Starting phenix.real_space_refine on Sat Feb 7 18:01:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p3y_71259/02_2026/9p3y_71259.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p3y_71259/02_2026/9p3y_71259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9p3y_71259/02_2026/9p3y_71259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p3y_71259/02_2026/9p3y_71259.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p3y_71259/02_2026/9p3y_71259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p3y_71259/02_2026/9p3y_71259.map" } resolution = 3.3 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 ------------------------------------------------------------------------------- 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= 0.047 sd= 0.568 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 292 5.16 5 C 21828 2.51 5 N 5740 2.21 5 O 6776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34636 Number of models: 1 Model: "" Number of chains: 28 Chain: "I" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 917 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain breaks: 1 Chain: "J" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "K" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 917 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain breaks: 1 Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "M" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 917 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain breaks: 1 Chain: "N" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "O" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 917 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain breaks: 1 Chain: "P" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} 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': 20, 'TRANS': 437} Chain: "B" Number of atoms: 3296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3296 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 21, 'TRANS': 409} 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': 20, 'TRANS': 437} Chain: "D" Number of atoms: 3296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3296 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 21, 'TRANS': 409} 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': 20, 'TRANS': 437} Chain: "F" Number of atoms: 3296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3296 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 21, 'TRANS': 409} 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': 20, 'TRANS': 437} Chain: "H" Number of atoms: 3296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3296 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 21, 'TRANS': 409} Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 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: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.07, per 1000 atoms: 0.26 Number of scatterers: 34636 At special positions: 0 Unit cell: (213.824, 213.824, 126.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 292 16.00 O 6776 8.00 N 5740 7.00 C 21828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=100, symmetry=0 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 132 " distance=2.03 Simple disulfide: pdb=" SG CYS A 137 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 250 " distance=2.03 Simple disulfide: pdb=" SG CYS A 239 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 438 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 408 " - pdb=" SG CYS A 427 " distance=2.03 Simple disulfide: pdb=" SG CYS A 455 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 742 " - pdb=" SG CYS B 780 " distance=2.03 Simple disulfide: pdb=" SG CYS B 754 " - pdb=" SG CYS B 887 " distance=2.03 Simple disulfide: pdb=" SG CYS B 768 " - pdb=" SG CYS B 898 " distance=2.03 Simple disulfide: pdb=" SG CYS B 783 " - pdb=" SG CYS B 906 " distance=2.03 Simple disulfide: pdb=" SG CYS B 809 " - pdb=" SG CYS B 818 " distance=2.03 Simple disulfide: pdb=" SG CYS B 826 " - pdb=" SG CYS B 835 " distance=2.03 Simple disulfide: pdb=" SG CYS B 866 " - pdb=" SG CYS B 870 " distance=2.03 Simple disulfide: pdb=" SG CYS B 972 " - pdb=" SG CYS B1002 " distance=2.03 Simple disulfide: pdb=" SG CYS B 995 " - pdb=" SG CYS B1047 " distance=2.03 Simple disulfide: pdb=" SG CYS B1012 " - pdb=" SG CYS B1017 " distance=2.03 Simple disulfide: pdb=" SG CYS B1048 " - pdb=" SG CYS B1053 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 132 " distance=2.03 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 189 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 250 " distance=2.03 Simple disulfide: pdb=" SG CYS C 239 " - pdb=" SG CYS C 354 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 438 " distance=2.03 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 408 " - pdb=" SG CYS C 427 " distance=2.03 Simple disulfide: pdb=" SG CYS C 455 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 742 " - pdb=" SG CYS D 780 " distance=2.03 Simple disulfide: pdb=" SG CYS D 754 " - pdb=" SG CYS D 887 " distance=2.03 Simple disulfide: pdb=" SG CYS D 768 " - pdb=" SG CYS D 898 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS E 408 " - pdb=" SG CYS E 427 " distance=2.03 Simple disulfide: pdb=" SG CYS E 455 " - pdb=" SG CYS E 478 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 773 " distance=2.03 Simple disulfide: pdb=" SG CYS F 742 " - pdb=" SG CYS F 780 " distance=2.03 Simple disulfide: pdb=" SG CYS F 754 " - pdb=" SG CYS F 887 " distance=2.03 Simple disulfide: pdb=" SG CYS F 768 " - pdb=" SG CYS F 898 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS H 742 " - pdb=" SG CYS H 780 " distance=2.03 Simple disulfide: pdb=" SG CYS H 754 " - pdb=" SG CYS H 887 " distance=2.03 Simple disulfide: pdb=" SG CYS H 768 " - pdb=" SG CYS H 898 " distance=2.02 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA Q 3 " - " MAN Q 5 " " BMA S 3 " - " MAN S 5 " " BMA U 3 " - " MAN U 5 " " BMA W 3 " - " MAN W 5 " BETA1-4 " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A 701 " - " ASN A 402 " " NAG C 701 " - " ASN C 402 " " NAG E 701 " - " ASN E 402 " " NAG G 701 " - " ASN G 402 " " NAG Q 1 " - " ASN A 138 " " NAG R 1 " - " ASN A 350 " " NAG S 1 " - " ASN C 138 " " NAG T 1 " - " ASN C 350 " " NAG U 1 " - " ASN E 138 " " NAG V 1 " - " ASN E 350 " " NAG W 1 " - " ASN G 138 " " NAG X 1 " - " ASN G 350 " Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 1.7 seconds 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8216 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 60 sheets defined 10.0% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'I' and resid 83 through 87 removed outlier: 4.084A pdb=" N THR I 87 " --> pdb=" O ALA I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.563A pdb=" N VAL J 83 " --> pdb=" O ALA J 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.562A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.564A pdb=" N VAL N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.562A pdb=" N VAL P 83 " --> pdb=" O ALA P 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 removed outlier: 3.811A pdb=" N ILE A 58 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.870A pdb=" N SER A 72 " --> pdb=" O HIS A 69 " (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: 3.504A 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: 3.768A pdb=" N SER B 752 " --> pdb=" O TRP B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 858 removed outlier: 3.617A 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: 3.573A pdb=" N LEU B 967 " --> pdb=" O SER B 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 58 removed outlier: 3.815A pdb=" N ILE C 58 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 73 removed outlier: 3.868A pdb=" N SER C 72 " --> pdb=" O HIS C 69 " (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 225 through 234 Processing helix chain 'C' and resid 266 through 279 Processing helix chain 'C' and resid 446 through 463 removed outlier: 3.505A 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: 3.768A pdb=" N SER D 752 " --> pdb=" O TRP D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 858 removed outlier: 3.618A 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: 3.574A pdb=" N LEU D 967 " --> pdb=" O SER D 963 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 58 removed outlier: 3.811A pdb=" N ILE E 58 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 73 removed outlier: 3.868A pdb=" N SER E 72 " --> pdb=" O HIS E 69 " (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: 3.508A 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: 3.765A pdb=" N SER F 752 " --> pdb=" O TRP F 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 854 through 858 removed outlier: 3.600A 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: 3.575A pdb=" N LEU F 967 " --> pdb=" O SER F 963 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 58 removed outlier: 3.813A pdb=" N ILE G 58 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 73 removed outlier: 3.869A pdb=" N SER G 72 " --> pdb=" O HIS G 69 " (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: 3.506A 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: 3.768A pdb=" N SER H 752 " --> pdb=" O TRP H 749 " (cutoff:3.500A) Processing helix chain 'H' and resid 854 through 858 removed outlier: 3.598A 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: 3.575A pdb=" N LEU H 967 " --> pdb=" O SER H 963 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'I' and resid 56 through 59 removed outlier: 3.565A pdb=" N LYS I 56 " --> pdb=" O TRP I 52 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N TRP I 52 " --> pdb=" O TYR I 32 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N TYR I 32 " --> pdb=" O TRP I 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AA4, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.831A pdb=" N GLU J 104 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY J 84 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'K' and resid 56 through 59 removed outlier: 3.558A pdb=" N LYS K 56 " --> pdb=" O TRP K 52 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TRP K 52 " --> pdb=" O TYR K 32 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N TYR K 32 " --> pdb=" O TRP K 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.834A pdb=" N GLU L 104 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY L 84 " --> pdb=" O VAL L 103 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'M' and resid 56 through 59 removed outlier: 3.557A pdb=" N LYS M 56 " --> pdb=" O TRP M 52 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N TRP M 52 " --> pdb=" O TYR M 32 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N TYR M 32 " --> pdb=" O TRP M 52 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 4 through 5 Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.833A pdb=" N GLU N 104 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY N 84 " --> pdb=" O VAL N 103 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'O' and resid 56 through 59 removed outlier: 3.565A pdb=" N LYS O 56 " --> pdb=" O TRP O 52 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N MET O 34 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TRP O 52 " --> pdb=" O TYR O 32 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N TYR O 32 " --> pdb=" O TRP O 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 4 through 5 Processing sheet with id=AB7, first strand: chain 'P' and resid 10 through 12 removed outlier: 3.833A pdb=" N GLU P 104 " --> pdb=" O LEU P 11 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY P 84 " --> pdb=" O VAL P 103 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 23 through 30 removed outlier: 3.532A pdb=" N GLU A 61 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 40 through 46 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 40 through 46 current: chain 'A' and resid 141 through 151 No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 100 through 110 removed outlier: 4.505A pdb=" N PHE A 339 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU A 338 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 183 through 185 Processing sheet with id=AC3, 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 821 current: chain 'B' and resid 859 through 862 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 859 through 862 current: chain 'B' and resid 884 through 886 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 884 through 886 current: chain 'B' and resid 940 through 944 Processing sheet with id=AC4, first strand: chain 'A' and resid 299 through 303 Processing sheet with id=AC5, first strand: chain 'A' and resid 379 through 386 Processing sheet with id=AC6, first strand: chain 'A' and resid 411 through 413 removed outlier: 4.532A pdb=" N LYS A 442 " --> pdb=" O GLY H1070 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 663 through 664 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 663 through 664 current: chain 'B' and resid 991 through 1012 removed outlier: 8.432A pdb=" N GLU B1001 " --> pdb=" O ALA B1026 " (cutoff:3.500A) removed outlier: 11.395A pdb=" N ALA B1026 " --> pdb=" O GLU B1001 " (cutoff:3.500A) removed outlier: 9.808A pdb=" N ASN B1024 " --> pdb=" O PRO B1003 " (cutoff:3.500A) removed outlier: 11.155A pdb=" N PHE B1005 " --> pdb=" O VAL B1022 " (cutoff:3.500A) removed outlier: 9.850A pdb=" N VAL B1022 " --> pdb=" O PHE B1005 " (cutoff:3.500A) removed outlier: 11.275A pdb=" N THR B1007 " --> pdb=" O SER B1020 " (cutoff:3.500A) removed outlier: 9.847A pdb=" N SER B1020 " --> pdb=" O THR B1007 " (cutoff:3.500A) removed outlier: 11.454A pdb=" N ILE B1009 " --> pdb=" O TYR B1018 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N TYR B1018 " --> pdb=" O ILE B1009 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA B1011 " --> pdb=" O MET B1016 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N MET B1016 " --> pdb=" O ALA B1011 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1016 through 1036 current: chain 'B' and resid 1052 through 1053 Processing sheet with id=AC8, first strand: chain 'B' and resid 676 through 683 removed outlier: 3.689A pdb=" N GLY B 838 " --> pdb=" O HIS B 953 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN B 955 " --> pdb=" O ILE B 836 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ILE B 836 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL B 957 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL B 834 " --> pdb=" O VAL B 957 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 893 through 898 Processing sheet with id=AD1, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 4.513A pdb=" N LYS C 442 " --> pdb=" O GLY B1070 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 23 through 30 removed outlier: 3.541A pdb=" N GLU C 61 " --> pdb=" O SER C 164 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 40 through 46 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 40 through 46 current: chain 'C' and resid 141 through 151 No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 100 through 110 removed outlier: 4.494A pdb=" N PHE C 339 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU C 338 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 183 through 185 Processing sheet with id=AD6, 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 821 current: chain 'D' and resid 859 through 862 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 859 through 862 current: chain 'D' and resid 884 through 886 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 884 through 886 current: chain 'D' and resid 940 through 944 Processing sheet with id=AD7, first strand: chain 'C' and resid 299 through 303 Processing sheet with id=AD8, first strand: chain 'C' and resid 379 through 386 Processing sheet with id=AD9, first strand: chain 'D' and resid 663 through 664 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 663 through 664 current: chain 'D' and resid 991 through 1012 removed outlier: 8.433A pdb=" N GLU D1001 " --> pdb=" O ALA D1026 " (cutoff:3.500A) removed outlier: 11.398A pdb=" N ALA D1026 " --> pdb=" O GLU D1001 " (cutoff:3.500A) removed outlier: 9.834A pdb=" N ASN D1024 " --> pdb=" O PRO D1003 " (cutoff:3.500A) removed outlier: 11.216A pdb=" N PHE D1005 " --> pdb=" O VAL D1022 " (cutoff:3.500A) removed outlier: 9.906A pdb=" N VAL D1022 " --> pdb=" O PHE D1005 " (cutoff:3.500A) removed outlier: 11.237A pdb=" N THR D1007 " --> pdb=" O SER D1020 " (cutoff:3.500A) removed outlier: 9.810A pdb=" N SER D1020 " --> pdb=" O THR D1007 " (cutoff:3.500A) removed outlier: 11.414A pdb=" N ILE D1009 " --> pdb=" O TYR D1018 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N TYR D1018 " --> pdb=" O ILE D1009 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA D1011 " --> pdb=" O MET D1016 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N MET D1016 " --> pdb=" O ALA D1011 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 1016 through 1036 current: chain 'D' and resid 1052 through 1053 Processing sheet with id=AE1, first strand: chain 'D' and resid 676 through 683 removed outlier: 3.683A pdb=" N GLY D 838 " --> pdb=" O HIS D 953 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASN D 955 " --> pdb=" O ILE D 836 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ILE D 836 " --> pdb=" O ASN D 955 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL D 957 " --> pdb=" O VAL D 834 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL D 834 " --> pdb=" O VAL D 957 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 893 through 898 Processing sheet with id=AE3, first strand: chain 'D' and resid 1069 through 1070 removed outlier: 4.534A pdb=" N LYS E 442 " --> pdb=" O GLY D1070 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 23 through 30 removed outlier: 3.538A pdb=" N GLU E 61 " --> pdb=" O SER E 164 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 40 through 46 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 40 through 46 current: chain 'E' and resid 141 through 151 No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 100 through 110 removed outlier: 4.496A pdb=" N PHE E 339 " --> pdb=" O SER E 77 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU E 338 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 183 through 185 Processing sheet with id=AE8, 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 940 through 944 Processing sheet with id=AE9, first strand: chain 'E' and resid 299 through 303 Processing sheet with id=AF1, first strand: chain 'E' and resid 379 through 386 Processing sheet with id=AF2, first strand: chain 'F' and resid 663 through 664 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 663 through 664 current: chain 'F' and resid 991 through 1012 removed outlier: 8.419A pdb=" N GLU F1001 " --> pdb=" O ALA F1026 " (cutoff:3.500A) removed outlier: 11.380A pdb=" N ALA F1026 " --> pdb=" O GLU F1001 " (cutoff:3.500A) removed outlier: 9.711A pdb=" N ASN F1024 " --> pdb=" O PRO F1003 " (cutoff:3.500A) removed outlier: 10.914A pdb=" N PHE F1005 " --> pdb=" O VAL F1022 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N VAL F1022 " --> pdb=" O PHE F1005 " (cutoff:3.500A) removed outlier: 11.297A pdb=" N THR F1007 " --> pdb=" O SER F1020 " (cutoff:3.500A) removed outlier: 9.850A pdb=" N SER F1020 " --> pdb=" O THR F1007 " (cutoff:3.500A) removed outlier: 11.415A pdb=" N ILE F1009 " --> pdb=" O TYR F1018 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N TYR F1018 " --> pdb=" O ILE F1009 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA F1011 " --> pdb=" O MET F1016 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N MET F1016 " --> pdb=" O ALA F1011 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 1016 through 1036 current: chain 'F' and resid 1052 through 1053 Processing sheet with id=AF3, first strand: chain 'F' and resid 676 through 683 removed outlier: 3.685A pdb=" N GLY F 838 " --> pdb=" O HIS F 953 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN F 955 " --> pdb=" O ILE F 836 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILE F 836 " --> pdb=" O ASN F 955 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL F 957 " --> pdb=" O VAL F 834 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL F 834 " --> pdb=" O VAL F 957 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 893 through 898 Processing sheet with id=AF5, first strand: chain 'F' and resid 1069 through 1070 removed outlier: 4.529A pdb=" N LYS G 442 " --> pdb=" O GLY F1070 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 23 through 30 removed outlier: 3.537A pdb=" N GLU G 61 " --> pdb=" O SER G 164 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 40 through 46 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 40 through 46 current: chain 'G' and resid 141 through 151 No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'G' and resid 100 through 110 removed outlier: 4.494A pdb=" N PHE G 339 " --> pdb=" O SER G 77 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU G 338 " --> pdb=" O LEU G 331 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 183 through 185 Processing sheet with id=AG1, 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 821 current: chain 'H' and resid 859 through 862 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 859 through 862 current: chain 'H' and resid 884 through 886 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 884 through 886 current: chain 'H' and resid 940 through 944 Processing sheet with id=AG2, first strand: chain 'G' and resid 299 through 303 Processing sheet with id=AG3, first strand: chain 'G' and resid 379 through 386 Processing sheet with id=AG4, first strand: chain 'H' and resid 663 through 664 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 663 through 664 current: chain 'H' and resid 991 through 1012 removed outlier: 8.434A pdb=" N GLU H1001 " --> pdb=" O ALA H1026 " (cutoff:3.500A) removed outlier: 11.393A pdb=" N ALA H1026 " --> pdb=" O GLU H1001 " (cutoff:3.500A) removed outlier: 9.795A pdb=" N ASN H1024 " --> pdb=" O PRO H1003 " (cutoff:3.500A) removed outlier: 11.077A pdb=" N PHE H1005 " --> pdb=" O VAL H1022 " (cutoff:3.500A) removed outlier: 9.753A pdb=" N VAL H1022 " --> pdb=" O PHE H1005 " (cutoff:3.500A) removed outlier: 11.251A pdb=" N THR H1007 " --> pdb=" O SER H1020 " (cutoff:3.500A) removed outlier: 9.824A pdb=" N SER H1020 " --> pdb=" O THR H1007 " (cutoff:3.500A) removed outlier: 11.419A pdb=" N ILE H1009 " --> pdb=" O TYR H1018 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N TYR H1018 " --> pdb=" O ILE H1009 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA H1011 " --> pdb=" O MET H1016 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N MET H1016 " --> pdb=" O ALA H1011 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 1016 through 1036 current: chain 'H' and resid 1052 through 1053 Processing sheet with id=AG5, first strand: chain 'H' and resid 676 through 683 removed outlier: 3.685A pdb=" N GLY H 838 " --> pdb=" O HIS H 953 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN H 955 " --> pdb=" O ILE H 836 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILE H 836 " --> pdb=" O ASN H 955 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL H 957 " --> pdb=" O VAL H 834 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL H 834 " --> pdb=" O VAL H 957 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 893 through 898 1013 hydrogen bonds defined for protein. 2592 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.81 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11011 1.34 - 1.47: 8657 1.47 - 1.59: 15356 1.59 - 1.71: 0 1.71 - 1.84: 384 Bond restraints: 35408 Sorted by residual: bond pdb=" N LEU O 82C" pdb=" CA LEU O 82C" ideal model delta sigma weight residual 1.457 1.492 -0.036 1.31e-02 5.83e+03 7.43e+00 bond pdb=" N LEU I 82C" pdb=" CA LEU I 82C" ideal model delta sigma weight residual 1.457 1.492 -0.035 1.28e-02 6.10e+03 7.38e+00 bond pdb=" N LEU K 82C" pdb=" CA LEU K 82C" ideal model delta sigma weight residual 1.457 1.492 -0.035 1.31e-02 5.83e+03 7.25e+00 bond pdb=" N LEU M 82C" pdb=" CA LEU M 82C" ideal model delta sigma weight residual 1.457 1.492 -0.035 1.31e-02 5.83e+03 7.20e+00 bond pdb=" CG1 ILE A 426 " pdb=" CD1 ILE A 426 " ideal model delta sigma weight residual 1.513 1.409 0.104 3.90e-02 6.57e+02 7.09e+00 ... (remaining 35403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 47518 2.37 - 4.75: 511 4.75 - 7.12: 50 7.12 - 9.50: 0 9.50 - 11.87: 5 Bond angle restraints: 48084 Sorted by residual: angle pdb=" CG1 ILE E 288 " pdb=" CB ILE E 288 " pdb=" CG2 ILE E 288 " ideal model delta sigma weight residual 110.70 122.57 -11.87 3.00e+00 1.11e-01 1.57e+01 angle pdb=" CG1 ILE G 288 " pdb=" CB ILE G 288 " pdb=" CG2 ILE G 288 " ideal model delta sigma weight residual 110.70 122.53 -11.83 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CG1 ILE C 288 " pdb=" CB ILE C 288 " pdb=" CG2 ILE C 288 " ideal model delta sigma weight residual 110.70 122.50 -11.80 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CG1 ILE A 288 " pdb=" CB ILE A 288 " pdb=" CG2 ILE A 288 " ideal model delta sigma weight residual 110.70 122.44 -11.74 3.00e+00 1.11e-01 1.53e+01 angle pdb=" C GLN A 289 " pdb=" N ASN A 290 " pdb=" CA ASN A 290 " ideal model delta sigma weight residual 121.54 128.16 -6.62 1.91e+00 2.74e-01 1.20e+01 ... (remaining 48079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.31: 21122 24.31 - 48.61: 535 48.61 - 72.92: 87 72.92 - 97.22: 20 97.22 - 121.53: 12 Dihedral angle restraints: 21776 sinusoidal: 8952 harmonic: 12824 Sorted by residual: dihedral pdb=" CB CYS A 137 " pdb=" SG CYS A 137 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual 93.00 35.26 57.74 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CB CYS E 137 " pdb=" SG CYS E 137 " pdb=" SG CYS E 142 " pdb=" CB CYS E 142 " ideal model delta sinusoidal sigma weight residual 93.00 36.08 56.92 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CB CYS C 137 " pdb=" SG CYS C 137 " pdb=" SG CYS C 142 " pdb=" CB CYS C 142 " ideal model delta sinusoidal sigma weight residual 93.00 36.13 56.87 1 1.00e+01 1.00e-02 4.35e+01 ... (remaining 21773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 5457 0.117 - 0.233: 135 0.233 - 0.350: 0 0.350 - 0.466: 0 0.466 - 0.583: 4 Chirality restraints: 5596 Sorted by residual: chirality pdb=" CB ILE E 288 " pdb=" CA ILE E 288 " pdb=" CG1 ILE E 288 " pdb=" CG2 ILE E 288 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.58 2.00e-01 2.50e+01 8.49e+00 chirality pdb=" CB ILE G 288 " pdb=" CA ILE G 288 " pdb=" CG1 ILE G 288 " pdb=" CG2 ILE G 288 " both_signs ideal model delta sigma weight residual False 2.64 2.07 0.58 2.00e-01 2.50e+01 8.40e+00 chirality pdb=" CB ILE C 288 " pdb=" CA ILE C 288 " pdb=" CG1 ILE C 288 " pdb=" CG2 ILE C 288 " both_signs ideal model delta sigma weight residual False 2.64 2.07 0.58 2.00e-01 2.50e+01 8.35e+00 ... (remaining 5593 not shown) Planarity restraints: 6076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 393 " 0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" CD GLU C 393 " -0.059 2.00e-02 2.50e+03 pdb=" OE1 GLU C 393 " 0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU C 393 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 766 " 0.041 2.00e-02 2.50e+03 2.12e-02 1.12e+01 pdb=" CG TRP D 766 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP D 766 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP D 766 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP D 766 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP D 766 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 766 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 766 " 0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 766 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 766 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 766 " -0.041 2.00e-02 2.50e+03 2.12e-02 1.12e+01 pdb=" CG TRP F 766 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP F 766 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP F 766 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP F 766 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP F 766 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 766 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 766 " -0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 766 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP F 766 " 0.003 2.00e-02 2.50e+03 ... (remaining 6073 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 8544 2.81 - 3.33: 29071 3.33 - 3.85: 56120 3.85 - 4.38: 66428 4.38 - 4.90: 116261 Nonbonded interactions: 276424 Sorted by model distance: nonbonded pdb=" OG SER K 7 " pdb=" OG SER K 21 " model vdw 2.286 3.040 nonbonded pdb=" OG SER M 7 " pdb=" OG SER M 21 " model vdw 2.287 3.040 nonbonded pdb=" OG SER O 7 " pdb=" OG SER O 21 " model vdw 2.288 3.040 nonbonded pdb=" OG SER I 7 " pdb=" OG SER I 21 " model vdw 2.289 3.040 nonbonded pdb=" NH2 ARG H 691 " pdb=" OD1 ASP H1050 " model vdw 2.303 3.120 ... (remaining 276419 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: 0.02 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 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'R' selection = chain 'T' selection = chain 'V' 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: 8.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 36.690 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 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 : 0.003 0.104 35540 Z= 0.150 Angle : 0.643 11.874 48380 Z= 0.341 Chirality : 0.048 0.583 5596 Planarity : 0.004 0.047 6064 Dihedral : 11.498 121.527 13260 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.10 % Allowed : 0.08 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.63 (0.12), residues: 4424 helix: 1.19 (0.34), residues: 268 sheet: 0.22 (0.13), residues: 1720 loop : -1.08 (0.11), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 84 TYR 0.009 0.001 TYR E 133 PHE 0.020 0.002 PHE F1005 TRP 0.045 0.002 TRP F 766 HIS 0.015 0.002 HIS H 820 Details of bonding type rmsd covalent geometry : bond 0.00304 (35408) covalent geometry : angle 0.63338 (48084) SS BOND : bond 0.00337 ( 100) SS BOND : angle 1.38325 ( 200) hydrogen bonds : bond 0.11654 ( 1013) hydrogen bonds : angle 6.67207 ( 2592) link_ALPHA1-3 : bond 0.00719 ( 4) link_ALPHA1-3 : angle 1.51231 ( 12) link_ALPHA1-6 : bond 0.00340 ( 4) link_ALPHA1-6 : angle 1.52610 ( 12) link_BETA1-4 : bond 0.00601 ( 12) link_BETA1-4 : angle 1.85528 ( 36) link_NAG-ASN : bond 0.00153 ( 12) link_NAG-ASN : angle 2.15175 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 947 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 34 MET cc_start: 0.8949 (mmm) cc_final: 0.8604 (mmt) REVERT: J 22 SER cc_start: 0.8940 (m) cc_final: 0.8611 (t) REVERT: J 85 VAL cc_start: 0.8668 (t) cc_final: 0.8320 (p) REVERT: K 92 CYS cc_start: 0.5141 (t) cc_final: 0.4304 (t) REVERT: L 4 MET cc_start: 0.8392 (mmm) cc_final: 0.8114 (mmm) REVERT: M 92 CYS cc_start: 0.5208 (t) cc_final: 0.4548 (t) REVERT: N 27 LEU cc_start: 0.8154 (mt) cc_final: 0.7704 (mt) REVERT: O 82 MET cc_start: 0.6810 (mtp) cc_final: 0.6520 (mtp) REVERT: O 92 CYS cc_start: 0.5119 (t) cc_final: 0.4472 (t) REVERT: O 96 LEU cc_start: 0.8895 (tp) cc_final: 0.8532 (tt) REVERT: P 36 TYR cc_start: 0.7864 (m-80) cc_final: 0.7488 (m-80) REVERT: P 46 LEU cc_start: 0.8773 (tp) cc_final: 0.8560 (tp) REVERT: A 36 LEU cc_start: 0.9079 (mm) cc_final: 0.8794 (mt) REVERT: A 276 MET cc_start: 0.8826 (mtt) cc_final: 0.8621 (mtt) REVERT: A 431 ASP cc_start: 0.8883 (m-30) cc_final: 0.8590 (m-30) REVERT: B 673 LYS cc_start: 0.9031 (mmpt) cc_final: 0.8828 (mmmt) REVERT: B 693 LYS cc_start: 0.9260 (ttmm) cc_final: 0.8912 (mtpp) REVERT: B 933 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8576 (tm-30) REVERT: D 1014 LEU cc_start: 0.8961 (tt) cc_final: 0.8756 (mm) REVERT: E 89 THR cc_start: 0.8710 (m) cc_final: 0.8260 (p) REVERT: E 278 VAL cc_start: 0.7389 (t) cc_final: 0.7152 (m) REVERT: E 353 THR cc_start: 0.7758 (m) cc_final: 0.7275 (t) REVERT: F 693 LYS cc_start: 0.9220 (ttmm) cc_final: 0.8803 (ttmm) REVERT: F 760 TYR cc_start: 0.6155 (m-80) cc_final: 0.5921 (m-80) REVERT: F 762 TYR cc_start: 0.5490 (t80) cc_final: 0.5050 (t80) REVERT: F 763 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7424 (pm20) REVERT: F 829 THR cc_start: 0.7097 (p) cc_final: 0.6499 (p) REVERT: F 847 ASP cc_start: 0.8363 (m-30) cc_final: 0.8123 (m-30) REVERT: F 970 ASN cc_start: 0.9111 (m-40) cc_final: 0.8797 (t0) REVERT: F 1077 ASP cc_start: 0.8124 (p0) cc_final: 0.7803 (p0) REVERT: G 353 THR cc_start: 0.7986 (m) cc_final: 0.7756 (p) REVERT: H 760 TYR cc_start: 0.7805 (m-80) cc_final: 0.7433 (m-80) REVERT: H 905 VAL cc_start: 0.7429 (t) cc_final: 0.7115 (m) REVERT: H 964 PHE cc_start: 0.8379 (m-80) cc_final: 0.8023 (m-10) REVERT: H 970 ASN cc_start: 0.8770 (m-40) cc_final: 0.8333 (t0) REVERT: H 1030 ASN cc_start: 0.7891 (m-40) cc_final: 0.7681 (m-40) REVERT: H 1077 ASP cc_start: 0.7878 (p0) cc_final: 0.7513 (p0) outliers start: 4 outliers final: 0 residues processed: 947 average time/residue: 0.2510 time to fit residues: 368.0687 Evaluate side-chains 647 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 647 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 35 HIS K 35 HIS K 39 GLN L 27DHIS M 35 HIS N 27DHIS N 90 GLN ** O 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 743 GLN B 816 GLN B 953 HIS B 970 ASN B 977 HIS B1030 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 699 ASN D 707 HIS D 743 GLN D 953 HIS D1030 ASN E 75 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 HIS E 428 GLN F 707 HIS F 743 GLN F 816 GLN F 949 ASN F1030 ASN F1073 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 351 HIS G 398 ASN G 428 GLN H 743 GLN H 761 GLN H 816 GLN H 949 ASN H 977 HIS H1030 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.052962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.044292 restraints weight = 116636.951| |-----------------------------------------------------------------------------| r_work (start): 0.2608 rms_B_bonded: 2.73 r_work: 0.2504 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2387 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 35540 Z= 0.304 Angle : 0.853 15.424 48380 Z= 0.441 Chirality : 0.052 0.263 5596 Planarity : 0.006 0.058 6064 Dihedral : 7.755 103.033 5392 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.85 % Allowed : 9.65 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.70 (0.12), residues: 4424 helix: 0.18 (0.31), residues: 296 sheet: 0.36 (0.13), residues: 1652 loop : -1.15 (0.11), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 886 TYR 0.047 0.003 TYR P 28 PHE 0.033 0.003 PHE G 166 TRP 0.026 0.003 TRP M 103 HIS 0.031 0.002 HIS L 93 Details of bonding type rmsd covalent geometry : bond 0.00703 (35408) covalent geometry : angle 0.83769 (48084) SS BOND : bond 0.00769 ( 100) SS BOND : angle 2.14546 ( 200) hydrogen bonds : bond 0.04832 ( 1013) hydrogen bonds : angle 5.71480 ( 2592) link_ALPHA1-3 : bond 0.00756 ( 4) link_ALPHA1-3 : angle 2.83299 ( 12) link_ALPHA1-6 : bond 0.00393 ( 4) link_ALPHA1-6 : angle 1.73412 ( 12) link_BETA1-4 : bond 0.00971 ( 12) link_BETA1-4 : angle 2.51310 ( 36) link_NAG-ASN : bond 0.01450 ( 12) link_NAG-ASN : angle 2.39028 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 693 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 3 GLN cc_start: 0.9194 (mt0) cc_final: 0.8755 (mp10) REVERT: I 19 ARG cc_start: 0.8818 (ttt180) cc_final: 0.8423 (ttt90) REVERT: I 58 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8469 (t0) REVERT: J 22 SER cc_start: 0.9319 (m) cc_final: 0.9020 (t) REVERT: K 13 GLN cc_start: 0.8035 (mp10) cc_final: 0.7641 (mm110) REVERT: K 59 TYR cc_start: 0.8915 (m-80) cc_final: 0.8442 (m-80) REVERT: K 78 LEU cc_start: 0.8890 (tp) cc_final: 0.8662 (mt) REVERT: K 82 SER cc_start: 0.9089 (t) cc_final: 0.8824 (p) REVERT: K 86 ASP cc_start: 0.8690 (p0) cc_final: 0.8413 (p0) REVERT: L 17 GLU cc_start: 0.8360 (mp0) cc_final: 0.7921 (pm20) REVERT: L 22 SER cc_start: 0.8993 (m) cc_final: 0.8774 (p) REVERT: M 13 GLN cc_start: 0.7800 (mp10) cc_final: 0.7382 (mm110) REVERT: M 19 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7900 (ptm160) REVERT: M 86 ASP cc_start: 0.8559 (p0) cc_final: 0.8261 (p0) REVERT: N 11 LEU cc_start: 0.8598 (tp) cc_final: 0.8342 (tt) REVERT: N 33 LEU cc_start: 0.8809 (tp) cc_final: 0.8591 (tp) REVERT: N 38 GLN cc_start: 0.9088 (tt0) cc_final: 0.8756 (tt0) REVERT: N 101 THR cc_start: 0.8923 (m) cc_final: 0.8639 (t) REVERT: O 19 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8401 (ptm160) REVERT: O 66 ARG cc_start: 0.7434 (mtm-85) cc_final: 0.7039 (mtp180) REVERT: O 96 LEU cc_start: 0.9280 (tp) cc_final: 0.9078 (tp) REVERT: P 27 GLN cc_start: 0.9101 (mp10) cc_final: 0.8785 (mp10) REVERT: P 31 ASN cc_start: 0.8990 (m110) cc_final: 0.8727 (t0) REVERT: P 42 GLN cc_start: 0.8572 (mp10) cc_final: 0.8191 (mp10) REVERT: P 71 PHE cc_start: 0.8882 (m-80) cc_final: 0.8358 (m-10) REVERT: P 93 HIS cc_start: 0.8934 (t-90) cc_final: 0.8526 (t-90) REVERT: A 84 ARG cc_start: 0.8829 (ttp80) cc_final: 0.7877 (ptp90) REVERT: A 101 GLU cc_start: 0.8953 (pt0) cc_final: 0.8294 (pm20) REVERT: A 431 ASP cc_start: 0.8896 (m-30) cc_final: 0.8591 (m-30) REVERT: B 673 LYS cc_start: 0.9050 (mmpt) cc_final: 0.8824 (mmmt) REVERT: B 815 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8154 (tm-30) REVERT: B 895 ARG cc_start: 0.8775 (ptt90) cc_final: 0.8559 (ptt90) REVERT: B 933 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8858 (tm-30) REVERT: B 947 ASP cc_start: 0.8492 (p0) cc_final: 0.8287 (p0) REVERT: C 84 ARG cc_start: 0.8429 (ttp-170) cc_final: 0.8146 (ptp90) REVERT: C 101 GLU cc_start: 0.8759 (tt0) cc_final: 0.8312 (tm-30) REVERT: C 162 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8711 (ttt) REVERT: D 656 MET cc_start: 0.8973 (mmp) cc_final: 0.8511 (mmp) REVERT: D 833 LYS cc_start: 0.8974 (mmtm) cc_final: 0.8221 (ttpp) REVERT: D 933 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8386 (tm-30) REVERT: E 118 GLU cc_start: 0.9200 (pm20) cc_final: 0.8968 (pm20) REVERT: E 393 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8504 (tm-30) REVERT: F 933 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8644 (tm-30) REVERT: F 962 VAL cc_start: 0.8699 (t) cc_final: 0.8231 (p) REVERT: F 1014 LEU cc_start: 0.9345 (tt) cc_final: 0.9119 (mm) REVERT: G 156 MET cc_start: 0.8659 (mmp) cc_final: 0.8445 (mmt) REVERT: G 431 ASP cc_start: 0.8799 (OUTLIER) cc_final: 0.8556 (p0) REVERT: H 963 SER cc_start: 0.8783 (t) cc_final: 0.8469 (t) REVERT: H 1001 GLU cc_start: 0.8609 (mp0) cc_final: 0.8323 (mp0) REVERT: H 1052 ASP cc_start: 0.8760 (t0) cc_final: 0.8494 (t0) REVERT: H 1077 ASP cc_start: 0.8635 (p0) cc_final: 0.8242 (p0) outliers start: 111 outliers final: 59 residues processed: 759 average time/residue: 0.2398 time to fit residues: 286.7980 Evaluate side-chains 651 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 585 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 45 GLN Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 19 ARG Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain O residue 19 ARG Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 45 GLN Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 1043 SER Chi-restraints excluded: chain B residue 1072 ASN Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain D residue 766 TRP Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 891 THR Chi-restraints excluded: chain D residue 957 VAL Chi-restraints excluded: chain D residue 967 LEU Chi-restraints excluded: chain D residue 1041 SER Chi-restraints excluded: chain D residue 1072 ASN Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 393 GLU Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain F residue 662 ASP Chi-restraints excluded: chain F residue 766 TRP Chi-restraints excluded: chain F residue 913 ILE Chi-restraints excluded: chain F residue 1053 CYS Chi-restraints excluded: chain F residue 1072 ASN Chi-restraints excluded: chain G residue 308 THR Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain H residue 766 TRP Chi-restraints excluded: chain H residue 913 ILE Chi-restraints excluded: chain H residue 1051 THR Chi-restraints excluded: chain H residue 1072 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 105 optimal weight: 2.9990 chunk 328 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 27DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 27DHIS ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN N 27DHIS ** O 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN B 707 HIS B 977 HIS B1030 ASN C 279 HIS C 428 GLN D 707 HIS D 816 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 909 GLN F 965 GLN F1030 ASN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 HIS G 398 ASN H 707 HIS H 769 ASN H 953 HIS H 977 HIS H1030 ASN ** H1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.051942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.043365 restraints weight = 116955.794| |-----------------------------------------------------------------------------| r_work (start): 0.2587 rms_B_bonded: 2.77 r_work: 0.2480 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2363 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 35540 Z= 0.165 Angle : 0.631 10.471 48380 Z= 0.325 Chirality : 0.045 0.234 5596 Planarity : 0.005 0.093 6064 Dihedral : 7.018 100.199 5392 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.01 % Allowed : 11.32 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.56 (0.12), residues: 4424 helix: 0.79 (0.33), residues: 296 sheet: 0.49 (0.14), residues: 1468 loop : -1.04 (0.11), residues: 2660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 415 TYR 0.014 0.001 TYR E 247 PHE 0.025 0.002 PHE B 900 TRP 0.015 0.001 TRP O 47 HIS 0.009 0.001 HIS P 93 Details of bonding type rmsd covalent geometry : bond 0.00379 (35408) covalent geometry : angle 0.61737 (48084) SS BOND : bond 0.00485 ( 100) SS BOND : angle 1.44012 ( 200) hydrogen bonds : bond 0.03687 ( 1013) hydrogen bonds : angle 5.28016 ( 2592) link_ALPHA1-3 : bond 0.01133 ( 4) link_ALPHA1-3 : angle 2.89799 ( 12) link_ALPHA1-6 : bond 0.00701 ( 4) link_ALPHA1-6 : angle 1.37382 ( 12) link_BETA1-4 : bond 0.00553 ( 12) link_BETA1-4 : angle 2.34117 ( 36) link_NAG-ASN : bond 0.00420 ( 12) link_NAG-ASN : angle 2.46108 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 629 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 3 GLN cc_start: 0.9054 (mt0) cc_final: 0.8577 (mp10) REVERT: I 58 ASP cc_start: 0.8756 (t0) cc_final: 0.8362 (t0) REVERT: J 22 SER cc_start: 0.9331 (m) cc_final: 0.8971 (t) REVERT: K 13 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7348 (mm-40) REVERT: K 68 THR cc_start: 0.8993 (m) cc_final: 0.8761 (p) REVERT: K 86 ASP cc_start: 0.8691 (p0) cc_final: 0.8464 (p0) REVERT: L 17 GLU cc_start: 0.8400 (mp0) cc_final: 0.8127 (pm20) REVERT: L 22 SER cc_start: 0.8929 (m) cc_final: 0.8668 (p) REVERT: L 71 PHE cc_start: 0.8782 (m-10) cc_final: 0.8443 (m-10) REVERT: L 102 LYS cc_start: 0.9415 (ttmm) cc_final: 0.9187 (ttpp) REVERT: L 104 GLU cc_start: 0.7757 (pp20) cc_final: 0.7041 (tt0) REVERT: M 16 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7852 (mtt180) REVERT: M 86 ASP cc_start: 0.8584 (p0) cc_final: 0.8306 (p0) REVERT: N 38 GLN cc_start: 0.9123 (tt0) cc_final: 0.8794 (tt0) REVERT: O 86 ASP cc_start: 0.8656 (p0) cc_final: 0.8444 (p0) REVERT: O 96 LEU cc_start: 0.9267 (tp) cc_final: 0.8933 (tt) REVERT: P 42 GLN cc_start: 0.8621 (mp10) cc_final: 0.8275 (mp10) REVERT: P 46 LEU cc_start: 0.9182 (tp) cc_final: 0.8970 (tp) REVERT: P 71 PHE cc_start: 0.8881 (m-80) cc_final: 0.8267 (m-80) REVERT: A 84 ARG cc_start: 0.8893 (ttp80) cc_final: 0.7939 (ttp-170) REVERT: A 101 GLU cc_start: 0.8904 (pt0) cc_final: 0.8386 (pm20) REVERT: B 673 LYS cc_start: 0.9014 (mmpt) cc_final: 0.8757 (mmmt) REVERT: B 679 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8042 (t0) REVERT: B 933 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8884 (tm-30) REVERT: B 955 ASN cc_start: 0.8947 (t0) cc_final: 0.8480 (t0) REVERT: C 84 ARG cc_start: 0.8666 (ttp-170) cc_final: 0.8245 (ptp90) REVERT: C 162 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8886 (ttt) REVERT: D 656 MET cc_start: 0.8911 (mmp) cc_final: 0.8489 (mmp) REVERT: D 833 LYS cc_start: 0.9047 (mmtm) cc_final: 0.8781 (mmtm) REVERT: D 842 LYS cc_start: 0.9036 (mmmm) cc_final: 0.8769 (mtpp) REVERT: D 844 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8706 (mp10) REVERT: D 933 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8311 (tm-30) REVERT: E 73 MET cc_start: 0.9190 (mmt) cc_final: 0.8937 (mmt) REVERT: E 84 ARG cc_start: 0.8727 (ptt90) cc_final: 0.8246 (ptt90) REVERT: E 101 GLU cc_start: 0.7643 (tm-30) cc_final: 0.6974 (tm-30) REVERT: E 408 CYS cc_start: 0.8375 (m) cc_final: 0.8154 (m) REVERT: F 933 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8596 (tm-30) REVERT: F 1006 MET cc_start: 0.9329 (tpp) cc_final: 0.8853 (tpp) REVERT: F 1014 LEU cc_start: 0.9357 (tt) cc_final: 0.9140 (mm) REVERT: G 26 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8301 (tt) REVERT: G 84 ARG cc_start: 0.8536 (ptt90) cc_final: 0.7833 (ptt90) REVERT: G 415 ARG cc_start: 0.7632 (mtt180) cc_final: 0.7270 (mtt180) REVERT: G 429 ARG cc_start: 0.9256 (mtp85) cc_final: 0.8914 (mtp85) REVERT: G 431 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8443 (p0) REVERT: H 696 ASN cc_start: 0.8657 (t0) cc_final: 0.8363 (t0) REVERT: H 963 SER cc_start: 0.8723 (t) cc_final: 0.8459 (t) REVERT: H 1052 ASP cc_start: 0.8796 (t0) cc_final: 0.8519 (t0) outliers start: 117 outliers final: 59 residues processed: 694 average time/residue: 0.2411 time to fit residues: 262.6809 Evaluate side-chains 640 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 574 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain J residue 45 GLN Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain K residue 13 GLN Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 19 ARG Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 679 ASP Chi-restraints excluded: chain B residue 766 TRP Chi-restraints excluded: chain B residue 1072 ASN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 401 PHE Chi-restraints excluded: chain D residue 670 ILE Chi-restraints excluded: chain D residue 766 TRP Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 844 GLN Chi-restraints excluded: chain D residue 913 ILE Chi-restraints excluded: chain D residue 957 VAL Chi-restraints excluded: chain D residue 1041 SER Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1072 ASN Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain F residue 662 ASP Chi-restraints excluded: chain F residue 815 GLU Chi-restraints excluded: chain F residue 913 ILE Chi-restraints excluded: chain F residue 1072 ASN Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain G residue 291 SER Chi-restraints excluded: chain G residue 375 LYS Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain H residue 766 TRP Chi-restraints excluded: chain H residue 913 ILE Chi-restraints excluded: chain H residue 1072 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 312 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 328 optimal weight: 0.1980 chunk 370 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 198 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 27DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 HIS P 31 ASN A 289 GLN B 707 HIS ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 707 HIS D 965 GLN ** F 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN H 707 HIS H 977 HIS H1030 ASN ** H1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.048856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.040450 restraints weight = 117405.247| |-----------------------------------------------------------------------------| r_work (start): 0.2504 rms_B_bonded: 2.78 r_work: 0.2393 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2274 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 35540 Z= 0.256 Angle : 0.707 9.618 48380 Z= 0.366 Chirality : 0.048 0.209 5596 Planarity : 0.005 0.049 6064 Dihedral : 6.800 93.899 5392 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.58 % Allowed : 12.94 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.12), residues: 4424 helix: 0.78 (0.33), residues: 296 sheet: 0.65 (0.13), residues: 1592 loop : -1.17 (0.12), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 84 TYR 0.019 0.002 TYR K 91 PHE 0.032 0.002 PHE D 900 TRP 0.014 0.002 TRP M 52 HIS 0.007 0.001 HIS I 100G Details of bonding type rmsd covalent geometry : bond 0.00602 (35408) covalent geometry : angle 0.69259 (48084) SS BOND : bond 0.00598 ( 100) SS BOND : angle 1.76035 ( 200) hydrogen bonds : bond 0.04233 ( 1013) hydrogen bonds : angle 5.29271 ( 2592) link_ALPHA1-3 : bond 0.01059 ( 4) link_ALPHA1-3 : angle 3.40774 ( 12) link_ALPHA1-6 : bond 0.00502 ( 4) link_ALPHA1-6 : angle 1.64122 ( 12) link_BETA1-4 : bond 0.00658 ( 12) link_BETA1-4 : angle 2.19880 ( 36) link_NAG-ASN : bond 0.00514 ( 12) link_NAG-ASN : angle 2.13818 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 608 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 3 GLN cc_start: 0.9014 (mt0) cc_final: 0.8485 (mp10) REVERT: I 19 ARG cc_start: 0.8956 (ttt180) cc_final: 0.8677 (ttm170) REVERT: I 58 ASP cc_start: 0.8953 (t0) cc_final: 0.8697 (t0) REVERT: J 22 SER cc_start: 0.9341 (m) cc_final: 0.8975 (p) REVERT: K 13 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7524 (mm-40) REVERT: K 68 THR cc_start: 0.9132 (m) cc_final: 0.8746 (p) REVERT: K 86 ASP cc_start: 0.8807 (p0) cc_final: 0.8597 (p0) REVERT: L 11 LEU cc_start: 0.9131 (tp) cc_final: 0.8902 (tt) REVERT: L 17 GLU cc_start: 0.8462 (mp0) cc_final: 0.8243 (pm20) REVERT: L 22 SER cc_start: 0.9053 (m) cc_final: 0.8725 (p) REVERT: L 104 GLU cc_start: 0.7722 (pp20) cc_final: 0.7238 (tt0) REVERT: M 68 THR cc_start: 0.9023 (m) cc_final: 0.8682 (p) REVERT: M 86 ASP cc_start: 0.8791 (p0) cc_final: 0.8584 (p0) REVERT: M 96 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8897 (tt) REVERT: N 38 GLN cc_start: 0.9076 (tt0) cc_final: 0.8751 (tt0) REVERT: N 72 THR cc_start: 0.9337 (m) cc_final: 0.9050 (p) REVERT: N 101 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8909 (t) REVERT: O 81 GLN cc_start: 0.9092 (tp40) cc_final: 0.8871 (tp40) REVERT: O 86 ASP cc_start: 0.8829 (p0) cc_final: 0.8616 (p0) REVERT: O 96 LEU cc_start: 0.9291 (tp) cc_final: 0.9006 (tt) REVERT: P 31 ASN cc_start: 0.9137 (m-40) cc_final: 0.8871 (m-40) REVERT: P 42 GLN cc_start: 0.8757 (mp10) cc_final: 0.8420 (mp10) REVERT: P 46 LEU cc_start: 0.9229 (tp) cc_final: 0.9015 (tp) REVERT: A 28 MET cc_start: 0.9423 (mmm) cc_final: 0.8907 (mtp) REVERT: A 68 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8947 (mp) REVERT: A 84 ARG cc_start: 0.8876 (ttp80) cc_final: 0.7777 (ttp-170) REVERT: A 101 GLU cc_start: 0.8985 (pt0) cc_final: 0.8451 (pm20) REVERT: B 933 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8851 (tm-30) REVERT: C 68 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9020 (mp) REVERT: C 162 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8908 (ttt) REVERT: C 408 CYS cc_start: 0.8399 (m) cc_final: 0.8185 (m) REVERT: D 656 MET cc_start: 0.9018 (mmp) cc_final: 0.8791 (mmp) REVERT: D 833 LYS cc_start: 0.8953 (mmtm) cc_final: 0.8394 (ttpp) REVERT: D 842 LYS cc_start: 0.8976 (mmmm) cc_final: 0.8565 (mtpp) REVERT: D 844 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8304 (mp10) REVERT: D 933 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8156 (tm-30) REVERT: E 68 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9097 (mp) REVERT: E 73 MET cc_start: 0.9207 (mmt) cc_final: 0.8921 (mmt) REVERT: E 84 ARG cc_start: 0.8979 (ptt90) cc_final: 0.8752 (ptt-90) REVERT: F 933 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8575 (tm-30) REVERT: G 68 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8998 (mp) REVERT: G 101 GLU cc_start: 0.8310 (tt0) cc_final: 0.8072 (pt0) REVERT: G 415 ARG cc_start: 0.7829 (mtt180) cc_final: 0.7496 (mtt180) REVERT: G 429 ARG cc_start: 0.9310 (mtp85) cc_final: 0.9091 (mtp85) REVERT: H 933 GLU cc_start: 0.9252 (pt0) cc_final: 0.8909 (pp20) REVERT: H 955 ASN cc_start: 0.8873 (t0) cc_final: 0.8616 (t0) REVERT: H 963 SER cc_start: 0.8851 (t) cc_final: 0.8596 (t) outliers start: 139 outliers final: 91 residues processed: 699 average time/residue: 0.2426 time to fit residues: 267.0574 Evaluate side-chains 673 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 573 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain J residue 45 GLN Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain K residue 13 GLN Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 19 ARG Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 74 LYS Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain B residue 766 TRP Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 1072 ASN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain D residue 670 ILE Chi-restraints excluded: chain D residue 766 TRP Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 844 GLN Chi-restraints excluded: chain D residue 913 ILE Chi-restraints excluded: chain D residue 957 VAL Chi-restraints excluded: chain D residue 967 LEU Chi-restraints excluded: chain D residue 1041 SER Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1072 ASN Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 113 CYS Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain F residue 662 ASP Chi-restraints excluded: chain F residue 670 ILE Chi-restraints excluded: chain F residue 913 ILE Chi-restraints excluded: chain F residue 1072 ASN Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 375 LYS Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain H residue 766 TRP Chi-restraints excluded: chain H residue 829 THR Chi-restraints excluded: chain H residue 867 THR Chi-restraints excluded: chain H residue 913 ILE Chi-restraints excluded: chain H residue 1051 THR Chi-restraints excluded: chain H residue 1072 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 75 optimal weight: 6.9990 chunk 247 optimal weight: 4.9990 chunk 411 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 271 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 435 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 396 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 27DHIS L 6 GLN L 27DHIS M 35 HIS ** O 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 GLN P 6 GLN ** P 27DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 ASN A 289 GLN B 977 HIS ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 707 HIS D 965 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 965 GLN H 707 HIS H 824 ASN H 977 HIS H1030 ASN ** H1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.047979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.039660 restraints weight = 117996.881| |-----------------------------------------------------------------------------| r_work (start): 0.2477 rms_B_bonded: 2.77 r_work: 0.2366 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2248 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.6333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 35540 Z= 0.264 Angle : 0.712 8.976 48380 Z= 0.367 Chirality : 0.048 0.219 5596 Planarity : 0.005 0.051 6064 Dihedral : 6.669 85.030 5392 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.09 % Allowed : 13.81 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.12), residues: 4424 helix: 0.82 (0.33), residues: 296 sheet: 0.54 (0.13), residues: 1588 loop : -1.15 (0.12), residues: 2540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 895 TYR 0.021 0.002 TYR K 91 PHE 0.026 0.002 PHE H 900 TRP 0.013 0.002 TRP K 47 HIS 0.007 0.001 HIS I 100G Details of bonding type rmsd covalent geometry : bond 0.00621 (35408) covalent geometry : angle 0.69662 (48084) SS BOND : bond 0.00620 ( 100) SS BOND : angle 1.75051 ( 200) hydrogen bonds : bond 0.04174 ( 1013) hydrogen bonds : angle 5.32491 ( 2592) link_ALPHA1-3 : bond 0.01306 ( 4) link_ALPHA1-3 : angle 3.57926 ( 12) link_ALPHA1-6 : bond 0.00448 ( 4) link_ALPHA1-6 : angle 1.54131 ( 12) link_BETA1-4 : bond 0.00563 ( 12) link_BETA1-4 : angle 2.50230 ( 36) link_NAG-ASN : bond 0.00391 ( 12) link_NAG-ASN : angle 2.03298 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 615 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 3 GLN cc_start: 0.9006 (mt0) cc_final: 0.8498 (mp10) REVERT: I 19 ARG cc_start: 0.8967 (ttt180) cc_final: 0.8640 (ttm170) REVERT: I 20 LEU cc_start: 0.9031 (mp) cc_final: 0.8770 (mp) REVERT: I 47 TRP cc_start: 0.9375 (t60) cc_final: 0.9139 (t60) REVERT: I 58 ASP cc_start: 0.9018 (t0) cc_final: 0.8604 (t0) REVERT: I 67 PHE cc_start: 0.8975 (m-80) cc_final: 0.8520 (m-80) REVERT: I 80 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8810 (tt) REVERT: I 105 GLN cc_start: 0.9182 (tp40) cc_final: 0.8965 (mm-40) REVERT: J 11 LEU cc_start: 0.9412 (tp) cc_final: 0.9143 (tt) REVERT: J 22 SER cc_start: 0.9343 (m) cc_final: 0.9016 (p) REVERT: K 13 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7536 (mm110) REVERT: L 22 SER cc_start: 0.9151 (m) cc_final: 0.8834 (p) REVERT: L 72 THR cc_start: 0.9411 (m) cc_final: 0.9161 (p) REVERT: L 104 GLU cc_start: 0.7615 (pp20) cc_final: 0.7336 (tt0) REVERT: M 96 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8869 (tt) REVERT: N 38 GLN cc_start: 0.9063 (tt0) cc_final: 0.8765 (tt0) REVERT: N 72 THR cc_start: 0.9297 (m) cc_final: 0.8923 (p) REVERT: N 74 LYS cc_start: 0.9236 (mtpp) cc_final: 0.9022 (mtmm) REVERT: N 104 GLU cc_start: 0.6172 (tm-30) cc_final: 0.5954 (tm-30) REVERT: O 19 ARG cc_start: 0.8940 (ttm170) cc_final: 0.8664 (ttm170) REVERT: O 81 GLN cc_start: 0.9078 (tp40) cc_final: 0.8865 (tp40) REVERT: O 96 LEU cc_start: 0.9280 (tp) cc_final: 0.9063 (tt) REVERT: O 97 ILE cc_start: 0.9521 (OUTLIER) cc_final: 0.9306 (pp) REVERT: P 34 ASP cc_start: 0.9031 (m-30) cc_final: 0.8779 (m-30) REVERT: P 74 LYS cc_start: 0.9452 (OUTLIER) cc_final: 0.9002 (mtmm) REVERT: P 89 MET cc_start: 0.9083 (ttp) cc_final: 0.8570 (ttp) REVERT: P 104 GLU cc_start: 0.6604 (tm-30) cc_final: 0.6375 (tm-30) REVERT: A 84 ARG cc_start: 0.8876 (ttp80) cc_final: 0.7792 (ttp-170) REVERT: A 101 GLU cc_start: 0.8971 (pt0) cc_final: 0.8501 (pm20) REVERT: A 304 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.8895 (mtmm) REVERT: A 431 ASP cc_start: 0.8921 (m-30) cc_final: 0.8648 (m-30) REVERT: B 842 LYS cc_start: 0.9134 (mtpp) cc_final: 0.8823 (mtpp) REVERT: B 933 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8851 (tm-30) REVERT: B 955 ASN cc_start: 0.8990 (t0) cc_final: 0.8543 (t0) REVERT: B 964 PHE cc_start: 0.8867 (m-10) cc_final: 0.8652 (m-10) REVERT: C 68 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9002 (mp) REVERT: C 84 ARG cc_start: 0.8993 (ttp-170) cc_final: 0.7628 (ttp-170) REVERT: C 101 GLU cc_start: 0.8574 (tt0) cc_final: 0.8102 (pm20) REVERT: C 237 THR cc_start: 0.8820 (m) cc_final: 0.8479 (p) REVERT: C 408 CYS cc_start: 0.8433 (m) cc_final: 0.8217 (m) REVERT: D 833 LYS cc_start: 0.8852 (mmtm) cc_final: 0.8581 (tmtt) REVERT: D 842 LYS cc_start: 0.8993 (mmmm) cc_final: 0.8535 (mmmm) REVERT: D 844 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8355 (mp10) REVERT: D 933 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8123 (tm-30) REVERT: E 237 THR cc_start: 0.9034 (m) cc_final: 0.8732 (p) REVERT: E 408 CYS cc_start: 0.8441 (m) cc_final: 0.8239 (m) REVERT: F 833 LYS cc_start: 0.8929 (mmtm) cc_final: 0.8374 (tmtt) REVERT: F 885 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8854 (mtm) REVERT: F 933 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8475 (tm-30) REVERT: F 952 ASP cc_start: 0.8960 (t0) cc_final: 0.8725 (t0) REVERT: G 68 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9011 (mp) REVERT: G 101 GLU cc_start: 0.8660 (tt0) cc_final: 0.8292 (pm20) REVERT: G 156 MET cc_start: 0.8970 (mmp) cc_final: 0.8052 (mmt) REVERT: G 415 ARG cc_start: 0.7944 (mtt180) cc_final: 0.6656 (mtt180) REVERT: G 429 ARG cc_start: 0.9323 (mtp85) cc_final: 0.9118 (mtp85) REVERT: H 672 MET cc_start: 0.8614 (mmm) cc_final: 0.8198 (mtp) REVERT: H 933 GLU cc_start: 0.9279 (pt0) cc_final: 0.8973 (pp20) REVERT: H 955 ASN cc_start: 0.8848 (t0) cc_final: 0.8578 (t0) REVERT: H 963 SER cc_start: 0.8880 (t) cc_final: 0.8679 (t) outliers start: 159 outliers final: 111 residues processed: 712 average time/residue: 0.2437 time to fit residues: 272.2392 Evaluate side-chains 702 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 581 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain K residue 13 GLN Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 19 ARG Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 74 LYS Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain B residue 679 ASP Chi-restraints excluded: chain B residue 766 TRP Chi-restraints excluded: chain B residue 1006 MET Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain B residue 1072 ASN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain D residue 670 ILE Chi-restraints excluded: chain D residue 766 TRP Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 844 GLN Chi-restraints excluded: chain D residue 913 ILE Chi-restraints excluded: chain D residue 957 VAL Chi-restraints excluded: chain D residue 967 LEU Chi-restraints excluded: chain D residue 1041 SER Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1072 ASN Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 292 GLN Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain F residue 662 ASP Chi-restraints excluded: chain F residue 670 ILE Chi-restraints excluded: chain F residue 710 MET Chi-restraints excluded: chain F residue 815 GLU Chi-restraints excluded: chain F residue 885 MET Chi-restraints excluded: chain F residue 913 ILE Chi-restraints excluded: chain F residue 1049 HIS Chi-restraints excluded: chain F residue 1072 ASN Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 291 SER Chi-restraints excluded: chain G residue 324 MET Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 375 LYS Chi-restraints excluded: chain H residue 766 TRP Chi-restraints excluded: chain H residue 829 THR Chi-restraints excluded: chain H residue 867 THR Chi-restraints excluded: chain H residue 913 ILE Chi-restraints excluded: chain H residue 1051 THR Chi-restraints excluded: chain H residue 1072 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 190 optimal weight: 0.9980 chunk 195 optimal weight: 0.8980 chunk 242 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 275 optimal weight: 1.9990 chunk 428 optimal weight: 0.3980 chunk 157 optimal weight: 2.9990 chunk 397 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 260 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 35 HIS O 35 HIS P 6 GLN ** P 27DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 ASN B1073 GLN C 255 HIS D 707 HIS ** D 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 HIS F 965 GLN H 824 ASN H 977 HIS ** H1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.049067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.040720 restraints weight = 117085.245| |-----------------------------------------------------------------------------| r_work (start): 0.2518 rms_B_bonded: 2.76 r_work: 0.2408 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2290 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.6435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 35540 Z= 0.145 Angle : 0.638 9.248 48380 Z= 0.327 Chirality : 0.045 0.304 5596 Planarity : 0.004 0.046 6064 Dihedral : 6.287 71.033 5392 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.47 % Allowed : 15.30 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.45 (0.12), residues: 4424 helix: 1.02 (0.34), residues: 296 sheet: 0.52 (0.13), residues: 1640 loop : -1.06 (0.12), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 84 TYR 0.016 0.001 TYR F1018 PHE 0.022 0.001 PHE H 900 TRP 0.010 0.001 TRP K 47 HIS 0.006 0.001 HIS P 27D Details of bonding type rmsd covalent geometry : bond 0.00337 (35408) covalent geometry : angle 0.62459 (48084) SS BOND : bond 0.00535 ( 100) SS BOND : angle 1.41004 ( 200) hydrogen bonds : bond 0.03435 ( 1013) hydrogen bonds : angle 5.10630 ( 2592) link_ALPHA1-3 : bond 0.01600 ( 4) link_ALPHA1-3 : angle 3.34229 ( 12) link_ALPHA1-6 : bond 0.00433 ( 4) link_ALPHA1-6 : angle 1.59193 ( 12) link_BETA1-4 : bond 0.00544 ( 12) link_BETA1-4 : angle 2.31721 ( 36) link_NAG-ASN : bond 0.00242 ( 12) link_NAG-ASN : angle 2.12630 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 604 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 3 GLN cc_start: 0.8954 (mt0) cc_final: 0.8433 (mp10) REVERT: I 19 ARG cc_start: 0.8956 (ttt180) cc_final: 0.8736 (ttm170) REVERT: I 47 TRP cc_start: 0.9363 (t60) cc_final: 0.9154 (t60) REVERT: I 82 MET cc_start: 0.8407 (mmm) cc_final: 0.7997 (mmm) REVERT: I 91 TYR cc_start: 0.9181 (m-80) cc_final: 0.8857 (m-80) REVERT: I 105 GLN cc_start: 0.9167 (tp40) cc_final: 0.8926 (mm-40) REVERT: J 11 LEU cc_start: 0.9422 (tp) cc_final: 0.9103 (tt) REVERT: J 22 SER cc_start: 0.9334 (m) cc_final: 0.9008 (p) REVERT: J 74 LYS cc_start: 0.9462 (mtmm) cc_final: 0.8878 (mppt) REVERT: K 13 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7492 (mm110) REVERT: K 43 LYS cc_start: 0.8932 (mmtm) cc_final: 0.8724 (mmtm) REVERT: L 22 SER cc_start: 0.9133 (m) cc_final: 0.8857 (p) REVERT: L 72 THR cc_start: 0.9393 (m) cc_final: 0.9136 (p) REVERT: L 104 GLU cc_start: 0.7661 (pp20) cc_final: 0.7444 (tt0) REVERT: M 6 GLU cc_start: 0.8536 (pm20) cc_final: 0.8331 (pm20) REVERT: M 96 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8880 (tt) REVERT: N 38 GLN cc_start: 0.9076 (tt0) cc_final: 0.8814 (tt0) REVERT: N 72 THR cc_start: 0.9310 (m) cc_final: 0.8817 (p) REVERT: N 87 TYR cc_start: 0.9122 (m-80) cc_final: 0.8913 (m-80) REVERT: N 103 VAL cc_start: 0.9361 (t) cc_final: 0.8973 (m) REVERT: O 19 ARG cc_start: 0.8898 (ttm170) cc_final: 0.8380 (ttm-80) REVERT: O 97 ILE cc_start: 0.9523 (OUTLIER) cc_final: 0.9317 (pp) REVERT: P 11 LEU cc_start: 0.9397 (tp) cc_final: 0.9149 (tt) REVERT: P 34 ASP cc_start: 0.9042 (m-30) cc_final: 0.8799 (m-30) REVERT: P 72 THR cc_start: 0.9461 (m) cc_final: 0.9002 (p) REVERT: P 74 LYS cc_start: 0.9458 (OUTLIER) cc_final: 0.9002 (mtmm) REVERT: P 89 MET cc_start: 0.9101 (ttp) cc_final: 0.8785 (ttp) REVERT: P 103 VAL cc_start: 0.9400 (t) cc_final: 0.9132 (m) REVERT: A 38 GLN cc_start: 0.9272 (mp10) cc_final: 0.9024 (mp10) REVERT: A 84 ARG cc_start: 0.8825 (ttp80) cc_final: 0.7939 (ttp-170) REVERT: A 101 GLU cc_start: 0.9012 (pt0) cc_final: 0.8586 (pm20) REVERT: A 355 ASP cc_start: 0.9262 (OUTLIER) cc_final: 0.8978 (m-30) REVERT: B 933 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8876 (tm-30) REVERT: B 955 ASN cc_start: 0.8919 (t0) cc_final: 0.8467 (t0) REVERT: C 84 ARG cc_start: 0.8985 (ttp-170) cc_final: 0.8091 (ttp-110) REVERT: C 101 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8204 (pm20) REVERT: C 237 THR cc_start: 0.8792 (m) cc_final: 0.8461 (p) REVERT: C 408 CYS cc_start: 0.8408 (m) cc_final: 0.8185 (m) REVERT: D 833 LYS cc_start: 0.8867 (mmtm) cc_final: 0.8500 (tmtt) REVERT: D 842 LYS cc_start: 0.8993 (mmmm) cc_final: 0.8766 (mmmm) REVERT: D 844 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8648 (mp10) REVERT: D 933 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8384 (tm-30) REVERT: E 237 THR cc_start: 0.8986 (m) cc_final: 0.8688 (p) REVERT: E 408 CYS cc_start: 0.8329 (m) cc_final: 0.8114 (m) REVERT: F 833 LYS cc_start: 0.8924 (mmtm) cc_final: 0.8722 (mmtt) REVERT: F 885 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8941 (mtm) REVERT: F 933 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8621 (tm-30) REVERT: F 951 ARG cc_start: 0.9000 (mtm-85) cc_final: 0.8668 (mtm-85) REVERT: F 952 ASP cc_start: 0.8942 (t0) cc_final: 0.8721 (t0) REVERT: G 101 GLU cc_start: 0.8646 (tt0) cc_final: 0.8341 (pm20) REVERT: G 156 MET cc_start: 0.8926 (mmp) cc_final: 0.8038 (mmt) REVERT: G 415 ARG cc_start: 0.7725 (mtt180) cc_final: 0.6502 (mtt180) REVERT: H 672 MET cc_start: 0.8532 (mmm) cc_final: 0.8113 (mtp) REVERT: H 933 GLU cc_start: 0.9281 (pt0) cc_final: 0.9019 (pp20) REVERT: H 951 ARG cc_start: 0.9130 (mtm-85) cc_final: 0.8641 (mtm-85) REVERT: H 955 ASN cc_start: 0.8827 (t0) cc_final: 0.8505 (t0) outliers start: 135 outliers final: 97 residues processed: 692 average time/residue: 0.2489 time to fit residues: 270.4229 Evaluate side-chains 683 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 578 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain K residue 13 GLN Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 19 ARG Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 74 LYS Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain B residue 679 ASP Chi-restraints excluded: chain B residue 766 TRP Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 1001 GLU Chi-restraints excluded: chain B residue 1072 ASN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain D residue 670 ILE Chi-restraints excluded: chain D residue 766 TRP Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 844 GLN Chi-restraints excluded: chain D residue 913 ILE Chi-restraints excluded: chain D residue 957 VAL Chi-restraints excluded: chain D residue 1041 SER Chi-restraints excluded: chain D residue 1072 ASN Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain F residue 662 ASP Chi-restraints excluded: chain F residue 670 ILE Chi-restraints excluded: chain F residue 815 GLU Chi-restraints excluded: chain F residue 885 MET Chi-restraints excluded: chain F residue 913 ILE Chi-restraints excluded: chain F residue 1049 HIS Chi-restraints excluded: chain F residue 1072 ASN Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain G residue 324 MET Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 375 LYS Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain H residue 766 TRP Chi-restraints excluded: chain H residue 829 THR Chi-restraints excluded: chain H residue 835 CYS Chi-restraints excluded: chain H residue 867 THR Chi-restraints excluded: chain H residue 913 ILE Chi-restraints excluded: chain H residue 962 VAL Chi-restraints excluded: chain H residue 1051 THR Chi-restraints excluded: chain H residue 1072 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 231 optimal weight: 7.9990 chunk 232 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 252 optimal weight: 0.7980 chunk 290 optimal weight: 0.4980 chunk 366 optimal weight: 4.9990 chunk 378 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 35 HIS ** P 27DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 ASN B1049 HIS B1073 GLN D 707 HIS D 965 GLN E 103 GLN F 965 GLN H 824 ASN H 977 HIS ** H1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.047996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.039706 restraints weight = 118108.058| |-----------------------------------------------------------------------------| r_work (start): 0.2484 rms_B_bonded: 2.74 r_work: 0.2374 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2255 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.6618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 35540 Z= 0.222 Angle : 0.693 9.038 48380 Z= 0.357 Chirality : 0.047 0.203 5596 Planarity : 0.005 0.072 6064 Dihedral : 6.253 49.234 5392 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.14 % Allowed : 15.07 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.48 (0.12), residues: 4424 helix: 0.95 (0.34), residues: 296 sheet: 0.57 (0.13), residues: 1672 loop : -1.14 (0.12), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 429 TYR 0.027 0.002 TYR J 87 PHE 0.041 0.002 PHE I 67 TRP 0.012 0.001 TRP K 47 HIS 0.009 0.001 HIS O 100G Details of bonding type rmsd covalent geometry : bond 0.00524 (35408) covalent geometry : angle 0.67921 (48084) SS BOND : bond 0.00570 ( 100) SS BOND : angle 1.56540 ( 200) hydrogen bonds : bond 0.03897 ( 1013) hydrogen bonds : angle 5.16889 ( 2592) link_ALPHA1-3 : bond 0.01303 ( 4) link_ALPHA1-3 : angle 3.56751 ( 12) link_ALPHA1-6 : bond 0.00340 ( 4) link_ALPHA1-6 : angle 1.65800 ( 12) link_BETA1-4 : bond 0.00537 ( 12) link_BETA1-4 : angle 2.44146 ( 36) link_NAG-ASN : bond 0.00372 ( 12) link_NAG-ASN : angle 1.96590 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 595 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 3 GLN cc_start: 0.8962 (mt0) cc_final: 0.8426 (mp10) REVERT: I 19 ARG cc_start: 0.8991 (ttt180) cc_final: 0.8647 (ttm170) REVERT: I 80 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8929 (tt) REVERT: J 11 LEU cc_start: 0.9458 (tp) cc_final: 0.9140 (tt) REVERT: J 22 SER cc_start: 0.9329 (m) cc_final: 0.9014 (p) REVERT: J 89 MET cc_start: 0.9235 (ttp) cc_final: 0.9012 (ttp) REVERT: J 104 GLU cc_start: 0.6500 (tt0) cc_final: 0.6203 (tt0) REVERT: K 13 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7584 (mm110) REVERT: L 22 SER cc_start: 0.9175 (m) cc_final: 0.8931 (p) REVERT: L 72 THR cc_start: 0.9412 (m) cc_final: 0.9138 (p) REVERT: M 96 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8917 (tt) REVERT: M 110 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.8142 (t) REVERT: N 38 GLN cc_start: 0.9061 (tt0) cc_final: 0.8745 (tt0) REVERT: N 103 VAL cc_start: 0.9371 (t) cc_final: 0.8946 (m) REVERT: P 34 ASP cc_start: 0.9112 (m-30) cc_final: 0.8908 (m-30) REVERT: P 61 ARG cc_start: 0.8223 (ptp-170) cc_final: 0.7552 (ptp-170) REVERT: P 72 THR cc_start: 0.9441 (m) cc_final: 0.9015 (p) REVERT: P 74 LYS cc_start: 0.9461 (OUTLIER) cc_final: 0.9048 (mtmm) REVERT: P 89 MET cc_start: 0.9174 (ttp) cc_final: 0.8802 (ttp) REVERT: P 103 VAL cc_start: 0.9397 (t) cc_final: 0.9151 (m) REVERT: A 28 MET cc_start: 0.9396 (mmm) cc_final: 0.8910 (mtp) REVERT: A 68 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8945 (mp) REVERT: A 84 ARG cc_start: 0.8894 (ttp80) cc_final: 0.7881 (ttp-170) REVERT: A 101 GLU cc_start: 0.8983 (pt0) cc_final: 0.8547 (pm20) REVERT: A 237 THR cc_start: 0.8905 (m) cc_final: 0.8581 (p) REVERT: A 304 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.8918 (mtmm) REVERT: B 842 LYS cc_start: 0.9031 (mtpp) cc_final: 0.8818 (mmmm) REVERT: B 933 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8810 (tm-30) REVERT: B 947 ASP cc_start: 0.8048 (p0) cc_final: 0.7795 (p0) REVERT: B 949 ASN cc_start: 0.8516 (m-40) cc_final: 0.8305 (m110) REVERT: B 955 ASN cc_start: 0.8982 (t0) cc_final: 0.8522 (t0) REVERT: C 68 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8989 (mp) REVERT: C 84 ARG cc_start: 0.8989 (ttp-170) cc_final: 0.7912 (ttp-170) REVERT: C 101 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8254 (pm20) REVERT: C 237 THR cc_start: 0.8889 (m) cc_final: 0.8597 (p) REVERT: C 408 CYS cc_start: 0.8443 (m) cc_final: 0.8225 (m) REVERT: D 833 LYS cc_start: 0.8783 (mmtm) cc_final: 0.8475 (tmtt) REVERT: D 842 LYS cc_start: 0.8983 (mmmm) cc_final: 0.8737 (mmmm) REVERT: D 844 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8654 (mp10) REVERT: D 933 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8277 (tm-30) REVERT: E 101 GLU cc_start: 0.8565 (pp20) cc_final: 0.8353 (pp20) REVERT: E 237 THR cc_start: 0.9078 (m) cc_final: 0.8832 (p) REVERT: E 408 CYS cc_start: 0.8382 (m) cc_final: 0.8177 (m) REVERT: F 885 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8888 (mtm) REVERT: F 933 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8624 (tm-30) REVERT: F 951 ARG cc_start: 0.9024 (mtm-85) cc_final: 0.8683 (mtm-85) REVERT: F 952 ASP cc_start: 0.8936 (t0) cc_final: 0.8692 (t0) REVERT: G 68 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9019 (mp) REVERT: G 101 GLU cc_start: 0.8661 (tt0) cc_final: 0.8323 (pm20) REVERT: H 679 ASP cc_start: 0.8599 (t0) cc_final: 0.8235 (t0) REVERT: H 933 GLU cc_start: 0.9268 (pt0) cc_final: 0.9052 (pp20) REVERT: H 951 ARG cc_start: 0.9121 (mtm-85) cc_final: 0.8689 (mtm-85) REVERT: H 955 ASN cc_start: 0.8821 (t0) cc_final: 0.8378 (t0) outliers start: 161 outliers final: 126 residues processed: 699 average time/residue: 0.2391 time to fit residues: 262.8349 Evaluate side-chains 716 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 578 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain K residue 13 GLN Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 19 ARG Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 45 GLN Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 74 LYS Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 679 ASP Chi-restraints excluded: chain B residue 766 TRP Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1072 ASN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain D residue 670 ILE Chi-restraints excluded: chain D residue 766 TRP Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 844 GLN Chi-restraints excluded: chain D residue 913 ILE Chi-restraints excluded: chain D residue 957 VAL Chi-restraints excluded: chain D residue 1016 MET Chi-restraints excluded: chain D residue 1041 SER Chi-restraints excluded: chain D residue 1072 ASN Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain F residue 662 ASP Chi-restraints excluded: chain F residue 673 LYS Chi-restraints excluded: chain F residue 710 MET Chi-restraints excluded: chain F residue 766 TRP Chi-restraints excluded: chain F residue 885 MET Chi-restraints excluded: chain F residue 913 ILE Chi-restraints excluded: chain F residue 1016 MET Chi-restraints excluded: chain F residue 1049 HIS Chi-restraints excluded: chain F residue 1059 LEU Chi-restraints excluded: chain F residue 1072 ASN Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 324 MET Chi-restraints excluded: chain G residue 355 ASP Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 375 LYS Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain H residue 766 TRP Chi-restraints excluded: chain H residue 815 GLU Chi-restraints excluded: chain H residue 829 THR Chi-restraints excluded: chain H residue 835 CYS Chi-restraints excluded: chain H residue 867 THR Chi-restraints excluded: chain H residue 913 ILE Chi-restraints excluded: chain H residue 962 VAL Chi-restraints excluded: chain H residue 1051 THR Chi-restraints excluded: chain H residue 1072 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 38 optimal weight: 2.9990 chunk 401 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 chunk 381 optimal weight: 2.9990 chunk 423 optimal weight: 0.8980 chunk 288 optimal weight: 0.9990 chunk 411 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 156 optimal weight: 0.7980 chunk 313 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 35 HIS ** L 27DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN ** N 27DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN B1073 GLN D 707 HIS E 103 GLN H 824 ASN H 977 HIS ** H1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1049 HIS ** H1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.049285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.040945 restraints weight = 117041.334| |-----------------------------------------------------------------------------| r_work (start): 0.2527 rms_B_bonded: 2.75 r_work: 0.2418 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2300 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.6667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35540 Z= 0.134 Angle : 0.645 10.383 48380 Z= 0.331 Chirality : 0.044 0.203 5596 Planarity : 0.004 0.040 6064 Dihedral : 5.954 51.165 5392 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.32 % Allowed : 16.67 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.43 (0.12), residues: 4424 helix: 1.10 (0.34), residues: 296 sheet: 0.64 (0.13), residues: 1596 loop : -1.10 (0.12), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 429 TYR 0.018 0.001 TYR L 87 PHE 0.027 0.001 PHE I 67 TRP 0.015 0.001 TRP I 47 HIS 0.006 0.001 HIS P 27D Details of bonding type rmsd covalent geometry : bond 0.00312 (35408) covalent geometry : angle 0.63380 (48084) SS BOND : bond 0.00524 ( 100) SS BOND : angle 1.28768 ( 200) hydrogen bonds : bond 0.03279 ( 1013) hydrogen bonds : angle 4.98037 ( 2592) link_ALPHA1-3 : bond 0.01461 ( 4) link_ALPHA1-3 : angle 2.89599 ( 12) link_ALPHA1-6 : bond 0.00302 ( 4) link_ALPHA1-6 : angle 1.61732 ( 12) link_BETA1-4 : bond 0.00562 ( 12) link_BETA1-4 : angle 2.20222 ( 36) link_NAG-ASN : bond 0.00234 ( 12) link_NAG-ASN : angle 2.07635 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 605 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 3 GLN cc_start: 0.8930 (mt0) cc_final: 0.8302 (mp10) REVERT: I 19 ARG cc_start: 0.8976 (ttt180) cc_final: 0.8629 (ttm170) REVERT: I 80 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8726 (tt) REVERT: J 11 LEU cc_start: 0.9467 (tp) cc_final: 0.9149 (tt) REVERT: J 22 SER cc_start: 0.9314 (m) cc_final: 0.8975 (p) REVERT: J 74 LYS cc_start: 0.9488 (mtmm) cc_final: 0.8820 (mmtm) REVERT: K 13 GLN cc_start: 0.8161 (mp10) cc_final: 0.7562 (mm110) REVERT: K 43 LYS cc_start: 0.8931 (mmtm) cc_final: 0.8670 (mmtm) REVERT: L 22 SER cc_start: 0.9161 (m) cc_final: 0.8912 (p) REVERT: L 72 THR cc_start: 0.9387 (m) cc_final: 0.9103 (p) REVERT: M 96 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8674 (tt) REVERT: M 110 THR cc_start: 0.8337 (OUTLIER) cc_final: 0.8122 (t) REVERT: N 38 GLN cc_start: 0.9019 (tt0) cc_final: 0.8722 (tt0) REVERT: N 79 GLU cc_start: 0.8517 (pp20) cc_final: 0.8278 (pp20) REVERT: N 103 VAL cc_start: 0.9355 (t) cc_final: 0.9004 (m) REVERT: O 91 TYR cc_start: 0.8912 (m-80) cc_final: 0.8630 (m-80) REVERT: P 72 THR cc_start: 0.9422 (m) cc_final: 0.8978 (p) REVERT: P 74 LYS cc_start: 0.9443 (ttmm) cc_final: 0.9041 (mtmm) REVERT: P 89 MET cc_start: 0.9112 (ttp) cc_final: 0.8817 (ttp) REVERT: A 68 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8912 (mp) REVERT: A 84 ARG cc_start: 0.8824 (ttp80) cc_final: 0.8001 (ttp-170) REVERT: A 101 GLU cc_start: 0.9025 (pt0) cc_final: 0.8768 (pm20) REVERT: A 103 GLN cc_start: 0.8083 (mp10) cc_final: 0.7178 (mt0) REVERT: A 237 THR cc_start: 0.8863 (m) cc_final: 0.8524 (p) REVERT: B 673 LYS cc_start: 0.9075 (mmmt) cc_final: 0.8824 (mmmt) REVERT: B 933 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8838 (tm-30) REVERT: C 84 ARG cc_start: 0.8963 (ttp-170) cc_final: 0.8082 (ttp-110) REVERT: C 101 GLU cc_start: 0.8565 (tt0) cc_final: 0.8244 (pm20) REVERT: C 237 THR cc_start: 0.8866 (m) cc_final: 0.8571 (p) REVERT: C 408 CYS cc_start: 0.8412 (m) cc_final: 0.8187 (m) REVERT: D 656 MET cc_start: 0.8965 (mmp) cc_final: 0.8473 (mmp) REVERT: D 833 LYS cc_start: 0.8793 (mmtm) cc_final: 0.8541 (tmtt) REVERT: D 933 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8303 (tm-30) REVERT: E 101 GLU cc_start: 0.8550 (pp20) cc_final: 0.8188 (pp20) REVERT: E 237 THR cc_start: 0.9044 (m) cc_final: 0.8788 (p) REVERT: E 353 THR cc_start: 0.9252 (m) cc_final: 0.9016 (p) REVERT: E 408 CYS cc_start: 0.8323 (m) cc_final: 0.8100 (m) REVERT: F 885 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8954 (mtm) REVERT: F 933 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8639 (tm-30) REVERT: F 952 ASP cc_start: 0.8926 (t0) cc_final: 0.8658 (t0) REVERT: F 962 VAL cc_start: 0.8946 (t) cc_final: 0.8671 (p) REVERT: G 101 GLU cc_start: 0.8622 (tt0) cc_final: 0.8274 (pm20) REVERT: G 156 MET cc_start: 0.8875 (mmt) cc_final: 0.7987 (mmt) REVERT: G 415 ARG cc_start: 0.7727 (mtt180) cc_final: 0.6447 (mtt180) REVERT: H 933 GLU cc_start: 0.9298 (pt0) cc_final: 0.9077 (pp20) REVERT: H 955 ASN cc_start: 0.8801 (t0) cc_final: 0.8497 (t0) outliers start: 129 outliers final: 102 residues processed: 691 average time/residue: 0.2385 time to fit residues: 259.7951 Evaluate side-chains 690 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 583 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 401 PHE Chi-restraints excluded: chain B residue 679 ASP Chi-restraints excluded: chain B residue 766 TRP Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1072 ASN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 242 ASN Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain D residue 670 ILE Chi-restraints excluded: chain D residue 679 ASP Chi-restraints excluded: chain D residue 766 TRP Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain D residue 913 ILE Chi-restraints excluded: chain D residue 957 VAL Chi-restraints excluded: chain D residue 1016 MET Chi-restraints excluded: chain D residue 1041 SER Chi-restraints excluded: chain D residue 1072 ASN Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain F residue 673 LYS Chi-restraints excluded: chain F residue 766 TRP Chi-restraints excluded: chain F residue 815 GLU Chi-restraints excluded: chain F residue 885 MET Chi-restraints excluded: chain F residue 913 ILE Chi-restraints excluded: chain F residue 1016 MET Chi-restraints excluded: chain F residue 1049 HIS Chi-restraints excluded: chain F residue 1072 ASN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 324 MET Chi-restraints excluded: chain G residue 375 LYS Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain H residue 766 TRP Chi-restraints excluded: chain H residue 815 GLU Chi-restraints excluded: chain H residue 829 THR Chi-restraints excluded: chain H residue 835 CYS Chi-restraints excluded: chain H residue 913 ILE Chi-restraints excluded: chain H residue 962 VAL Chi-restraints excluded: chain H residue 1051 THR Chi-restraints excluded: chain H residue 1072 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 379 optimal weight: 0.8980 chunk 354 optimal weight: 3.9990 chunk 360 optimal weight: 0.0980 chunk 56 optimal weight: 6.9990 chunk 179 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 364 optimal weight: 1.9990 chunk 279 optimal weight: 0.8980 chunk 332 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 35 HIS ** L 27DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 ASN B 977 HIS B1073 GLN H 824 ASN H 927 GLN H 977 HIS ** H1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1073 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.049818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.041457 restraints weight = 116959.895| |-----------------------------------------------------------------------------| r_work (start): 0.2543 rms_B_bonded: 2.76 r_work: 0.2434 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2316 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.6724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35540 Z= 0.123 Angle : 0.638 10.238 48380 Z= 0.327 Chirality : 0.044 0.209 5596 Planarity : 0.004 0.040 6064 Dihedral : 5.709 50.303 5392 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.01 % Allowed : 17.46 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.23 (0.13), residues: 4424 helix: 1.63 (0.35), residues: 272 sheet: 0.76 (0.13), residues: 1608 loop : -1.00 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 429 TYR 0.025 0.001 TYR L 87 PHE 0.035 0.001 PHE I 67 TRP 0.019 0.001 TRP I 47 HIS 0.006 0.001 HIS P 27D Details of bonding type rmsd covalent geometry : bond 0.00291 (35408) covalent geometry : angle 0.62793 (48084) SS BOND : bond 0.00430 ( 100) SS BOND : angle 1.24473 ( 200) hydrogen bonds : bond 0.03123 ( 1013) hydrogen bonds : angle 4.84951 ( 2592) link_ALPHA1-3 : bond 0.01368 ( 4) link_ALPHA1-3 : angle 2.70121 ( 12) link_ALPHA1-6 : bond 0.00292 ( 4) link_ALPHA1-6 : angle 1.65464 ( 12) link_BETA1-4 : bond 0.00586 ( 12) link_BETA1-4 : angle 2.16236 ( 36) link_NAG-ASN : bond 0.00240 ( 12) link_NAG-ASN : angle 2.03995 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 604 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 3 GLN cc_start: 0.8900 (mt0) cc_final: 0.8399 (mp10) REVERT: I 19 ARG cc_start: 0.8952 (ttt180) cc_final: 0.8685 (ttm170) REVERT: I 80 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8504 (tt) REVERT: J 11 LEU cc_start: 0.9454 (tp) cc_final: 0.9134 (tt) REVERT: J 22 SER cc_start: 0.9291 (m) cc_final: 0.9020 (p) REVERT: J 74 LYS cc_start: 0.9494 (mtmm) cc_final: 0.8856 (mmtm) REVERT: K 13 GLN cc_start: 0.8144 (mp10) cc_final: 0.7549 (mm110) REVERT: K 43 LYS cc_start: 0.8880 (mmtm) cc_final: 0.8627 (mmtm) REVERT: L 22 SER cc_start: 0.9152 (m) cc_final: 0.8930 (p) REVERT: L 33 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8445 (mm) REVERT: L 72 THR cc_start: 0.9359 (m) cc_final: 0.9061 (p) REVERT: M 96 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8699 (tt) REVERT: N 38 GLN cc_start: 0.9008 (tt0) cc_final: 0.8691 (tt0) REVERT: N 74 LYS cc_start: 0.9219 (mtmm) cc_final: 0.8441 (mmtm) REVERT: N 79 GLU cc_start: 0.8531 (pp20) cc_final: 0.8021 (pp20) REVERT: N 81 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8090 (pp20) REVERT: N 87 TYR cc_start: 0.9179 (m-80) cc_final: 0.8869 (m-80) REVERT: N 103 VAL cc_start: 0.9358 (t) cc_final: 0.8993 (m) REVERT: O 91 TYR cc_start: 0.8851 (m-80) cc_final: 0.8570 (m-80) REVERT: P 11 LEU cc_start: 0.9513 (tp) cc_final: 0.9307 (tt) REVERT: P 72 THR cc_start: 0.9412 (m) cc_final: 0.8604 (p) REVERT: P 74 LYS cc_start: 0.9410 (ttmm) cc_final: 0.8921 (mtmm) REVERT: A 28 MET cc_start: 0.9394 (mmm) cc_final: 0.8823 (mtp) REVERT: A 68 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8919 (mp) REVERT: A 84 ARG cc_start: 0.8827 (ttp80) cc_final: 0.8020 (ttp-170) REVERT: A 101 GLU cc_start: 0.9016 (pt0) cc_final: 0.8780 (pm20) REVERT: A 103 GLN cc_start: 0.8065 (mp10) cc_final: 0.7108 (mt0) REVERT: A 237 THR cc_start: 0.8842 (m) cc_final: 0.8511 (p) REVERT: A 355 ASP cc_start: 0.9250 (OUTLIER) cc_final: 0.9035 (m-30) REVERT: B 933 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8844 (tm-30) REVERT: C 68 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8975 (mp) REVERT: C 84 ARG cc_start: 0.8945 (ttp-170) cc_final: 0.8083 (ttp-110) REVERT: C 101 GLU cc_start: 0.8565 (tt0) cc_final: 0.8325 (pm20) REVERT: C 237 THR cc_start: 0.8843 (m) cc_final: 0.8555 (p) REVERT: C 408 CYS cc_start: 0.8401 (m) cc_final: 0.8169 (m) REVERT: D 656 MET cc_start: 0.8926 (mmp) cc_final: 0.8442 (mmp) REVERT: D 833 LYS cc_start: 0.8898 (mmtm) cc_final: 0.8501 (tmtt) REVERT: D 842 LYS cc_start: 0.9092 (mmmm) cc_final: 0.8805 (mmmm) REVERT: D 933 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8323 (tm-30) REVERT: E 84 ARG cc_start: 0.9061 (ptt-90) cc_final: 0.8462 (ptt90) REVERT: E 237 THR cc_start: 0.9060 (m) cc_final: 0.8803 (p) REVERT: E 353 THR cc_start: 0.9247 (m) cc_final: 0.9026 (p) REVERT: E 408 CYS cc_start: 0.8342 (m) cc_final: 0.8119 (m) REVERT: F 885 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8960 (mtm) REVERT: F 933 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8640 (tm-30) REVERT: F 951 ARG cc_start: 0.8938 (mtm-85) cc_final: 0.8654 (mtm-85) REVERT: F 952 ASP cc_start: 0.8894 (t0) cc_final: 0.8606 (t0) REVERT: F 955 ASN cc_start: 0.8862 (t0) cc_final: 0.8538 (t0) REVERT: F 962 VAL cc_start: 0.8904 (t) cc_final: 0.8646 (p) REVERT: G 101 GLU cc_start: 0.8586 (tt0) cc_final: 0.8268 (pm20) REVERT: G 156 MET cc_start: 0.8873 (mmt) cc_final: 0.8007 (mmt) REVERT: G 415 ARG cc_start: 0.7649 (mtt180) cc_final: 0.6437 (mtt180) REVERT: H 679 ASP cc_start: 0.8553 (t0) cc_final: 0.8150 (t0) REVERT: H 955 ASN cc_start: 0.8768 (t0) cc_final: 0.8280 (t0) REVERT: H 1027 ARG cc_start: 0.9261 (tpp-160) cc_final: 0.8986 (mtp85) outliers start: 117 outliers final: 97 residues processed: 676 average time/residue: 0.2413 time to fit residues: 256.8059 Evaluate side-chains 688 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 583 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 679 ASP Chi-restraints excluded: chain B residue 766 TRP Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1072 ASN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 242 ASN Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain D residue 670 ILE Chi-restraints excluded: chain D residue 679 ASP Chi-restraints excluded: chain D residue 766 TRP Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain D residue 913 ILE Chi-restraints excluded: chain D residue 957 VAL Chi-restraints excluded: chain D residue 1016 MET Chi-restraints excluded: chain D residue 1041 SER Chi-restraints excluded: chain D residue 1072 ASN Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain F residue 673 LYS Chi-restraints excluded: chain F residue 766 TRP Chi-restraints excluded: chain F residue 815 GLU Chi-restraints excluded: chain F residue 885 MET Chi-restraints excluded: chain F residue 913 ILE Chi-restraints excluded: chain F residue 1016 MET Chi-restraints excluded: chain F residue 1049 HIS Chi-restraints excluded: chain F residue 1072 ASN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 291 SER Chi-restraints excluded: chain G residue 324 MET Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 375 LYS Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain H residue 766 TRP Chi-restraints excluded: chain H residue 815 GLU Chi-restraints excluded: chain H residue 829 THR Chi-restraints excluded: chain H residue 835 CYS Chi-restraints excluded: chain H residue 913 ILE Chi-restraints excluded: chain H residue 927 GLN Chi-restraints excluded: chain H residue 962 VAL Chi-restraints excluded: chain H residue 1072 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 353 optimal weight: 2.9990 chunk 374 optimal weight: 0.3980 chunk 174 optimal weight: 0.9990 chunk 153 optimal weight: 10.0000 chunk 388 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 310 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 27DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 HIS ** N 27DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 953 HIS H 824 ASN H 977 HIS ** H1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.050290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.041907 restraints weight = 117194.022| |-----------------------------------------------------------------------------| r_work (start): 0.2554 rms_B_bonded: 2.77 r_work: 0.2446 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2329 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.6753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35540 Z= 0.120 Angle : 0.644 12.310 48380 Z= 0.329 Chirality : 0.044 0.236 5596 Planarity : 0.004 0.044 6064 Dihedral : 5.564 48.518 5392 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.75 % Allowed : 18.06 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 4424 helix: 1.72 (0.35), residues: 272 sheet: 0.83 (0.13), residues: 1576 loop : -0.98 (0.12), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 429 TYR 0.021 0.001 TYR L 87 PHE 0.026 0.001 PHE I 67 TRP 0.029 0.001 TRP I 47 HIS 0.006 0.001 HIS J 27D Details of bonding type rmsd covalent geometry : bond 0.00283 (35408) covalent geometry : angle 0.63506 (48084) SS BOND : bond 0.00441 ( 100) SS BOND : angle 1.18332 ( 200) hydrogen bonds : bond 0.03041 ( 1013) hydrogen bonds : angle 4.78888 ( 2592) link_ALPHA1-3 : bond 0.01189 ( 4) link_ALPHA1-3 : angle 2.40765 ( 12) link_ALPHA1-6 : bond 0.00271 ( 4) link_ALPHA1-6 : angle 1.62044 ( 12) link_BETA1-4 : bond 0.00589 ( 12) link_BETA1-4 : angle 2.12705 ( 36) link_NAG-ASN : bond 0.00238 ( 12) link_NAG-ASN : angle 2.01930 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 603 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 3 GLN cc_start: 0.8869 (mt0) cc_final: 0.8377 (mp10) REVERT: I 19 ARG cc_start: 0.8923 (ttt180) cc_final: 0.8574 (ttm170) REVERT: I 80 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8845 (tt) REVERT: J 11 LEU cc_start: 0.9446 (tp) cc_final: 0.9122 (tt) REVERT: J 22 SER cc_start: 0.9294 (m) cc_final: 0.9033 (p) REVERT: J 74 LYS cc_start: 0.9498 (mtmm) cc_final: 0.8831 (mmtm) REVERT: K 13 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7511 (mm110) REVERT: K 43 LYS cc_start: 0.8879 (mmtm) cc_final: 0.8654 (mmtm) REVERT: L 33 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8583 (mm) REVERT: M 19 ARG cc_start: 0.8886 (ttm170) cc_final: 0.8330 (ttm-80) REVERT: M 96 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8668 (tt) REVERT: N 38 GLN cc_start: 0.8947 (tt0) cc_final: 0.8663 (tt0) REVERT: N 74 LYS cc_start: 0.9234 (mtmm) cc_final: 0.8564 (mmtm) REVERT: N 79 GLU cc_start: 0.8537 (pp20) cc_final: 0.8067 (pp20) REVERT: N 81 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8127 (pp20) REVERT: N 103 VAL cc_start: 0.9356 (t) cc_final: 0.8995 (m) REVERT: O 19 ARG cc_start: 0.8773 (ttm170) cc_final: 0.8522 (ttt90) REVERT: O 91 TYR cc_start: 0.8793 (m-80) cc_final: 0.8577 (m-80) REVERT: P 11 LEU cc_start: 0.9529 (tp) cc_final: 0.9315 (tt) REVERT: P 72 THR cc_start: 0.9403 (m) cc_final: 0.8919 (p) REVERT: P 74 LYS cc_start: 0.9398 (ttmm) cc_final: 0.9081 (mtmm) REVERT: A 68 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8890 (mp) REVERT: A 84 ARG cc_start: 0.8815 (ttp80) cc_final: 0.8049 (ttp-170) REVERT: A 101 GLU cc_start: 0.9024 (pt0) cc_final: 0.8767 (pm20) REVERT: A 103 GLN cc_start: 0.8070 (mp10) cc_final: 0.7155 (mt0) REVERT: A 237 THR cc_start: 0.8820 (m) cc_final: 0.8493 (p) REVERT: A 355 ASP cc_start: 0.9221 (OUTLIER) cc_final: 0.9007 (m-30) REVERT: A 397 GLU cc_start: 0.8106 (tp30) cc_final: 0.7731 (tp30) REVERT: B 842 LYS cc_start: 0.8910 (mtpp) cc_final: 0.8585 (mmmt) REVERT: B 933 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8854 (tm-30) REVERT: B 960 ARG cc_start: 0.8133 (ptm160) cc_final: 0.7859 (mtp-110) REVERT: B 964 PHE cc_start: 0.8700 (m-10) cc_final: 0.8495 (m-10) REVERT: C 68 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8965 (mp) REVERT: C 84 ARG cc_start: 0.8936 (ttp-170) cc_final: 0.8086 (ttp-110) REVERT: C 101 GLU cc_start: 0.8522 (tt0) cc_final: 0.8287 (pm20) REVERT: C 237 THR cc_start: 0.8817 (m) cc_final: 0.8526 (p) REVERT: D 656 MET cc_start: 0.8918 (mmp) cc_final: 0.8421 (mmp) REVERT: D 833 LYS cc_start: 0.8909 (mmtm) cc_final: 0.8587 (tmtt) REVERT: D 933 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8225 (tm-30) REVERT: E 101 GLU cc_start: 0.8558 (pp20) cc_final: 0.8145 (pp20) REVERT: E 237 THR cc_start: 0.9061 (m) cc_final: 0.8811 (p) REVERT: E 353 THR cc_start: 0.9245 (m) cc_final: 0.9032 (p) REVERT: F 885 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8952 (mtm) REVERT: F 933 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8648 (tm-30) REVERT: F 951 ARG cc_start: 0.8957 (mtm-85) cc_final: 0.8650 (mtm-85) REVERT: F 952 ASP cc_start: 0.8880 (t0) cc_final: 0.8607 (t0) REVERT: F 955 ASN cc_start: 0.8868 (t0) cc_final: 0.8531 (t0) REVERT: F 962 VAL cc_start: 0.8910 (t) cc_final: 0.8662 (p) REVERT: G 101 GLU cc_start: 0.8605 (tt0) cc_final: 0.8274 (pm20) REVERT: G 156 MET cc_start: 0.8847 (mmt) cc_final: 0.7984 (mmt) REVERT: G 415 ARG cc_start: 0.7620 (mtt180) cc_final: 0.6429 (mtt180) REVERT: H 679 ASP cc_start: 0.8549 (t0) cc_final: 0.8144 (t0) REVERT: H 927 GLN cc_start: 0.8369 (mt0) cc_final: 0.8080 (mt0) REVERT: H 955 ASN cc_start: 0.8730 (t0) cc_final: 0.8243 (t0) REVERT: H 1027 ARG cc_start: 0.9266 (tpp-160) cc_final: 0.9026 (mtp85) outliers start: 107 outliers final: 91 residues processed: 673 average time/residue: 0.2397 time to fit residues: 254.3879 Evaluate side-chains 681 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 582 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain K residue 13 GLN Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 45 GLN Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 401 PHE Chi-restraints excluded: chain B residue 679 ASP Chi-restraints excluded: chain B residue 766 TRP Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1072 ASN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain D residue 670 ILE Chi-restraints excluded: chain D residue 679 ASP Chi-restraints excluded: chain D residue 766 TRP Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain D residue 913 ILE Chi-restraints excluded: chain D residue 1041 SER Chi-restraints excluded: chain D residue 1072 ASN Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain F residue 673 LYS Chi-restraints excluded: chain F residue 815 GLU Chi-restraints excluded: chain F residue 885 MET Chi-restraints excluded: chain F residue 913 ILE Chi-restraints excluded: chain F residue 1016 MET Chi-restraints excluded: chain F residue 1049 HIS Chi-restraints excluded: chain F residue 1072 ASN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 375 LYS Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain H residue 766 TRP Chi-restraints excluded: chain H residue 815 GLU Chi-restraints excluded: chain H residue 829 THR Chi-restraints excluded: chain H residue 835 CYS Chi-restraints excluded: chain H residue 913 ILE Chi-restraints excluded: chain H residue 962 VAL Chi-restraints excluded: chain H residue 1072 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 119 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 287 optimal weight: 0.7980 chunk 219 optimal weight: 6.9990 chunk 419 optimal weight: 0.0470 chunk 271 optimal weight: 3.9990 chunk 280 optimal weight: 3.9990 chunk 409 optimal weight: 7.9990 chunk 225 optimal weight: 0.1980 chunk 178 optimal weight: 3.9990 chunk 231 optimal weight: 6.9990 overall best weight: 1.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 949 ASN B 977 HIS E 103 GLN H 824 ASN H 977 HIS ** H1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.048609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.040323 restraints weight = 116986.648| |-----------------------------------------------------------------------------| r_work (start): 0.2502 rms_B_bonded: 2.74 r_work: 0.2394 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2275 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.6844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 35540 Z= 0.201 Angle : 0.704 13.228 48380 Z= 0.361 Chirality : 0.046 0.280 5596 Planarity : 0.004 0.042 6064 Dihedral : 5.764 48.105 5392 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.88 % Allowed : 18.13 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.34 (0.12), residues: 4424 helix: 1.08 (0.34), residues: 300 sheet: 0.81 (0.13), residues: 1576 loop : -1.10 (0.12), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 429 TYR 0.032 0.002 TYR P 36 PHE 0.027 0.002 PHE H 900 TRP 0.023 0.001 TRP I 47 HIS 0.007 0.001 HIS P 27D Details of bonding type rmsd covalent geometry : bond 0.00475 (35408) covalent geometry : angle 0.69335 (48084) SS BOND : bond 0.00521 ( 100) SS BOND : angle 1.43820 ( 200) hydrogen bonds : bond 0.03659 ( 1013) hydrogen bonds : angle 4.96919 ( 2592) link_ALPHA1-3 : bond 0.00985 ( 4) link_ALPHA1-3 : angle 2.83398 ( 12) link_ALPHA1-6 : bond 0.00141 ( 4) link_ALPHA1-6 : angle 1.70574 ( 12) link_BETA1-4 : bond 0.00493 ( 12) link_BETA1-4 : angle 2.35119 ( 36) link_NAG-ASN : bond 0.00296 ( 12) link_NAG-ASN : angle 1.86153 ( 36) =============================================================================== Job complete usr+sys time: 10246.58 seconds wall clock time: 176 minutes 20.23 seconds (10580.23 seconds total)