Starting phenix.real_space_refine on Wed Oct 28 18:41:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30xt_58134/10_2026/30xt_58134.cif Found real_map, /net/cci-nas-00/data/ceres_data/30xt_58134/10_2026/30xt_58134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/30xt_58134/10_2026/30xt_58134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30xt_58134/10_2026/30xt_58134.map" model { file = "/net/cci-nas-00/data/ceres_data/30xt_58134/10_2026/30xt_58134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30xt_58134/10_2026/30xt_58134.cif" } resolution = 2.55 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= 0.014 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 258 5.16 5 C 18057 2.51 5 N 4716 2.21 5 O 5718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28749 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3523 Classifications: {'peptide': 460} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 436} Chain: "B" Number of atoms: 3308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3308 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain: "C" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3523 Classifications: {'peptide': 460} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 436} Chain: "D" Number of atoms: 3308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3308 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain: "E" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3523 Classifications: {'peptide': 460} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 436} Chain: "F" Number of atoms: 3308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3308 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain: "G" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3523 Classifications: {'peptide': 460} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 436} Chain: "H" Number of atoms: 3308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3308 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain: "Y" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 801 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 94} Chain: "I" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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: "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: 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: "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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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 Time building chain proxies: 6.52, per 1000 atoms: 0.23 Number of scatterers: 28749 At special positions: 0 Unit cell: (147.609, 149.846, 107.352, 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 258 16.00 O 5718 8.00 N 4716 7.00 C 18057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=93, 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=2.04 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=2.04 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=2.04 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=2.04 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 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=2.04 Simple disulfide: pdb=" SG CYS D 742 " - pdb=" SG CYS D 780 " distance=2.04 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 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=2.04 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 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=2.04 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=2.06 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 Y 123 " - pdb=" SG CYS Y 132 " 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=2, 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 " 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 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 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 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 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 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.1 seconds 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6802 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 48 sheets defined 11.4% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.550A pdb=" N SER A 56 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 3.703A 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 225 through 234 Processing helix chain 'A' and resid 266 through 279 Processing helix chain 'A' and resid 446 through 463 removed outlier: 3.502A pdb=" N LEU A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 479 Processing helix chain 'B' and resid 747 through 752 removed outlier: 3.836A pdb=" N SER B 752 " --> pdb=" O TRP B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 858 removed outlier: 3.742A 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: 3.671A pdb=" N SER B 968 " --> pdb=" O PHE B 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 58 removed outlier: 3.519A pdb=" N SER C 56 " --> pdb=" O GLU C 53 " (cutoff:3.500A) removed outlier: 3.677A 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 removed outlier: 3.530A pdb=" N LEU C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 479 Processing helix chain 'D' and resid 747 through 752 removed outlier: 3.832A pdb=" N SER D 752 " --> pdb=" O TRP D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 858 removed outlier: 3.721A 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: 3.581A pdb=" N LEU D 967 " --> pdb=" O SER D 963 " (cutoff:3.500A) removed outlier: 3.628A 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 'E' and resid 52 through 58 removed outlier: 3.528A pdb=" N SER E 56 " --> pdb=" O GLU E 53 " (cutoff:3.500A) removed outlier: 3.673A 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 225 through 234 Processing helix chain 'E' and resid 266 through 279 Processing helix chain 'E' and resid 446 through 463 removed outlier: 3.559A pdb=" N LEU E 450 " --> pdb=" O LEU E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 479 Processing helix chain 'F' and resid 747 through 752 removed outlier: 3.824A pdb=" N SER F 752 " --> pdb=" O TRP F 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 854 through 858 removed outlier: 3.733A 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: 3.539A pdb=" N LEU F 967 " --> pdb=" O SER F 963 " (cutoff:3.500A) removed outlier: 3.612A 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 'G' and resid 52 through 58 removed outlier: 3.509A pdb=" N SER G 56 " --> pdb=" O GLU G 53 " (cutoff:3.500A) removed outlier: 3.718A 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 225 through 234 Processing helix chain 'G' and resid 266 through 279 Processing helix chain 'G' and resid 446 through 463 removed outlier: 3.522A pdb=" N LEU G 450 " --> pdb=" O LEU G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 469 through 479 Processing helix chain 'H' and resid 747 through 752 removed outlier: 3.844A pdb=" N SER H 752 " --> pdb=" O TRP H 749 " (cutoff:3.500A) Processing helix chain 'H' and resid 854 through 858 removed outlier: 3.746A 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: 3.570A pdb=" N SER H 968 " --> pdb=" O PHE H 964 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 81 Processing helix chain 'Y' and resid 120 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 30 removed outlier: 6.316A pdb=" N THR A 22 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLN A 171 " --> pdb=" O THR A 22 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N TYR A 24 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ILE A 173 " --> pdb=" O TYR A 24 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU A 26 " --> pdb=" O ILE A 173 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLU A 175 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 6.281A 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: 10.978A pdb=" N PHE A 339 " --> pdb=" O GLN A 75 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N SER A 77 " --> pdb=" O PHE A 339 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N PHE A 341 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 5.739A 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 710 current: chain 'B' and resid 781 through 812 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 815 through 822 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 297 through 303 Processing sheet with id=AA7, first strand: chain 'A' and resid 380 through 386 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 676 through 683 removed outlier: 3.648A pdb=" N LEU B 676 " --> pdb=" O LEU B 958 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY B 838 " --> pdb=" O HIS B 953 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASN B 955 " --> pdb=" O ILE B 836 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ILE B 836 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VAL B 957 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL B 834 " --> pdb=" O VAL B 957 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 893 through 898 Processing sheet with id=AB2, first strand: chain 'B' and resid 973 through 975 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 973 through 975 current: chain 'B' and resid 990 through 1012 removed outlier: 8.204A pdb=" N GLU B1001 " --> pdb=" O ALA B1026 " (cutoff:3.500A) removed outlier: 11.159A pdb=" N ALA B1026 " --> pdb=" O GLU B1001 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N ASN B1024 " --> pdb=" O PRO B1003 " (cutoff:3.500A) removed outlier: 11.232A pdb=" N PHE B1005 " --> pdb=" O VAL B1022 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N VAL B1022 " --> pdb=" O PHE B1005 " (cutoff:3.500A) removed outlier: 11.489A pdb=" N THR B1007 " --> pdb=" O SER B1020 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N SER B1020 " --> pdb=" O THR B1007 " (cutoff:3.500A) removed outlier: 11.701A pdb=" N ILE B1009 " --> pdb=" O TYR B1018 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N TYR B1018 " --> pdb=" O ILE B1009 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1017 through 1036 current: chain 'B' and resid 1052 through 1053 Processing sheet with id=AB3, first strand: chain 'C' and resid 23 through 30 removed outlier: 6.322A pdb=" N TYR C 24 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE C 173 " --> pdb=" O TYR C 24 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU C 26 " --> pdb=" O ILE C 173 " (cutoff:3.500A) removed outlier: 7.083A 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 75 through 85 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 710 current: chain 'D' and resid 781 through 812 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 815 through 822 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 940 through 944 Processing sheet with id=AB8, first strand: chain 'C' and resid 297 through 303 Processing sheet with id=AB9, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AC1, first strand: chain 'C' and resid 379 through 386 Processing sheet with id=AC2, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AC3, first strand: chain 'D' and resid 676 through 683 removed outlier: 6.751A pdb=" N ARG D 951 " --> pdb=" O THR D 839 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N THR D 839 " --> pdb=" O ARG D 951 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N HIS D 953 " --> pdb=" O VAL D 837 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL D 834 " --> pdb=" O LEU D 827 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU D 827 " --> pdb=" O VAL D 834 " (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 'D' and resid 973 through 975 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 973 through 975 current: chain 'D' and resid 990 through 1012 removed outlier: 8.365A pdb=" N GLU D1001 " --> pdb=" O ALA D1026 " (cutoff:3.500A) removed outlier: 11.232A pdb=" N ALA D1026 " --> pdb=" O GLU D1001 " (cutoff:3.500A) removed outlier: 9.686A pdb=" N ASN D1024 " --> pdb=" O PRO D1003 " (cutoff:3.500A) removed outlier: 11.103A pdb=" N PHE D1005 " --> pdb=" O VAL D1022 " (cutoff:3.500A) removed outlier: 9.545A pdb=" N VAL D1022 " --> pdb=" O PHE D1005 " (cutoff:3.500A) removed outlier: 11.157A pdb=" N THR D1007 " --> pdb=" O SER D1020 " (cutoff:3.500A) removed outlier: 9.704A pdb=" N SER D1020 " --> pdb=" O THR D1007 " (cutoff:3.500A) removed outlier: 11.187A pdb=" N ILE D1009 " --> pdb=" O TYR D1018 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N TYR D1018 " --> pdb=" O ILE D1009 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 1017 through 1036 current: chain 'D' and resid 1052 through 1053 Processing sheet with id=AC6, first strand: chain 'E' and resid 22 through 30 removed outlier: 6.280A pdb=" N THR E 22 " --> pdb=" O ARG E 169 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLN E 171 " --> pdb=" O THR E 22 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR E 24 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE E 173 " --> pdb=" O TYR E 24 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU E 26 " --> pdb=" O ILE E 173 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU E 175 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N MET E 28 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 130 through 137 Processing sheet with id=AC8, first strand: chain 'E' and resid 75 through 85 removed outlier: 3.550A pdb=" N ARG E 84 " --> pdb=" O GLU E 101 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 183 through 184 removed outlier: 3.503A pdb=" N ASP E 206 " --> pdb=" O GLY E 371 " (cutoff:3.500A) Processing sheet with id=AD1, 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 710 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=AD2, first strand: chain 'E' and resid 297 through 303 Processing sheet with id=AD3, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AD4, first strand: chain 'E' and resid 379 through 386 Processing sheet with id=AD5, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AD6, first strand: chain 'F' and resid 677 through 683 removed outlier: 6.447A pdb=" N ASN F 955 " --> pdb=" O ILE F 836 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE F 836 " --> pdb=" O ASN F 955 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL F 957 " --> pdb=" O VAL F 834 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL F 834 " --> pdb=" O VAL F 957 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 893 through 898 Processing sheet with id=AD8, first strand: chain 'F' and resid 973 through 984 removed outlier: 5.484A pdb=" N VAL F 974 " --> pdb=" O THR F1000 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N THR F1000 " --> pdb=" O VAL F 974 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU F 976 " --> pdb=" O GLY F 998 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY F 998 " --> pdb=" O LEU F 976 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N THR F 978 " --> pdb=" O THR F 996 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N THR F 996 " --> pdb=" O THR F 978 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA F 980 " --> pdb=" O THR F 994 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY F 990 " --> pdb=" O ALA F 984 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU F 993 " --> pdb=" O GLY F1036 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLY F1036 " --> pdb=" O LEU F 993 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N CYS F 995 " --> pdb=" O VAL F1034 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL F1034 " --> pdb=" O CYS F 995 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL F 997 " --> pdb=" O VAL F1032 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL F1032 " --> pdb=" O VAL F 997 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU F 999 " --> pdb=" O ASN F1030 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ASN F1030 " --> pdb=" O LEU F 999 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N GLU F1001 " --> pdb=" O GLY F1028 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N GLY F1028 " --> pdb=" O GLU F1001 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ALA F1026 " --> pdb=" O PRO F1003 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N PHE F1005 " --> pdb=" O ASN F1024 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASN F1024 " --> pdb=" O PHE F1005 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR F1007 " --> pdb=" O VAL F1022 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL F1022 " --> pdb=" O THR F1007 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE F1009 " --> pdb=" O SER F1020 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER F1020 " --> pdb=" O ILE F1009 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA F1011 " --> pdb=" O TYR F1018 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 1017 through 1036 current: chain 'F' and resid 1052 through 1053 Processing sheet with id=AD9, first strand: chain 'G' and resid 22 through 30 removed outlier: 6.146A pdb=" N THR G 22 " --> pdb=" O ARG G 169 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLN G 171 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR G 24 " --> pdb=" O GLN G 171 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE G 173 " --> pdb=" O TYR G 24 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU G 26 " --> pdb=" O ILE G 173 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU G 175 " --> pdb=" O LEU G 26 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N MET G 28 " --> pdb=" O GLU G 175 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 130 through 137 Processing sheet with id=AE2, first strand: chain 'G' and resid 100 through 110 removed outlier: 3.586A pdb=" N GLU G 101 " --> pdb=" O ARG G 84 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG G 84 " --> pdb=" O GLU G 101 " (cutoff:3.500A) removed outlier: 10.975A pdb=" N PHE G 339 " --> pdb=" O GLN G 75 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N SER G 77 " --> pdb=" O PHE G 339 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N PHE G 341 " --> pdb=" O SER G 77 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N THR G 79 " --> pdb=" O PHE G 341 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 183 through 184 Processing sheet with id=AE4, 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 710 current: chain 'H' and resid 781 through 812 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 815 through 822 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=AE5, first strand: chain 'G' and resid 297 through 303 Processing sheet with id=AE6, first strand: chain 'G' and resid 379 through 386 Processing sheet with id=AE7, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AE8, first strand: chain 'H' and resid 676 through 683 removed outlier: 3.655A pdb=" N GLY H 838 " --> pdb=" O HIS H 953 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN H 955 " --> pdb=" O ILE H 836 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE H 836 " --> pdb=" O ASN H 955 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL H 957 " --> pdb=" O VAL H 834 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL H 834 " --> pdb=" O VAL H 957 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 893 through 898 Processing sheet with id=AF1, first strand: chain 'H' and resid 973 through 975 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 973 through 975 current: chain 'H' and resid 990 through 1012 removed outlier: 8.331A pdb=" N GLU H1001 " --> pdb=" O ALA H1026 " (cutoff:3.500A) removed outlier: 11.179A pdb=" N ALA H1026 " --> pdb=" O GLU H1001 " (cutoff:3.500A) removed outlier: 9.745A pdb=" N ASN H1024 " --> pdb=" O PRO H1003 " (cutoff:3.500A) removed outlier: 11.147A pdb=" N PHE H1005 " --> pdb=" O VAL H1022 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N VAL H1022 " --> pdb=" O PHE H1005 " (cutoff:3.500A) removed outlier: 11.396A pdb=" N THR H1007 " --> pdb=" O SER H1020 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N SER H1020 " --> pdb=" O THR H1007 " (cutoff:3.500A) removed outlier: 11.468A pdb=" N ILE H1009 " --> pdb=" O TYR H1018 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N TYR H1018 " --> pdb=" O ILE H1009 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 1017 through 1036 current: chain 'H' and resid 1052 through 1053 Processing sheet with id=AF2, first strand: chain 'Y' and resid 60 through 65 removed outlier: 4.507A pdb=" N CYS Y 132 " --> pdb=" O VAL Y 158 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLU Y 137 " --> pdb=" O GLU Y 93 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Y' and resid 73 through 76 removed outlier: 7.166A pdb=" N LEU Y 73 " --> pdb=" O THR Y 110 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR Y 110 " --> pdb=" O LEU Y 73 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY Y 75 " --> pdb=" O ILE Y 108 " (cutoff:3.500A) 778 hydrogen bonds defined for protein. 2043 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: 5.59 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9067 1.34 - 1.46: 6758 1.46 - 1.59: 13208 1.59 - 1.71: 1 1.71 - 1.84: 330 Bond restraints: 29364 Sorted by residual: bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C1 NAG W 1 " pdb=" O5 NAG W 1 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.27e+01 ... (remaining 29359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 39479 3.24 - 6.48: 355 6.48 - 9.71: 47 9.71 - 12.95: 2 12.95 - 16.19: 4 Bond angle restraints: 39887 Sorted by residual: angle pdb=" CA CYS H 738 " pdb=" CB CYS H 738 " pdb=" SG CYS H 738 " ideal model delta sigma weight residual 114.40 130.59 -16.19 2.30e+00 1.89e-01 4.95e+01 angle pdb=" CA CYS H 773 " pdb=" CB CYS H 773 " pdb=" SG CYS H 773 " ideal model delta sigma weight residual 114.40 129.70 -15.30 2.30e+00 1.89e-01 4.43e+01 angle pdb=" CA MET D1016 " pdb=" CB MET D1016 " pdb=" CG MET D1016 " ideal model delta sigma weight residual 114.10 123.76 -9.66 2.00e+00 2.50e-01 2.33e+01 angle pdb=" C VAL G 126 " pdb=" N LYS G 127 " pdb=" CA LYS G 127 " ideal model delta sigma weight residual 122.77 116.61 6.16 1.33e+00 5.65e-01 2.14e+01 angle pdb=" CB ASN B 930 " pdb=" CG ASN B 930 " pdb=" ND2 ASN B 930 " ideal model delta sigma weight residual 116.40 123.30 -6.90 1.50e+00 4.44e-01 2.11e+01 ... (remaining 39882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.71: 16608 20.71 - 41.43: 1432 41.43 - 62.14: 311 62.14 - 82.86: 92 82.86 - 103.57: 44 Dihedral angle restraints: 18487 sinusoidal: 7903 harmonic: 10584 Sorted by residual: dihedral pdb=" CB CYS H 738 " pdb=" SG CYS H 738 " pdb=" SG CYS H 773 " pdb=" CB CYS H 773 " ideal model delta sinusoidal sigma weight residual -86.00 -171.73 85.73 1 1.00e+01 1.00e-02 8.89e+01 dihedral pdb=" CB CYS H 742 " pdb=" SG CYS H 742 " pdb=" SG CYS H 780 " pdb=" CB CYS H 780 " ideal model delta sinusoidal sigma weight residual 93.00 152.94 -59.94 1 1.00e+01 1.00e-02 4.79e+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 93.00 148.89 -55.89 1 1.00e+01 1.00e-02 4.22e+01 ... (remaining 18484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 4459 0.101 - 0.201: 273 0.201 - 0.302: 17 0.302 - 0.403: 3 0.403 - 0.503: 2 Chirality restraints: 4754 Sorted by residual: chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN G 350 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.33e+00 chirality pdb=" CA CYS H 738 " pdb=" N CYS H 738 " pdb=" C CYS H 738 " pdb=" CB CYS H 738 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN E 350 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.68e+00 ... (remaining 4751 not shown) Planarity restraints: 5030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 692 " -0.370 9.50e-02 1.11e+02 1.67e-01 2.21e+01 pdb=" NE ARG H 692 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG H 692 " -0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG H 692 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG H 692 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 692 " 0.379 9.50e-02 1.11e+02 1.71e-01 2.18e+01 pdb=" NE ARG B 692 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG B 692 " 0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG B 692 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG B 692 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 692 " 0.379 9.50e-02 1.11e+02 1.71e-01 2.18e+01 pdb=" NE ARG F 692 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG F 692 " 0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG F 692 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG F 692 " 0.002 2.00e-02 2.50e+03 ... (remaining 5027 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 289 2.66 - 3.22: 24781 3.22 - 3.78: 40955 3.78 - 4.34: 58446 4.34 - 4.90: 98123 Nonbonded interactions: 222594 Sorted by model distance: nonbonded pdb=" OG SER C 221 " pdb=" OE1 GLN C 223 " model vdw 2.094 3.040 nonbonded pdb=" OD1 ASN B 930 " pdb=" N2 NAG L 1 " model vdw 2.156 3.120 nonbonded pdb=" NH2 ARG A 333 " pdb=" OD1 ASP A 355 " model vdw 2.160 3.120 nonbonded pdb=" N ASP E 88 " pdb=" OD1 ASP E 88 " model vdw 2.167 3.120 nonbonded pdb=" OG SER F 684 " pdb=" OE1 GLN F 713 " model vdw 2.167 3.040 ... (remaining 222589 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: 0.00 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 'J' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'W' 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: 7.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.170 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 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:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 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 : 0.004 0.085 29507 Z= 0.203 Angle : 0.831 16.189 40217 Z= 0.420 Chirality : 0.052 0.503 4754 Planarity : 0.006 0.171 5014 Dihedral : 17.106 103.572 11406 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.21 % Favored : 97.73 % Rotamer: Outliers : 1.08 % Allowed : 21.67 % Favored : 77.25 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.14), residues: 3657 helix: 0.94 (0.33), residues: 282 sheet: 0.52 (0.14), residues: 1452 loop : -0.52 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.002 ARG H 692 TYR 0.018 0.001 TYR G 120 PHE 0.021 0.002 PHE H 706 TRP 0.013 0.001 TRP F 660 HIS 0.005 0.001 HIS H 820 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (29364) covalent geometry : angle 0.80516 / 0.41 (39887) SS BOND : bond 0.00437 / 0.27 ( 93) SS BOND : angle 1.61502 / 1.06 ( 186) hydrogen bonds : bond 0.21965 / 14.64 ( 778) hydrogen bonds : angle 7.77042 / 5.46 ( 2043) Misc. bond : bond 0.00033 / 0.02 ( 2) link_ALPHA1-3 : bond 0.00527 / 0.25 ( 8) link_ALPHA1-3 : angle 1.31562 / 0.76 ( 24) link_BETA1-4 : bond 0.00914 / 0.57 ( 24) link_BETA1-4 : angle 2.74056 / 1.65 ( 72) link_NAG-ASN : bond 0.01583 / 0.86 ( 16) link_NAG-ASN : angle 4.18242 / 2.63 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 224 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8228 (mm-30) REVERT: C 175 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7825 (mt-10) REVERT: E 429 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7758 (mmt180) REVERT: F 710 MET cc_start: 0.7460 (ttm) cc_final: 0.7236 (ttm) REVERT: G 125 LYS cc_start: 0.7041 (OUTLIER) cc_final: 0.6807 (mtmt) REVERT: G 476 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8682 (tm-30) REVERT: H 817 THR cc_start: 0.7512 (m) cc_final: 0.7078 (p) REVERT: Y 142 ASP cc_start: 0.8636 (p0) cc_final: 0.8346 (t0) outliers start: 35 outliers final: 13 residues processed: 245 average time/residue: 0.7632 time to fit residues: 214.7402 Evaluate side-chains 211 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 354 CYS Chi-restraints excluded: chain E residue 429 ARG Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 125 LYS Chi-restraints excluded: chain H residue 773 CYS Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 141 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 GLN ** B 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1030 ASN D 820 HIS ** G 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1072 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.142994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.086266 restraints weight = 44780.496| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.27 r_work: 0.2988 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29507 Z= 0.110 Angle : 0.562 10.080 40217 Z= 0.284 Chirality : 0.044 0.242 4754 Planarity : 0.004 0.089 5014 Dihedral : 9.897 74.211 4879 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.74 % Allowed : 19.90 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.14), residues: 3657 helix: 0.95 (0.32), residues: 306 sheet: 0.67 (0.15), residues: 1392 loop : -0.56 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 951 TYR 0.011 0.001 TYR E 120 PHE 0.012 0.001 PHE H 736 TRP 0.009 0.001 TRP F 749 HIS 0.003 0.001 HIS F 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (29364) covalent geometry : angle 0.54492 / 0.28 (39887) SS BOND : bond 0.00217 / 0.13 ( 93) SS BOND : angle 0.73690 / 0.51 ( 186) hydrogen bonds : bond 0.03929 / 2.65 ( 778) hydrogen bonds : angle 5.64480 / 3.99 ( 2043) Misc. bond : bond 0.00177 / 0.09 ( 2) link_ALPHA1-3 : bond 0.01057 / 0.50 ( 8) link_ALPHA1-3 : angle 1.95638 / 1.19 ( 24) link_BETA1-4 : bond 0.00515 / 0.32 ( 24) link_BETA1-4 : angle 1.95106 / 1.16 ( 72) link_NAG-ASN : bond 0.00589 / 0.34 ( 16) link_NAG-ASN : angle 2.80846 / 1.90 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 211 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7646 (tp30) REVERT: B 672 MET cc_start: 0.6253 (tmt) cc_final: 0.6032 (tmt) REVERT: C 175 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8046 (mt-10) REVERT: C 462 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8841 (tm) REVERT: E 412 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8284 (tppt) REVERT: F 656 MET cc_start: 0.2268 (mpt) cc_final: 0.0818 (mpp) REVERT: G 84 ARG cc_start: 0.7124 (tmm160) cc_final: 0.6838 (ttm110) REVERT: G 420 GLU cc_start: 0.7925 (mp0) cc_final: 0.7684 (mp0) REVERT: G 476 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8794 (tm-30) REVERT: H 672 MET cc_start: 0.4045 (OUTLIER) cc_final: 0.3745 (ppp) REVERT: H 817 THR cc_start: 0.6933 (m) cc_final: 0.6511 (p) REVERT: H 951 ARG cc_start: 0.7461 (tpp80) cc_final: 0.7205 (ttm-80) REVERT: Y 80 ASP cc_start: 0.8627 (m-30) cc_final: 0.8402 (m-30) REVERT: Y 137 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6723 (tm-30) REVERT: Y 151 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8732 (tm) outliers start: 56 outliers final: 12 residues processed: 252 average time/residue: 0.7243 time to fit residues: 211.5539 Evaluate side-chains 207 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 354 CYS Chi-restraints excluded: chain E residue 412 LYS Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain H residue 672 MET Chi-restraints excluded: chain H residue 810 ILE Chi-restraints excluded: chain Y residue 111 THR Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 151 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: [285, 196, 87, 116, 299, 15, 206, 50, 226, 94, 174] chunk 285 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 299 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 206 optimal weight: 0.6980 chunk 50 optimal weight: 9.9990 chunk 226 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 174 optimal weight: 50.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 GLN B 707 HIS B 709 GLN F 955 ASN ** G 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.137776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.079914 restraints weight = 45054.676| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.21 r_work: 0.2884 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 29507 Z= 0.254 Angle : 0.652 9.544 40217 Z= 0.332 Chirality : 0.048 0.243 4754 Planarity : 0.005 0.068 5014 Dihedral : 8.260 59.717 4853 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.16 % Allowed : 17.92 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.13), residues: 3657 helix: 0.78 (0.31), residues: 306 sheet: 0.57 (0.14), residues: 1444 loop : -0.83 (0.13), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 296 TYR 0.018 0.002 TYR E 40 PHE 0.020 0.002 PHE E 459 TRP 0.010 0.001 TRP A 83 HIS 0.009 0.002 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.25 (29364) covalent geometry : angle 0.63358 / 0.33 (39887) SS BOND : bond 0.00485 / 0.28 ( 93) SS BOND : angle 1.13799 / 0.78 ( 186) hydrogen bonds : bond 0.05227 / 3.51 ( 778) hydrogen bonds : angle 5.49594 / 3.88 ( 2043) Misc. bond : bond 0.00169 / 0.09 ( 2) link_ALPHA1-3 : bond 0.01251 / 0.60 ( 8) link_ALPHA1-3 : angle 1.84706 / 1.18 ( 24) link_BETA1-4 : bond 0.00477 / 0.30 ( 24) link_BETA1-4 : angle 2.29242 / 1.42 ( 72) link_NAG-ASN : bond 0.00667 / 0.40 ( 16) link_NAG-ASN : angle 2.81841 / 1.93 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 188 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8945 (mtpp) REVERT: A 224 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8079 (mp) REVERT: A 372 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8063 (tp30) REVERT: B 672 MET cc_start: 0.6457 (tmt) cc_final: 0.6213 (tmt) REVERT: B 951 ARG cc_start: 0.7870 (ttm-80) cc_final: 0.7645 (ttm-80) REVERT: B 1016 MET cc_start: 0.6746 (mmp) cc_final: 0.6545 (mpp) REVERT: C 143 GLN cc_start: 0.9321 (OUTLIER) cc_final: 0.7761 (tp40) REVERT: C 175 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8401 (mt-10) REVERT: C 228 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8485 (mptt) REVERT: C 462 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8826 (tm) REVERT: E 143 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7298 (tm-30) REVERT: E 412 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8363 (tppt) REVERT: E 414 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7941 (mt0) REVERT: F 672 MET cc_start: 0.5479 (tmt) cc_final: 0.4469 (tmt) REVERT: F 951 ARG cc_start: 0.8177 (tpp80) cc_final: 0.7918 (tpp80) REVERT: G 103 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7605 (mt0) REVERT: G 476 GLU cc_start: 0.9169 (tm-30) cc_final: 0.8855 (tm-30) REVERT: H 672 MET cc_start: 0.3830 (ppp) cc_final: 0.3561 (ppp) REVERT: H 817 THR cc_start: 0.7207 (m) cc_final: 0.6804 (p) outliers start: 102 outliers final: 35 residues processed: 272 average time/residue: 0.6834 time to fit residues: 216.1473 Evaluate side-chains 220 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 972 CYS Chi-restraints excluded: chain B residue 1033 LYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 855 LEU Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 1058 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 412 LYS Chi-restraints excluded: chain E residue 414 GLN Chi-restraints excluded: chain E residue 468 ASP Chi-restraints excluded: chain F residue 835 CYS Chi-restraints excluded: chain F residue 895 ARG Chi-restraints excluded: chain F residue 972 CYS Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain H residue 972 CYS Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Y residue 111 THR Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 141 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: [338, 92, 246, 64, 180, 197, 238, 159, 301, 250, 332] chunk 338 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 246 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 301 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 chunk 332 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 GLN B 709 GLN E 103 GLN G 289 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.139312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.081667 restraints weight = 44505.456| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.23 r_work: 0.2933 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29507 Z= 0.124 Angle : 0.539 10.935 40217 Z= 0.271 Chirality : 0.044 0.246 4754 Planarity : 0.004 0.067 5014 Dihedral : 6.935 59.651 4852 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.51 % Allowed : 18.44 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.13), residues: 3657 helix: 1.00 (0.31), residues: 306 sheet: 0.55 (0.14), residues: 1404 loop : -0.79 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 417 TYR 0.013 0.001 TYR Y 98 PHE 0.013 0.001 PHE E 459 TRP 0.007 0.001 TRP D 766 HIS 0.003 0.001 HIS B 820 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (29364) covalent geometry : angle 0.52278 / 0.27 (39887) SS BOND : bond 0.00203 / 0.12 ( 93) SS BOND : angle 0.75284 / 0.52 ( 186) hydrogen bonds : bond 0.03528 / 2.39 ( 778) hydrogen bonds : angle 5.11945 / 3.63 ( 2043) Misc. bond : bond 0.00530 / 0.28 ( 2) link_ALPHA1-3 : bond 0.01238 / 0.59 ( 8) link_ALPHA1-3 : angle 1.50933 / 0.97 ( 24) link_BETA1-4 : bond 0.00460 / 0.28 ( 24) link_BETA1-4 : angle 1.93159 / 1.20 ( 72) link_NAG-ASN : bond 0.00542 / 0.31 ( 16) link_NAG-ASN : angle 2.71746 / 1.84 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 201 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8897 (mm-30) REVERT: A 143 GLN cc_start: 0.9354 (OUTLIER) cc_final: 0.8292 (tp40) REVERT: A 372 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8002 (tp30) REVERT: A 476 GLU cc_start: 0.8709 (tt0) cc_final: 0.8437 (tm-30) REVERT: B 656 MET cc_start: 0.5569 (mmt) cc_final: 0.5062 (mpt) REVERT: B 672 MET cc_start: 0.6446 (tmt) cc_final: 0.6135 (tmt) REVERT: B 951 ARG cc_start: 0.7867 (ttm-80) cc_final: 0.7625 (ttm-80) REVERT: B 1033 LYS cc_start: 0.9337 (mttp) cc_final: 0.8877 (mptt) REVERT: C 175 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8388 (mt-10) REVERT: C 223 GLN cc_start: 0.8434 (mp10) cc_final: 0.8023 (pm20) REVERT: C 462 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8782 (tm) REVERT: E 171 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: F 672 MET cc_start: 0.5580 (tmt) cc_final: 0.4416 (tmt) REVERT: F 951 ARG cc_start: 0.8190 (tpp80) cc_final: 0.7954 (tpp80) REVERT: G 476 GLU cc_start: 0.9163 (tm-30) cc_final: 0.8895 (tm-30) REVERT: H 672 MET cc_start: 0.3706 (OUTLIER) cc_final: 0.3389 (pmt) REVERT: H 706 PHE cc_start: 0.7179 (t80) cc_final: 0.6854 (t80) REVERT: H 817 THR cc_start: 0.7379 (m) cc_final: 0.6956 (p) REVERT: Y 104 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8720 (tmmt) REVERT: Y 137 GLU cc_start: 0.7341 (tm-30) cc_final: 0.6861 (tm-30) REVERT: Y 151 LEU cc_start: 0.9154 (tp) cc_final: 0.8813 (tm) outliers start: 81 outliers final: 39 residues processed: 264 average time/residue: 0.6951 time to fit residues: 213.4998 Evaluate side-chains 233 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 187 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 835 CYS Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 972 CYS Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 972 CYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 159 ARG Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 466 MET Chi-restraints excluded: chain F residue 808 VAL Chi-restraints excluded: chain F residue 835 CYS Chi-restraints excluded: chain F residue 855 LEU Chi-restraints excluded: chain F residue 962 VAL Chi-restraints excluded: chain F residue 972 CYS Chi-restraints excluded: chain F residue 1021 THR Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 266 ASP Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain H residue 672 MET Chi-restraints excluded: chain H residue 766 TRP Chi-restraints excluded: chain H residue 810 ILE Chi-restraints excluded: chain H residue 957 VAL Chi-restraints excluded: chain Y residue 104 LYS Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 133 ILE Chi-restraints excluded: chain Y residue 141 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: [263, 329, 336, 167, 39, 310, 81, 299, 115, 331, 163] chunk 263 optimal weight: 20.0000 chunk 329 optimal weight: 10.0000 chunk 336 optimal weight: 7.9990 chunk 167 optimal weight: 40.0000 chunk 39 optimal weight: 0.9980 chunk 310 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 299 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 331 optimal weight: 5.9990 chunk 163 optimal weight: 0.0570 overall best weight: 3.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 103 GLN ** G 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.137386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.079623 restraints weight = 44673.967| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.24 r_work: 0.2885 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 29507 Z= 0.205 Angle : 0.593 10.422 40217 Z= 0.299 Chirality : 0.046 0.247 4754 Planarity : 0.004 0.069 5014 Dihedral : 6.606 57.984 4852 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.01 % Allowed : 17.92 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.13), residues: 3657 helix: 0.86 (0.31), residues: 306 sheet: 0.54 (0.14), residues: 1444 loop : -0.90 (0.13), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 159 TYR 0.013 0.002 TYR E 40 PHE 0.020 0.002 PHE E 459 TRP 0.009 0.001 TRP A 83 HIS 0.024 0.001 HIS B 665 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.20 (29364) covalent geometry : angle 0.57526 / 0.29 (39887) SS BOND : bond 0.00299 / 0.18 ( 93) SS BOND : angle 0.96818 / 0.67 ( 186) hydrogen bonds : bond 0.04357 / 2.93 ( 778) hydrogen bonds : angle 5.20209 / 3.68 ( 2043) Misc. bond : bond 0.00176 / 0.09 ( 2) link_ALPHA1-3 : bond 0.01230 / 0.60 ( 8) link_ALPHA1-3 : angle 1.69433 / 1.09 ( 24) link_BETA1-4 : bond 0.00430 / 0.27 ( 24) link_BETA1-4 : angle 2.13863 / 1.34 ( 72) link_NAG-ASN : bond 0.00561 / 0.33 ( 16) link_NAG-ASN : angle 2.83092 / 1.94 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 183 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8915 (mm-30) REVERT: A 143 GLN cc_start: 0.9355 (OUTLIER) cc_final: 0.8316 (tp40) REVERT: A 372 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8059 (tp30) REVERT: A 476 GLU cc_start: 0.8720 (tt0) cc_final: 0.8424 (tm-30) REVERT: B 672 MET cc_start: 0.6604 (tmt) cc_final: 0.6157 (tmt) REVERT: B 951 ARG cc_start: 0.7906 (ttm-80) cc_final: 0.7686 (mtt-85) REVERT: C 143 GLN cc_start: 0.9300 (OUTLIER) cc_final: 0.7691 (tp40) REVERT: C 175 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8418 (mt-10) REVERT: C 223 GLN cc_start: 0.8376 (mp10) cc_final: 0.7968 (pm20) REVERT: C 228 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8555 (mptt) REVERT: C 462 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8824 (tm) REVERT: E 143 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7333 (tm-30) REVERT: F 951 ARG cc_start: 0.8231 (tpp80) cc_final: 0.7984 (tpp80) REVERT: G 476 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8851 (tm-30) REVERT: H 672 MET cc_start: 0.3713 (OUTLIER) cc_final: 0.3469 (pmt) REVERT: H 691 ARG cc_start: 0.5616 (OUTLIER) cc_final: 0.4567 (mmm160) REVERT: H 817 THR cc_start: 0.7440 (m) cc_final: 0.7016 (p) REVERT: Y 137 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7064 (tm-30) outliers start: 97 outliers final: 44 residues processed: 260 average time/residue: 0.6868 time to fit residues: 207.9838 Evaluate side-chains 227 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 174 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 835 CYS Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 972 CYS Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 1033 LYS Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 855 LEU Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 972 CYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain F residue 835 CYS Chi-restraints excluded: chain F residue 855 LEU Chi-restraints excluded: chain F residue 972 CYS Chi-restraints excluded: chain F residue 1021 THR Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 468 ASP Chi-restraints excluded: chain H residue 672 MET Chi-restraints excluded: chain H residue 691 ARG Chi-restraints excluded: chain H residue 766 TRP Chi-restraints excluded: chain H residue 972 CYS Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Y residue 111 THR Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 133 ILE Chi-restraints excluded: chain Y residue 141 THR Chi-restraints excluded: chain Y residue 152 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: [136, 128, 344, 209, 70, 174, 187, 245, 252, 43, 130] chunk 136 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 344 optimal weight: 20.0000 chunk 209 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 174 optimal weight: 30.0000 chunk 187 optimal weight: 2.9990 chunk 245 optimal weight: 4.9990 chunk 252 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.138260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.080883 restraints weight = 44916.633| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.21 r_work: 0.2917 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29507 Z= 0.139 Angle : 0.541 10.857 40217 Z= 0.272 Chirality : 0.044 0.244 4754 Planarity : 0.004 0.082 5014 Dihedral : 6.143 56.282 4852 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.73 % Allowed : 18.35 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.14), residues: 3657 helix: 1.01 (0.32), residues: 306 sheet: 0.47 (0.14), residues: 1424 loop : -0.89 (0.13), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 417 TYR 0.013 0.001 TYR Y 98 PHE 0.014 0.001 PHE E 459 TRP 0.008 0.001 TRP D 766 HIS 0.008 0.001 HIS B 665 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (29364) covalent geometry : angle 0.52417 / 0.27 (39887) SS BOND : bond 0.00234 / 0.14 ( 93) SS BOND : angle 0.78684 / 0.55 ( 186) hydrogen bonds : bond 0.03574 / 2.42 ( 778) hydrogen bonds : angle 5.04129 / 3.56 ( 2043) Misc. bond : bond 0.00086 / 0.04 ( 2) link_ALPHA1-3 : bond 0.01200 / 0.58 ( 8) link_ALPHA1-3 : angle 1.44585 / 0.95 ( 24) link_BETA1-4 : bond 0.00418 / 0.25 ( 24) link_BETA1-4 : angle 1.93638 / 1.21 ( 72) link_NAG-ASN : bond 0.00523 / 0.30 ( 16) link_NAG-ASN : angle 2.75888 / 1.88 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 185 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.9210 (OUTLIER) cc_final: 0.8911 (mm-30) REVERT: A 143 GLN cc_start: 0.9357 (OUTLIER) cc_final: 0.8294 (tp40) REVERT: A 372 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8053 (tp30) REVERT: A 476 GLU cc_start: 0.8722 (tt0) cc_final: 0.8453 (tm-30) REVERT: B 665 HIS cc_start: 0.6388 (OUTLIER) cc_final: 0.6035 (m-70) REVERT: B 672 MET cc_start: 0.6646 (tmt) cc_final: 0.6193 (tmt) REVERT: B 951 ARG cc_start: 0.7909 (ttm-80) cc_final: 0.7682 (mtt-85) REVERT: C 175 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8413 (mt-10) REVERT: C 223 GLN cc_start: 0.8463 (mp10) cc_final: 0.8035 (pm20) REVERT: C 228 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8639 (mptt) REVERT: C 462 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8801 (tm) REVERT: E 46 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8672 (mm-30) REVERT: E 414 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8230 (mt0) REVERT: F 672 MET cc_start: 0.3841 (tpt) cc_final: 0.2534 (tmt) REVERT: F 951 ARG cc_start: 0.8323 (tpp80) cc_final: 0.8066 (tpp80) REVERT: G 476 GLU cc_start: 0.9156 (tm-30) cc_final: 0.8917 (tm-30) REVERT: H 672 MET cc_start: 0.4110 (OUTLIER) cc_final: 0.3722 (pmt) REVERT: H 691 ARG cc_start: 0.5789 (mtp85) cc_final: 0.4774 (mmm160) REVERT: H 817 THR cc_start: 0.7645 (m) cc_final: 0.7236 (p) REVERT: Y 104 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8718 (tmmt) REVERT: Y 137 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.6870 (tm-30) REVERT: Y 151 LEU cc_start: 0.9156 (tp) cc_final: 0.8726 (tm) outliers start: 88 outliers final: 49 residues processed: 257 average time/residue: 0.6715 time to fit residues: 201.3463 Evaluate side-chains 239 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 179 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 835 CYS Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 972 CYS Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 855 LEU Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 972 CYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 266 ASP Chi-restraints excluded: chain E residue 401 PHE Chi-restraints excluded: chain E residue 414 GLN Chi-restraints excluded: chain E residue 445 ILE Chi-restraints excluded: chain F residue 808 VAL Chi-restraints excluded: chain F residue 855 LEU Chi-restraints excluded: chain F residue 972 CYS Chi-restraints excluded: chain F residue 1021 THR Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 266 ASP Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain H residue 672 MET Chi-restraints excluded: chain H residue 766 TRP Chi-restraints excluded: chain H residue 810 ILE Chi-restraints excluded: chain H residue 962 VAL Chi-restraints excluded: chain H residue 972 CYS Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 104 LYS Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 133 ILE Chi-restraints excluded: chain Y residue 137 GLU Chi-restraints excluded: chain Y residue 141 THR Chi-restraints excluded: chain Y residue 152 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: [168, 56, 212, 204, 301, 64, 284, 29, 106, 143, 224] chunk 168 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 212 optimal weight: 0.9990 chunk 204 optimal weight: 7.9990 chunk 301 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 284 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 224 optimal weight: 40.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 GLN B 955 ASN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.136172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.078698 restraints weight = 44716.611| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.19 r_work: 0.2878 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 29507 Z= 0.238 Angle : 0.625 10.133 40217 Z= 0.316 Chirality : 0.047 0.250 4754 Planarity : 0.005 0.071 5014 Dihedral : 6.295 59.510 4852 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.94 % Allowed : 18.13 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.13), residues: 3657 helix: 1.23 (0.33), residues: 282 sheet: 0.42 (0.14), residues: 1444 loop : -1.00 (0.13), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 84 TYR 0.014 0.002 TYR E 40 PHE 0.020 0.002 PHE E 459 TRP 0.011 0.001 TRP A 83 HIS 0.005 0.001 HIS E 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.24 (29364) covalent geometry : angle 0.60585 / 0.31 (39887) SS BOND : bond 0.00372 / 0.24 ( 93) SS BOND : angle 1.14843 / 0.78 ( 186) hydrogen bonds : bond 0.04651 / 3.13 ( 778) hydrogen bonds : angle 5.26755 / 3.72 ( 2043) Misc. bond : bond 0.00175 / 0.09 ( 2) link_ALPHA1-3 : bond 0.01123 / 0.54 ( 8) link_ALPHA1-3 : angle 1.69726 / 1.10 ( 24) link_BETA1-4 : bond 0.00401 / 0.24 ( 24) link_BETA1-4 : angle 2.24406 / 1.41 ( 72) link_NAG-ASN : bond 0.00583 / 0.35 ( 16) link_NAG-ASN : angle 2.90557 / 1.99 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 182 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8910 (mm-30) REVERT: A 143 GLN cc_start: 0.9379 (OUTLIER) cc_final: 0.8320 (tp40) REVERT: A 159 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8161 (mmm-85) REVERT: A 372 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8195 (tp30) REVERT: A 476 GLU cc_start: 0.8747 (tt0) cc_final: 0.8468 (tm-30) REVERT: B 656 MET cc_start: 0.5442 (mmt) cc_final: 0.4859 (mpt) REVERT: B 672 MET cc_start: 0.6704 (tmt) cc_final: 0.6239 (tmt) REVERT: B 780 CYS cc_start: 0.6564 (OUTLIER) cc_final: 0.5926 (t) REVERT: C 46 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8719 (tt0) REVERT: C 175 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8474 (mt-10) REVERT: C 223 GLN cc_start: 0.8444 (mp10) cc_final: 0.7983 (pm20) REVERT: C 462 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8871 (tm) REVERT: E 46 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8639 (mm-30) REVERT: E 317 THR cc_start: 0.8328 (m) cc_final: 0.8013 (t) REVERT: E 414 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8389 (mt0) REVERT: F 672 MET cc_start: 0.3917 (tpt) cc_final: 0.2775 (tmt) REVERT: F 951 ARG cc_start: 0.8348 (tpp80) cc_final: 0.8072 (tpp80) REVERT: G 476 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8874 (tm-30) REVERT: H 691 ARG cc_start: 0.5776 (OUTLIER) cc_final: 0.4895 (mmm160) REVERT: H 706 PHE cc_start: 0.7350 (t80) cc_final: 0.7041 (t80) REVERT: H 817 THR cc_start: 0.7849 (m) cc_final: 0.7424 (p) REVERT: Y 137 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7232 (tm-30) outliers start: 95 outliers final: 54 residues processed: 257 average time/residue: 0.6725 time to fit residues: 202.1020 Evaluate side-chains 242 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 178 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 159 ARG Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 835 CYS Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 972 CYS Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 855 LEU Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 972 CYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 401 PHE Chi-restraints excluded: chain E residue 414 GLN Chi-restraints excluded: chain E residue 445 ILE Chi-restraints excluded: chain E residue 468 ASP Chi-restraints excluded: chain F residue 855 LEU Chi-restraints excluded: chain F residue 895 ARG Chi-restraints excluded: chain F residue 972 CYS Chi-restraints excluded: chain F residue 1021 THR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 468 ASP Chi-restraints excluded: chain H residue 691 ARG Chi-restraints excluded: chain H residue 766 TRP Chi-restraints excluded: chain H residue 810 ILE Chi-restraints excluded: chain H residue 962 VAL Chi-restraints excluded: chain H residue 972 CYS Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 133 ILE Chi-restraints excluded: chain Y residue 137 GLU Chi-restraints excluded: chain Y residue 141 THR Chi-restraints excluded: chain Y residue 152 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: [224, 125, 248, 142, 165, 60, 229, 187, 68, 150, 23] chunk 224 optimal weight: 40.0000 chunk 125 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 165 optimal weight: 20.0000 chunk 60 optimal weight: 0.6980 chunk 229 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 68 optimal weight: 0.0870 chunk 150 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.138110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.080761 restraints weight = 44786.791| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.22 r_work: 0.2923 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29507 Z= 0.116 Angle : 0.536 11.076 40217 Z= 0.271 Chirality : 0.044 0.243 4754 Planarity : 0.004 0.051 5014 Dihedral : 5.750 55.913 4852 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.23 % Allowed : 18.94 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.14), residues: 3657 helix: 1.51 (0.33), residues: 278 sheet: 0.41 (0.14), residues: 1468 loop : -0.91 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 159 TYR 0.014 0.001 TYR Y 98 PHE 0.013 0.001 PHE E 459 TRP 0.010 0.001 TRP D 766 HIS 0.003 0.001 HIS D 953 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (29364) covalent geometry : angle 0.51963 / 0.27 (39887) SS BOND : bond 0.00202 / 0.12 ( 93) SS BOND : angle 0.83559 / 0.56 ( 186) hydrogen bonds : bond 0.03302 / 2.24 ( 778) hydrogen bonds : angle 4.97753 / 3.53 ( 2043) Misc. bond : bond 0.00566 / 0.30 ( 2) link_ALPHA1-3 : bond 0.01140 / 0.54 ( 8) link_ALPHA1-3 : angle 1.33437 / 0.87 ( 24) link_BETA1-4 : bond 0.00425 / 0.26 ( 24) link_BETA1-4 : angle 1.88196 / 1.19 ( 72) link_NAG-ASN : bond 0.00529 / 0.29 ( 16) link_NAG-ASN : angle 2.76140 / 1.87 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 187 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.9199 (OUTLIER) cc_final: 0.8905 (mm-30) REVERT: A 143 GLN cc_start: 0.9373 (OUTLIER) cc_final: 0.8300 (tp40) REVERT: A 159 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8137 (mmm-85) REVERT: A 372 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8072 (tp30) REVERT: A 476 GLU cc_start: 0.8706 (tt0) cc_final: 0.8445 (tm-30) REVERT: B 672 MET cc_start: 0.6743 (tmt) cc_final: 0.6303 (tmt) REVERT: B 780 CYS cc_start: 0.6478 (OUTLIER) cc_final: 0.5794 (t) REVERT: C 175 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8425 (mt-10) REVERT: C 223 GLN cc_start: 0.8438 (mp10) cc_final: 0.8022 (pm20) REVERT: C 462 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8791 (tm) REVERT: E 46 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8677 (mm-30) REVERT: E 412 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8366 (tppt) REVERT: E 414 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8300 (mt0) REVERT: F 672 MET cc_start: 0.3794 (tpt) cc_final: 0.2815 (tmt) REVERT: F 951 ARG cc_start: 0.8368 (tpp80) cc_final: 0.8084 (tpp80) REVERT: G 462 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8670 (tp) REVERT: G 476 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8848 (tm-30) REVERT: H 691 ARG cc_start: 0.5991 (mtp85) cc_final: 0.5074 (mmm160) REVERT: H 706 PHE cc_start: 0.7272 (t80) cc_final: 0.6985 (t80) REVERT: H 817 THR cc_start: 0.7838 (m) cc_final: 0.7448 (p) REVERT: H 962 VAL cc_start: 0.6503 (OUTLIER) cc_final: 0.6289 (t) REVERT: Y 104 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8740 (tmmt) REVERT: Y 137 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6839 (tm-30) REVERT: Y 151 LEU cc_start: 0.9176 (tp) cc_final: 0.8726 (tm) outliers start: 72 outliers final: 38 residues processed: 245 average time/residue: 0.6930 time to fit residues: 196.6018 Evaluate side-chains 233 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 182 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 159 ARG Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 835 CYS Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 972 CYS Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 812 LEU Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 855 LEU Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 972 CYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 401 PHE Chi-restraints excluded: chain E residue 412 LYS Chi-restraints excluded: chain E residue 414 GLN Chi-restraints excluded: chain F residue 808 VAL Chi-restraints excluded: chain F residue 855 LEU Chi-restraints excluded: chain F residue 972 CYS Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain H residue 766 TRP Chi-restraints excluded: chain H residue 810 ILE Chi-restraints excluded: chain H residue 962 VAL Chi-restraints excluded: chain H residue 972 CYS Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 104 LYS Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 137 GLU Chi-restraints excluded: chain Y residue 141 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: [221, 52, 149, 128, 55, 337, 178, 59, 72, 16, 312] chunk 221 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 337 optimal weight: 9.9990 chunk 178 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 312 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 289 GLN Y 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.137840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.080718 restraints weight = 44641.543| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.18 r_work: 0.2918 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29507 Z= 0.127 Angle : 0.546 13.865 40217 Z= 0.274 Chirality : 0.044 0.245 4754 Planarity : 0.004 0.054 5014 Dihedral : 5.470 56.693 4852 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.08 % Allowed : 19.03 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3657 helix: 1.59 (0.33), residues: 278 sheet: 0.45 (0.14), residues: 1468 loop : -0.88 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 159 TYR 0.009 0.001 TYR E 40 PHE 0.016 0.001 PHE E 459 TRP 0.009 0.001 TRP D 766 HIS 0.003 0.001 HIS D 953 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (29364) covalent geometry : angle 0.52896 / 0.27 (39887) SS BOND : bond 0.00211 / 0.13 ( 93) SS BOND : angle 0.84369 / 0.57 ( 186) hydrogen bonds : bond 0.03454 / 2.33 ( 778) hydrogen bonds : angle 4.90165 / 3.47 ( 2043) Misc. bond : bond 0.00098 / 0.05 ( 2) link_ALPHA1-3 : bond 0.01078 / 0.52 ( 8) link_ALPHA1-3 : angle 1.39677 / 0.90 ( 24) link_BETA1-4 : bond 0.00403 / 0.24 ( 24) link_BETA1-4 : angle 1.91432 / 1.20 ( 72) link_NAG-ASN : bond 0.00519 / 0.29 ( 16) link_NAG-ASN : angle 2.79000 / 1.89 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 185 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8907 (mm-30) REVERT: A 143 GLN cc_start: 0.9385 (OUTLIER) cc_final: 0.8338 (tp40) REVERT: A 159 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8109 (mmm-85) REVERT: A 372 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8060 (tp30) REVERT: A 476 GLU cc_start: 0.8711 (tt0) cc_final: 0.8440 (tm-30) REVERT: B 672 MET cc_start: 0.6760 (tmt) cc_final: 0.6321 (tmt) REVERT: B 709 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8172 (mm-40) REVERT: B 780 CYS cc_start: 0.6488 (OUTLIER) cc_final: 0.5817 (t) REVERT: B 951 ARG cc_start: 0.7738 (ttm-80) cc_final: 0.7448 (mtt-85) REVERT: C 175 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8467 (mt-10) REVERT: C 223 GLN cc_start: 0.8361 (mp10) cc_final: 0.7938 (pm20) REVERT: C 462 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8810 (tm) REVERT: E 46 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8646 (mm-30) REVERT: E 414 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8182 (mt0) REVERT: F 672 MET cc_start: 0.3874 (tpt) cc_final: 0.2998 (tmt) REVERT: F 951 ARG cc_start: 0.8397 (tpp80) cc_final: 0.8122 (tpp80) REVERT: G 223 GLN cc_start: 0.9125 (mp10) cc_final: 0.8821 (pm20) REVERT: G 462 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8703 (tp) REVERT: G 476 GLU cc_start: 0.9133 (tm-30) cc_final: 0.8898 (tm-30) REVERT: H 691 ARG cc_start: 0.6119 (mtp85) cc_final: 0.5248 (mmm160) REVERT: H 706 PHE cc_start: 0.7294 (t80) cc_final: 0.7011 (t80) REVERT: H 817 THR cc_start: 0.7865 (m) cc_final: 0.7484 (p) REVERT: Y 59 ARG cc_start: 0.6813 (ttm110) cc_final: 0.6275 (ttm-80) REVERT: Y 104 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8718 (tmmt) REVERT: Y 137 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6838 (tm-30) REVERT: Y 151 LEU cc_start: 0.9160 (tp) cc_final: 0.8678 (tm) outliers start: 67 outliers final: 40 residues processed: 239 average time/residue: 0.7090 time to fit residues: 196.1815 Evaluate side-chains 232 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 159 ARG Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain B residue 709 GLN Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 835 CYS Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 972 CYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain D residue 812 LEU Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 855 LEU Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 972 CYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 401 PHE Chi-restraints excluded: chain E residue 414 GLN Chi-restraints excluded: chain F residue 855 LEU Chi-restraints excluded: chain F residue 895 ARG Chi-restraints excluded: chain F residue 972 CYS Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain H residue 766 TRP Chi-restraints excluded: chain H residue 810 ILE Chi-restraints excluded: chain H residue 962 VAL Chi-restraints excluded: chain H residue 972 CYS Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 104 LYS Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 137 GLU Chi-restraints excluded: chain Y residue 141 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: [154, 312, 51, 328, 143, 234, 40, 175, 296, 10, 136] chunk 154 optimal weight: 4.9990 chunk 312 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 328 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 175 optimal weight: 8.9990 chunk 296 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 136 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 289 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.135429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.078126 restraints weight = 44734.534| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.20 r_work: 0.2871 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 29507 Z= 0.282 Angle : 0.658 10.506 40217 Z= 0.332 Chirality : 0.048 0.248 4754 Planarity : 0.005 0.058 5014 Dihedral : 5.960 59.594 4852 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.11 % Allowed : 18.88 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.13), residues: 3657 helix: 1.24 (0.32), residues: 282 sheet: 0.46 (0.14), residues: 1452 loop : -1.08 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 159 TYR 0.015 0.002 TYR Y 98 PHE 0.020 0.002 PHE E 459 TRP 0.011 0.002 TRP A 83 HIS 0.005 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00697 / 0.28 (29364) covalent geometry : angle 0.63865 / 0.33 (39887) SS BOND : bond 0.00391 / 0.24 ( 93) SS BOND : angle 1.25705 / 0.84 ( 186) hydrogen bonds : bond 0.04810 / 3.24 ( 778) hydrogen bonds : angle 5.23006 / 3.69 ( 2043) Misc. bond : bond 0.00185 / 0.10 ( 2) link_ALPHA1-3 : bond 0.01084 / 0.53 ( 8) link_ALPHA1-3 : angle 1.67694 / 1.09 ( 24) link_BETA1-4 : bond 0.00366 / 0.21 ( 24) link_BETA1-4 : angle 2.29533 / 1.44 ( 72) link_NAG-ASN : bond 0.00568 / 0.33 ( 16) link_NAG-ASN : angle 2.94313 / 2.01 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7314 Ramachandran restraints generated. 3657 Oldfield, 0 Emsley, 3657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 173 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 GLN cc_start: 0.9388 (OUTLIER) cc_final: 0.9135 (tm-30) REVERT: A 159 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8187 (mmm-85) REVERT: A 372 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8282 (tp30) REVERT: A 476 GLU cc_start: 0.8732 (tt0) cc_final: 0.8463 (tm-30) REVERT: B 656 MET cc_start: 0.3809 (mpt) cc_final: 0.3448 (mmt) REVERT: B 672 MET cc_start: 0.6857 (tmt) cc_final: 0.6382 (tmt) REVERT: B 709 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8252 (mm-40) REVERT: B 780 CYS cc_start: 0.6730 (OUTLIER) cc_final: 0.6149 (t) REVERT: B 951 ARG cc_start: 0.7876 (ttm-80) cc_final: 0.7599 (ttm-80) REVERT: C 175 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8480 (mt-10) REVERT: C 223 GLN cc_start: 0.8355 (mp10) cc_final: 0.7874 (pm20) REVERT: C 462 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8860 (tm) REVERT: E 46 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8637 (mm-30) REVERT: E 317 THR cc_start: 0.8327 (m) cc_final: 0.8035 (t) REVERT: F 672 MET cc_start: 0.3975 (tpt) cc_final: 0.3050 (tmt) REVERT: G 223 GLN cc_start: 0.9150 (mp10) cc_final: 0.8922 (pm20) REVERT: G 476 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8878 (tm-30) REVERT: H 691 ARG cc_start: 0.6018 (mtp85) cc_final: 0.5247 (mmm160) REVERT: H 706 PHE cc_start: 0.7386 (t80) cc_final: 0.7115 (t80) REVERT: H 817 THR cc_start: 0.7885 (m) cc_final: 0.7531 (p) REVERT: H 1016 MET cc_start: 0.7263 (tpt) cc_final: 0.6883 (mpp) REVERT: Y 137 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7007 (tm-30) REVERT: Y 151 LEU cc_start: 0.9198 (tp) cc_final: 0.8706 (tm) outliers start: 68 outliers final: 45 residues processed: 232 average time/residue: 0.7113 time to fit residues: 191.3399 Evaluate side-chains 225 residues out of total 3226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 172 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 159 ARG Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain B residue 709 GLN Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 835 CYS Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 972 CYS Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 812 LEU Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 855 LEU Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 972 CYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 401 PHE Chi-restraints excluded: chain F residue 855 LEU Chi-restraints excluded: chain F residue 972 CYS Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain H residue 766 TRP Chi-restraints excluded: chain H residue 810 ILE Chi-restraints excluded: chain H residue 962 VAL Chi-restraints excluded: chain H residue 972 CYS Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 137 GLU Chi-restraints excluded: chain Y residue 141 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: [310, 339, 221, 142, 255, 182, 353, 314, 347, 338, 91] chunk 310 optimal weight: 0.9980 chunk 339 optimal weight: 0.9990 chunk 221 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 255 optimal weight: 8.9990 chunk 182 optimal weight: 0.0060 chunk 353 optimal weight: 40.0000 chunk 314 optimal weight: 20.0000 chunk 347 optimal weight: 8.9990 chunk 338 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 289 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.138397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.081553 restraints weight = 44588.668| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.15 r_work: 0.2935 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 29507 Z= 0.096 Angle : 0.537 12.725 40217 Z= 0.270 Chirality : 0.043 0.244 4754 Planarity : 0.004 0.053 5014 Dihedral : 5.369 54.696 4852 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.55 % Allowed : 19.71 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3657 helix: 2.16 (0.34), residues: 254 sheet: 0.53 (0.14), residues: 1478 loop : -0.93 (0.13), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 415 TYR 0.008 0.001 TYR A 248 PHE 0.016 0.001 PHE E 416 TRP 0.012 0.001 TRP D 766 HIS 0.003 0.001 HIS D1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (29364) covalent geometry : angle 0.52132 / 0.27 (39887) SS BOND : bond 0.00187 / 0.11 ( 93) SS BOND : angle 0.75517 / 0.51 ( 186) hydrogen bonds : bond 0.02996 / 2.03 ( 778) hydrogen bonds : angle 4.82886 / 3.42 ( 2043) Misc. bond : bond 0.00054 / 0.03 ( 2) link_ALPHA1-3 : bond 0.01045 / 0.49 ( 8) link_ALPHA1-3 : angle 1.26057 / 0.80 ( 24) link_BETA1-4 : bond 0.00421 / 0.25 ( 24) link_BETA1-4 : angle 1.78507 / 1.12 ( 72) link_NAG-ASN : bond 0.00551 / 0.30 ( 16) link_NAG-ASN : angle 2.75049 / 1.85 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13980.90 seconds wall clock time: 237 minutes 21.19 seconds (14241.19 seconds total)