluded: chain H residue 1101 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 33 optimal weight: 6.9990 chunk 275 optimal weight: 0.9990 chunk 218 optimal weight: 4.9990 chunk 217 optimal weight: 0.9980 chunk 364 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 346 optimal weight: 20.0000 chunk 245 optimal weight: 30.0000 chunk 285 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 259 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1030 ASN B1107 ASN D1030 ASN D1107 ASN F1030 ASN F1107 ASN H1030 ASN H1107 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.086593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.057176 restraints weight = 56303.402| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 2.93 r_work: 0.2559 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2422 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 32004 Z= 0.187 Angle : 0.573 12.286 43676 Z= 0.282 Chirality : 0.043 0.195 5244 Planarity : 0.004 0.050 5336 Dihedral : 6.757 57.720 5371 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.41 % Allowed : 16.10 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.14), residues: 3940 helix: 2.78 (0.22), residues: 608 sheet: 0.51 (0.15), residues: 1324 loop : -0.59 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 960 TYR 0.010 0.001 TYR B 690 PHE 0.015 0.001 PHE A 459 TRP 0.019 0.001 TRP B1108 HIS 0.003 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00444 (31848) covalent geometry : angle 0.56056 (43304) SS BOND : bond 0.00254 ( 96) SS BOND : angle 0.78634 ( 192) hydrogen bonds : bond 0.03412 ( 1040) hydrogen bonds : angle 4.38700 ( 2796) link_ALPHA1-3 : bond 0.00972 ( 8) link_ALPHA1-3 : angle 1.57143 ( 24) link_ALPHA1-6 : bond 0.00498 ( 8) link_ALPHA1-6 : angle 1.77743 ( 24) link_BETA1-4 : bond 0.00454 ( 28) link_BETA1-4 : angle 1.83543 ( 84) link_NAG-ASN : bond 0.00272 ( 16) link_NAG-ASN : angle 2.09381 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7880 Ramachandran restraints generated. 3940 Oldfield, 0 Emsley, 3940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7880 Ramachandran restraints generated. 3940 Oldfield, 0 Emsley, 3940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 269 time to evaluate : 1.236 Fit side-chains REVERT: A 46 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8566 (mm-30) REVERT: A 414 GLN cc_start: 0.8685 (pp30) cc_final: 0.8250 (pp30) REVERT: B 656 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8739 (mmp) REVERT: B 691 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.8869 (ptm-80) REVERT: B 693 LYS cc_start: 0.9078 (ttpt) cc_final: 0.8588 (ttpp) REVERT: B 927 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8225 (mm-40) REVERT: B 1066 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7578 (tp30) REVERT: B 1093 PHE cc_start: 0.9136 (m-80) cc_final: 0.8910 (m-80) REVERT: C 46 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8769 (mm-30) REVERT: C 143 GLN cc_start: 0.9370 (OUTLIER) cc_final: 0.8825 (tp40) REVERT: C 414 GLN cc_start: 0.8690 (pp30) cc_final: 0.8258 (pp30) REVERT: C 429 ARG cc_start: 0.8916 (mtp85) cc_final: 0.8639 (mtp85) REVERT: C 431 ASP cc_start: 0.8932 (p0) cc_final: 0.8527 (p0) REVERT: D 656 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8739 (mmp) REVERT: D 691 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.8848 (ptm-80) REVERT: D 927 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8212 (mm-40) REVERT: D 1066 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7589 (tp30) REVERT: D 1093 PHE cc_start: 0.9133 (m-80) cc_final: 0.8912 (m-80) REVERT: E 46 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8512 (mm-30) REVERT: E 414 GLN cc_start: 0.8704 (pp30) cc_final: 0.8267 (pp30) REVERT: E 429 ARG cc_start: 0.8923 (mtp85) cc_final: 0.8654 (mtp85) REVERT: E 431 ASP cc_start: 0.8910 (p0) cc_final: 0.8511 (p0) REVERT: F 656 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8723 (mmp) REVERT: F 691 ARG cc_start: 0.9237 (OUTLIER) cc_final: 0.8490 (ptm-80) REVERT: F 693 LYS cc_start: 0.9101 (ttpt) cc_final: 0.8665 (ttpp) REVERT: F 927 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8228 (mm-40) REVERT: F 1066 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7601 (tp30) REVERT: F 1093 PHE cc_start: 0.9141 (m-80) cc_final: 0.8913 (m-80) REVERT: G 46 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8752 (mm-30) REVERT: G 143 GLN cc_start: 0.9374 (OUTLIER) cc_final: 0.8823 (tp40) REVERT: G 414 GLN cc_start: 0.8688 (pp30) cc_final: 0.8256 (pp30) REVERT: G 429 ARG cc_start: 0.8908 (mtp85) cc_final: 0.8636 (mtp85) REVERT: G 431 ASP cc_start: 0.8932 (p0) cc_final: 0.8533 (p0) REVERT: H 656 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8725 (mmp) REVERT: H 691 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8478 (ptm-80) REVERT: H 693 LYS cc_start: 0.9100 (ttpt) cc_final: 0.8671 (ttpp) REVERT: H 927 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8222 (mm-40) REVERT: H 1066 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7588 (tp30) REVERT: H 1093 PHE cc_start: 0.9144 (m-80) cc_final: 0.8924 (m-80) outliers start: 84 outliers final: 52 residues processed: 321 average time/residue: 0.8908 time to fit residues: 327.3810 Evaluate side-chains 322 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 260 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 1006 MET Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain D residue 691 ARG Chi-restraints excluded: chain D residue 768 CYS Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 932 THR Chi-restraints excluded: chain D residue 1006 MET Chi-restraints excluded: chain D residue 1101 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 644 ILE Chi-restraints excluded: chain F residue 656 MET Chi-restraints excluded: chain F residue 691 ARG Chi-restraints excluded: chain F residue 768 CYS Chi-restraints excluded: chain F residue 834 VAL Chi-restraints excluded: chain F residue 932 THR Chi-restraints excluded: chain F residue 1006 MET Chi-restraints excluded: chain F residue 1101 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 482 LEU Chi-restraints excluded: chain G residue 490 LEU Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain G residue 644 ILE Chi-restraints excluded: chain H residue 656 MET Chi-restraints excluded: chain H residue 691 ARG Chi-restraints excluded: chain H residue 768 CYS Chi-restraints excluded: chain H residue 834 VAL Chi-restraints excluded: chain H residue 932 THR Chi-restraints excluded: chain H residue 1006 MET Chi-restraints excluded: chain H residue 1101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 244 optimal weight: 20.0000 chunk 377 optimal weight: 1.9990 chunk 195 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 326 optimal weight: 2.9990 chunk 370 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 264 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 235 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1030 ASN B1107 ASN D1030 ASN D1107 ASN F1030 ASN F1107 ASN H1030 ASN H1107 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.086418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.057022 restraints weight = 56331.029| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 2.93 r_work: 0.2554 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2417 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 32004 Z= 0.196 Angle : 0.586 12.465 43676 Z= 0.288 Chirality : 0.043 0.196 5244 Planarity : 0.003 0.042 5336 Dihedral : 6.784 56.898 5371 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.07 % Allowed : 16.36 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.13), residues: 3940 helix: 2.43 (0.22), residues: 636 sheet: 0.61 (0.15), residues: 1292 loop : -0.74 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 960 TYR 0.010 0.001 TYR B 690 PHE 0.015 0.001 PHE E 459 TRP 0.021 0.001 TRP D1108 HIS 0.003 0.001 HIS C 279 Details of bonding type rmsd covalent geometry : bond 0.00465 (31848) covalent geometry : angle 0.57292 (43304) SS BOND : bond 0.00262 ( 96) SS BOND : angle 0.80480 ( 192) hydrogen bonds : bond 0.03447 ( 1040) hydrogen bonds : angle 4.40598 ( 2796) link_ALPHA1-3 : bond 0.00951 ( 8) link_ALPHA1-3 : angle 1.56313 ( 24) link_ALPHA1-6 : bond 0.00522 ( 8) link_ALPHA1-6 : angle 1.78300 ( 24) link_BETA1-4 : bond 0.00438 ( 28) link_BETA1-4 : angle 1.87509 ( 84) link_NAG-ASN : bond 0.00197 ( 16) link_NAG-ASN : angle 2.24792 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7880 Ramachandran restraints generated. 3940 Oldfield, 0 Emsley, 3940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7880 Ramachandran restraints generated. 3940 Oldfield, 0 Emsley, 3940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 260 time to evaluate : 1.263 Fit side-chains REVERT: A 46 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8576 (mm-30) REVERT: A 414 GLN cc_start: 0.8705 (pp30) cc_final: 0.8298 (pp30) REVERT: A 429 ARG cc_start: 0.8899 (mtp85) cc_final: 0.8619 (mtp85) REVERT: A 431 ASP cc_start: 0.9026 (p0) cc_final: 0.8662 (p0) REVERT: B 656 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8776 (OUTLIER) REVERT: B 691 ARG cc_start: 0.9209 (OUTLIER) cc_final: 0.8861 (ptm-80) REVERT: B 927 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8223 (mm-40) REVERT: B 960 ARG cc_start: 0.9074 (ttp80) cc_final: 0.8838 (ttp80) REVERT: B 1066 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7595 (tp30) REVERT: B 1093 PHE cc_start: 0.9125 (m-80) cc_final: 0.8905 (m-80) REVERT: C 46 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8771 (mm-30) REVERT: C 143 GLN cc_start: 0.9363 (OUTLIER) cc_final: 0.8826 (tp40) REVERT: C 414 GLN cc_start: 0.8711 (pp30) cc_final: 0.8299 (pp30) REVERT: D 656 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8755 (OUTLIER) REVERT: D 691 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.8841 (ptm-80) REVERT: D 927 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8221 (mm-40) REVERT: D 960 ARG cc_start: 0.9073 (ttp80) cc_final: 0.8839 (ttp80) REVERT: D 1066 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7596 (tp30) REVERT: D 1093 PHE cc_start: 0.9146 (m-80) cc_final: 0.8933 (m-80) REVERT: E 46 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8539 (mm-30) REVERT: E 414 GLN cc_start: 0.8720 (pp30) cc_final: 0.8274 (pp30) REVERT: F 656 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8788 (mmp) REVERT: F 691 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.8493 (ptm-80) REVERT: F 693 LYS cc_start: 0.9108 (ttpt) cc_final: 0.8632 (ttpp) REVERT: F 927 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8229 (mm-40) REVERT: F 960 ARG cc_start: 0.9070 (ttp80) cc_final: 0.8831 (ttp80) REVERT: F 1066 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7592 (tp30) REVERT: F 1093 PHE cc_start: 0.9141 (m-80) cc_final: 0.8927 (m-80) REVERT: G 46 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8762 (mm-30) REVERT: G 143 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.8817 (tp40) REVERT: G 414 GLN cc_start: 0.8713 (pp30) cc_final: 0.8266 (pp30) REVERT: H 656 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8757 (OUTLIER) REVERT: H 691 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.8490 (ptm-80) REVERT: H 693 LYS cc_start: 0.9105 (ttpt) cc_final: 0.8668 (ttpp) REVERT: H 927 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8228 (mm-40) REVERT: H 960 ARG cc_start: 0.9083 (ttp80) cc_final: 0.8842 (ttp80) REVERT: H 1066 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7604 (tp30) REVERT: H 1093 PHE cc_start: 0.9149 (m-80) cc_final: 0.8940 (m-80) outliers start: 72 outliers final: 56 residues processed: 303 average time/residue: 0.8834 time to fit residues: 305.8233 Evaluate side-chains 321 residues out of total 3484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 258 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 1006 MET Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain D residue 691 ARG Chi-restraints excluded: chain D residue 768 CYS Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 932 THR Chi-restraints excluded: chain D residue 1006 MET Chi-restraints excluded: chain D residue 1101 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 644 ILE Chi-restraints excluded: chain F residue 656 MET Chi-restraints excluded: chain F residue 691 ARG Chi-restraints excluded: chain F residue 768 CYS Chi-restraints excluded: chain F residue 834 VAL Chi-restraints excluded: chain F residue 932 THR Chi-restraints excluded: chain F residue 1006 MET Chi-restraints excluded: chain F residue 1101 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 482 LEU Chi-restraints excluded: chain G residue 490 LEU Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain G residue 644 ILE Chi-restraints excluded: chain H residue 656 MET Chi-restraints excluded: chain H residue 691 ARG Chi-restraints excluded: chain H residue 768 CYS Chi-restraints excluded: chain H residue 834 VAL Chi-restraints excluded: chain H residue 932 THR Chi-restraints excluded: chain H residue 1006 MET Chi-restraints excluded: chain H residue 1101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 292 optimal weight: 7.9990 chunk 376 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 276 optimal weight: 5.9990 chunk 328 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 271 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 248 optimal weight: 0.0970 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1030 ASN B1107 ASN D1030 ASN D1107 ASN F1030 ASN F1107 ASN H1030 ASN H1107 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.087775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.058353 restraints weight = 56288.189| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 2.95 r_work: 0.2581 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2443 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32004 Z= 0.109 Angle : 0.544 12.422 43676 Z= 0.267 Chirality : 0.042 0.196 5244 Planarity : 0.003 0.045 5336 Dihedral : 6.449 54.379 5371 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.81 % Allowed : 16.73 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.14), residues: 3940 helix: 2.76 (0.22), residues: 608 sheet: 0.53 (0.15), residues: 1300 loop : -0.62 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 960 TYR 0.009 0.001 TYR B 690 PHE 0.010 0.001 PHE A 459 TRP 0.021 0.001 TRP H1108 HIS 0.002 0.000 HIS B 820 Details of bonding type rmsd covalent geometry : bond 0.00254 (31848) covalent geometry : angle 0.53237 (43304) SS BOND : bond 0.00195 ( 96) SS BOND : angle 0.63055 ( 192) hydrogen bonds : bond 0.02923 ( 1040) hydrogen bonds : angle 4.26785 ( 2796) link_ALPHA1-3 : bond 0.01075 ( 8) link_ALPHA1-3 : angle 1.53180 ( 24) link_ALPHA1-6 : bond 0.00603 ( 8) link_ALPHA1-6 : angle 1.73230 ( 24) link_BETA1-4 : bond 0.00531 ( 28) link_BETA1-4 : angle 1.71619 ( 84) link_NAG-ASN : bond 0.00195 ( 16) link_NAG-ASN : angle 2.01506 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15834.93 seconds wall clock time: 269 minutes 14.42 seconds (16154.42 seconds total)