Starting phenix.real_space_refine on Thu Mar 5 22:25:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u7k_20672/03_2026/6u7k_20672_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u7k_20672/03_2026/6u7k_20672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6u7k_20672/03_2026/6u7k_20672.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u7k_20672/03_2026/6u7k_20672.map" model { file = "/net/cci-nas-00/data/ceres_data/6u7k_20672/03_2026/6u7k_20672_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u7k_20672/03_2026/6u7k_20672_neut.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.046 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 108 5.16 5 C 16191 2.51 5 N 4029 2.21 5 O 5187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25515 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8139 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 36, 'TRANS': 1027} Chain breaks: 6 Chain: "B" Number of atoms: 8139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8139 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 36, 'TRANS': 1027} Chain breaks: 6 Chain: "C" Number of atoms: 8139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8139 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 36, 'TRANS': 1027} Chain breaks: 6 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 6.28, per 1000 atoms: 0.25 Number of scatterers: 25515 At special positions: 0 Unit cell: (147.275, 155.875, 159.1, 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 108 16.00 O 5187 8.00 N 4029 7.00 C 16191 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 231 " distance=2.02 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 304 " distance=2.06 Simple disulfide: pdb=" SG CYS A 346 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 470 " distance=2.01 Simple disulfide: pdb=" SG CYS A 540 " - pdb=" SG CYS A 586 " distance=2.04 Simple disulfide: pdb=" SG CYS A 569 " - pdb=" SG CYS A 596 " distance=2.01 Simple disulfide: pdb=" SG CYS A 646 " - pdb=" SG CYS A 697 " distance=2.04 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 754 " distance=2.04 Simple disulfide: pdb=" SG CYS A 805 " - pdb=" SG CYS A 827 " distance=2.04 Simple disulfide: pdb=" SG CYS A 810 " - pdb=" SG CYS A 816 " distance=2.04 Simple disulfide: pdb=" SG CYS A 917 " - pdb=" SG CYS A 928 " distance=2.05 Simple disulfide: pdb=" SG CYS A1119 " - pdb=" SG CYS A1130 " distance=1.99 Simple disulfide: pdb=" SG CYS A1170 " - pdb=" SG CYS A1223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 227 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 304 " distance=2.01 Simple disulfide: pdb=" SG CYS B 346 " - pdb=" SG CYS B 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 461 " - pdb=" SG CYS B 470 " distance=2.00 Simple disulfide: pdb=" SG CYS B 540 " - pdb=" SG CYS B 586 " distance=2.04 Simple disulfide: pdb=" SG CYS B 569 " - pdb=" SG CYS B 596 " distance=2.00 Simple disulfide: pdb=" SG CYS B 646 " - pdb=" SG CYS B 697 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 754 " distance=2.00 Simple disulfide: pdb=" SG CYS B 805 " - pdb=" SG CYS B 827 " distance=2.04 Simple disulfide: pdb=" SG CYS B 810 " - pdb=" SG CYS B 816 " distance=2.10 Simple disulfide: pdb=" SG CYS B 917 " - pdb=" SG CYS B 928 " distance=2.05 Simple disulfide: pdb=" SG CYS B1119 " - pdb=" SG CYS B1130 " distance=1.99 Simple disulfide: pdb=" SG CYS B1170 " - pdb=" SG CYS B1223 " distance=2.04 Simple disulfide: pdb=" SG CYS C 227 " - pdb=" SG CYS C 231 " distance=2.02 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 304 " distance=2.02 Simple disulfide: pdb=" SG CYS C 346 " - pdb=" SG CYS C 370 " distance=2.05 Simple disulfide: pdb=" SG CYS C 461 " - pdb=" SG CYS C 470 " distance=2.00 Simple disulfide: pdb=" SG CYS C 540 " - pdb=" SG CYS C 586 " distance=2.04 Simple disulfide: pdb=" SG CYS C 569 " - pdb=" SG CYS C 596 " distance=2.03 Simple disulfide: pdb=" SG CYS C 646 " - pdb=" SG CYS C 697 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 754 " distance=2.03 Simple disulfide: pdb=" SG CYS C 805 " - pdb=" SG CYS C 827 " distance=2.03 Simple disulfide: pdb=" SG CYS C 810 " - pdb=" SG CYS C 816 " distance=2.04 Simple disulfide: pdb=" SG CYS C 917 " - pdb=" SG CYS C 928 " distance=2.01 Simple disulfide: pdb=" SG CYS C1119 " - pdb=" SG CYS C1130 " distance=2.00 Simple disulfide: pdb=" SG CYS C1170 " - pdb=" SG CYS C1223 " distance=2.05 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 Atom "HETATM24769 O5 NAG M 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM24953 O5 NAG R 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM24925 O5 NAG Q 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN I 4 " - " MAN I 5 " " MAN N 4 " - " MAN N 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA I 3 " - " MAN I 4 " " BMA N 3 " - " MAN N 4 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " " BMA I 3 " - " MAN I 6 " " BMA N 3 " - " MAN N 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1401 " - " ASN A 213 " " NAG A1408 " - " ASN A 297 " " NAG A1411 " - " ASN A 341 " " NAG A1412 " - " ASN A 348 " " NAG A1413 " - " ASN A 422 " " NAG A1416 " - " ASN A 553 " " NAG A1417 " - " ASN A 664 " " NAG A1420 " - " ASN A 723 " " NAG A1421 " - " ASN A 740 " " NAG A1422 " - " ASN A 778 " " NAG A1423 " - " ASN A 784 " " NAG A1426 " - " ASN A1006 " " NAG A1427 " - " ASN A1229 " " NAG B1401 " - " ASN B 213 " " NAG B1408 " - " ASN B 297 " " NAG B1411 " - " ASN B 341 " " NAG B1412 " - " ASN B 348 " " NAG B1413 " - " ASN B 422 " " NAG B1416 " - " ASN B 553 " " NAG B1417 " - " ASN B 664 " " NAG B1420 " - " ASN B 723 " " NAG B1421 " - " ASN B 740 " " NAG B1422 " - " ASN B 778 " " NAG B1423 " - " ASN B 784 " " NAG B1426 " - " ASN B1006 " " NAG B1427 " - " ASN B1229 " " NAG C1401 " - " ASN C 213 " " NAG C1408 " - " ASN C 297 " " NAG C1411 " - " ASN C 341 " " NAG C1412 " - " ASN C 348 " " NAG C1413 " - " ASN C 422 " " NAG C1416 " - " ASN C 553 " " NAG C1417 " - " ASN C 664 " " NAG C1420 " - " ASN C 723 " " NAG C1421 " - " ASN C 740 " " NAG C1422 " - " ASN C 778 " " NAG C1423 " - " ASN C 784 " " NAG C1426 " - " ASN C1006 " " NAG C1427 " - " ASN C1229 " " NAG D 1 " - " ASN A 261 " " NAG E 1 " - " ASN A 321 " " NAG F 1 " - " ASN A 511 " " NAG G 1 " - " ASN A 685 " " NAG H 1 " - " ASN A 870 " " NAG I 1 " - " ASN B 261 " " NAG J 1 " - " ASN B 321 " " NAG K 1 " - " ASN B 511 " " NAG L 1 " - " ASN B 685 " " NAG M 1 " - " ASN B 870 " " NAG N 1 " - " ASN C 261 " " NAG O 1 " - " ASN C 321 " " NAG P 1 " - " ASN C 511 " " NAG Q 1 " - " ASN C 685 " " NAG R 1 " - " ASN C 870 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.1 seconds 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5934 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 43 sheets defined 23.8% alpha, 35.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 242 through 246 removed outlier: 4.239A pdb=" N HIS A 246 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 463 through 470 Processing helix chain 'A' and resid 572 through 577 removed outlier: 3.694A pdb=" N ASN A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 811 Processing helix chain 'A' and resid 813 through 821 Processing helix chain 'A' and resid 827 through 849 removed outlier: 4.673A pdb=" N ALA A 833 " --> pdb=" O THR A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 860 removed outlier: 4.696A pdb=" N LEU A 858 " --> pdb=" O GLU A 854 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 876 removed outlier: 4.220A pdb=" N GLY A 876 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 903 removed outlier: 3.640A pdb=" N VAL A 902 " --> pdb=" O LEU A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 933 removed outlier: 3.675A pdb=" N TYR A 931 " --> pdb=" O VAL A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 957 Processing helix chain 'A' and resid 970 through 981 removed outlier: 3.678A pdb=" N ALA A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 981 " --> pdb=" O ALA A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1011 removed outlier: 3.905A pdb=" N SER A 999 " --> pdb=" O LEU A 995 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN A1006 " --> pdb=" O SER A1002 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER A1009 " --> pdb=" O GLY A1005 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A1010 " --> pdb=" O ASN A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1018 Processing helix chain 'A' and resid 1019 through 1024 removed outlier: 3.647A pdb=" N GLY A1024 " --> pdb=" O THR A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1040 Processing helix chain 'A' and resid 1043 through 1052 removed outlier: 3.775A pdb=" N GLN A1052 " --> pdb=" O GLN A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1055 No H-bonds generated for 'chain 'A' and resid 1053 through 1055' Processing helix chain 'A' and resid 1063 through 1068 Processing helix chain 'A' and resid 1072 through 1120 removed outlier: 4.293A pdb=" N VAL A1078 " --> pdb=" O LEU A1074 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A1082 " --> pdb=" O VAL A1078 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A1083 " --> pdb=" O GLN A1079 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A1107 " --> pdb=" O THR A1103 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER A1108 " --> pdb=" O GLU A1104 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A1111 " --> pdb=" O ALA A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1239 removed outlier: 3.823A pdb=" N VAL A1238 " --> pdb=" O GLN A1234 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 removed outlier: 3.692A pdb=" N ALA B 235 " --> pdb=" O THR B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 removed outlier: 4.240A pdb=" N HIS B 246 " --> pdb=" O SER B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 326 removed outlier: 3.509A pdb=" N ILE B 326 " --> pdb=" O THR B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 473 removed outlier: 3.681A pdb=" N LEU B 468 " --> pdb=" O PRO B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 577 removed outlier: 3.654A pdb=" N ASN B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 811 Processing helix chain 'B' and resid 813 through 821 removed outlier: 3.723A pdb=" N GLN B 818 " --> pdb=" O SER B 814 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU B 819 " --> pdb=" O ARG B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 847 removed outlier: 4.632A pdb=" N ALA B 833 " --> pdb=" O THR B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 860 removed outlier: 3.509A pdb=" N GLN B 857 " --> pdb=" O GLU B 853 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU B 858 " --> pdb=" O GLU B 854 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA B 859 " --> pdb=" O ALA B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 876 removed outlier: 4.258A pdb=" N GLY B 876 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 904 removed outlier: 3.990A pdb=" N VAL B 902 " --> pdb=" O LEU B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 919 removed outlier: 3.984A pdb=" N SER B 918 " --> pdb=" O TYR B 914 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASN B 919 " --> pdb=" O LYS B 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 914 through 919' Processing helix chain 'B' and resid 925 through 933 removed outlier: 3.837A pdb=" N TYR B 931 " --> pdb=" O VAL B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 957 Processing helix chain 'B' and resid 970 through 981 removed outlier: 3.510A pdb=" N ALA B 974 " --> pdb=" O PRO B 970 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 976 " --> pdb=" O SER B 972 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR B 981 " --> pdb=" O ALA B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1009 removed outlier: 3.860A pdb=" N SER B1002 " --> pdb=" O GLU B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1018 Processing helix chain 'B' and resid 1019 through 1024 removed outlier: 3.585A pdb=" N GLY B1024 " --> pdb=" O THR B1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1041 Processing helix chain 'B' and resid 1043 through 1052 removed outlier: 3.587A pdb=" N LEU B1049 " --> pdb=" O ALA B1045 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN B1052 " --> pdb=" O GLN B1048 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1070 Processing helix chain 'B' and resid 1072 through 1120 removed outlier: 3.850A pdb=" N ASP B1077 " --> pdb=" O ILE B1073 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL B1078 " --> pdb=" O LEU B1074 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG B1082 " --> pdb=" O VAL B1078 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B1107 " --> pdb=" O THR B1103 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B1108 " --> pdb=" O GLU B1104 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU B1111 " --> pdb=" O ALA B1107 " (cutoff:3.500A) Processing helix chain 'B' and resid 1234 through 1239 removed outlier: 3.825A pdb=" N VAL B1238 " --> pdb=" O GLN B1234 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 326 Processing helix chain 'C' and resid 463 through 472 removed outlier: 3.822A pdb=" N LEU C 468 " --> pdb=" O PRO C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 577 removed outlier: 3.679A pdb=" N ASN C 577 " --> pdb=" O LEU C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 811 Processing helix chain 'C' and resid 813 through 821 Processing helix chain 'C' and resid 825 through 849 removed outlier: 4.351A pdb=" N ALA C 833 " --> pdb=" O THR C 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 860 removed outlier: 4.912A pdb=" N LEU C 858 " --> pdb=" O GLU C 854 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA C 859 " --> pdb=" O ALA C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 876 removed outlier: 4.421A pdb=" N GLY C 876 " --> pdb=" O THR C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 901 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.903A pdb=" N ARG C 916 " --> pdb=" O ASP C 913 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER C 918 " --> pdb=" O LYS C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 933 removed outlier: 4.132A pdb=" N TYR C 931 " --> pdb=" O VAL C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 956 Processing helix chain 'C' and resid 957 through 960 Processing helix chain 'C' and resid 970 through 981 removed outlier: 3.609A pdb=" N ALA C 974 " --> pdb=" O PRO C 970 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 1009 Processing helix chain 'C' and resid 1014 through 1018 Processing helix chain 'C' and resid 1019 through 1024 removed outlier: 3.703A pdb=" N GLY C1024 " --> pdb=" O THR C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1027 through 1042 Processing helix chain 'C' and resid 1043 through 1052 removed outlier: 3.575A pdb=" N GLN C1052 " --> pdb=" O GLN C1048 " (cutoff:3.500A) Processing helix chain 'C' and resid 1063 through 1069 Processing helix chain 'C' and resid 1072 through 1119 removed outlier: 3.524A pdb=" N ASP C1077 " --> pdb=" O ILE C1073 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C1078 " --> pdb=" O LEU C1074 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG C1082 " --> pdb=" O VAL C1078 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA C1107 " --> pdb=" O THR C1103 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER C1108 " --> pdb=" O GLU C1104 " (cutoff:3.500A) Processing helix chain 'C' and resid 1234 through 1239 removed outlier: 3.529A pdb=" N VAL C1238 " --> pdb=" O GLN C1234 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 51 removed outlier: 4.262A pdb=" N TYR A 209 " --> pdb=" O CYS A 227 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR A 223 " --> pdb=" O ASN A 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 181 removed outlier: 3.504A pdb=" N GLY A 75 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 285 removed outlier: 3.544A pdb=" N LEU A 276 " --> pdb=" O ASN A 442 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN A 442 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL A 278 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER A 440 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS A 280 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 438 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A 282 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TRP A 436 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 437 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL A 403 " --> pdb=" O TYR A 410 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 268 through 285 removed outlier: 3.544A pdb=" N LEU A 276 " --> pdb=" O ASN A 442 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN A 442 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL A 278 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER A 440 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS A 280 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 438 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A 282 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TRP A 436 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ASP A 445 " --> pdb=" O TYR A 460 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N TYR A 460 " --> pdb=" O ASP A 445 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A 447 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE A 458 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU A 449 " --> pdb=" O GLN A 456 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 291 through 295 removed outlier: 3.548A pdb=" N GLN A 292 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 418 " --> pdb=" O HIS A 335 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE A 332 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR A 368 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL A 387 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N CYS A 370 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 480 through 485 removed outlier: 3.691A pdb=" N GLY A 712 " --> pdb=" O ALA A 704 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL A 706 " --> pdb=" O ILE A 710 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILE A 710 " --> pdb=" O VAL A 706 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 496 through 499 removed outlier: 4.301A pdb=" N VAL A 691 " --> pdb=" O THR A 663 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU A 681 " --> pdb=" O VAL A 694 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 525 through 533 removed outlier: 4.428A pdb=" N SER A 529 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER A 515 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR A 531 " --> pdb=" O THR A 513 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR A 513 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ILE A 533 " --> pdb=" O ASN A 511 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASN A 511 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 547 " --> pdb=" O SER A 508 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 516 " --> pdb=" O ASN A 553 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR A 616 " --> pdb=" O VAL A 587 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL A 587 " --> pdb=" O TYR A 616 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLN A 618 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE A 585 " --> pdb=" O GLN A 618 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR A 620 " --> pdb=" O SER A 583 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY A 622 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N SER A 581 " --> pdb=" O GLY A 622 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 525 through 533 removed outlier: 4.428A pdb=" N SER A 529 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER A 515 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR A 531 " --> pdb=" O THR A 513 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR A 513 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ILE A 533 " --> pdb=" O ASN A 511 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASN A 511 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 547 " --> pdb=" O SER A 508 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 516 " --> pdb=" O ASN A 553 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LYS A 611 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLY A 602 " --> pdb=" O LYS A 611 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER A 562 " --> pdb=" O TYR A 603 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 744 through 748 Processing sheet with id=AB2, first strand: chain 'A' and resid 778 through 782 Processing sheet with id=AB3, first strand: chain 'A' and resid 785 through 795 removed outlier: 7.071A pdb=" N GLY A1147 " --> pdb=" O ALA A1143 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ALA A1143 " --> pdb=" O GLY A1147 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU A1149 " --> pdb=" O VAL A1141 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL A1141 " --> pdb=" O LEU A1149 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU A1151 " --> pdb=" O SER A1139 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER A1139 " --> pdb=" O LEU A1151 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR A1153 " --> pdb=" O ILE A1137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 801 through 803 Processing sheet with id=AB5, first strand: chain 'A' and resid 1217 through 1220 removed outlier: 4.547A pdb=" N ALA A1176 " --> pdb=" O ILE A1220 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 46 through 49 removed outlier: 4.191A pdb=" N TYR B 209 " --> pdb=" O CYS B 227 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 177 through 181 removed outlier: 3.528A pdb=" N GLY B 162 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 268 through 285 removed outlier: 3.689A pdb=" N LEU B 276 " --> pdb=" O ASN B 442 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN B 442 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL B 278 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER B 440 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N CYS B 280 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 438 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU B 282 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP B 436 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B 403 " --> pdb=" O TYR B 410 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 268 through 285 removed outlier: 3.689A pdb=" N LEU B 276 " --> pdb=" O ASN B 442 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN B 442 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL B 278 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER B 440 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N CYS B 280 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 438 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU B 282 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP B 436 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ASP B 445 " --> pdb=" O TYR B 460 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TYR B 460 " --> pdb=" O ASP B 445 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU B 447 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE B 458 " --> pdb=" O LEU B 447 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU B 449 " --> pdb=" O GLN B 456 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 290 through 295 removed outlier: 6.949A pdb=" N HIS B 335 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL B 419 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL B 333 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE B 332 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TYR B 368 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL B 387 " --> pdb=" O TYR B 368 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N CYS B 370 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 480 through 485 removed outlier: 3.867A pdb=" N GLY B 712 " --> pdb=" O ALA B 704 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 706 " --> pdb=" O ILE B 710 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE B 710 " --> pdb=" O VAL B 706 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 496 through 499 removed outlier: 4.286A pdb=" N VAL B 691 " --> pdb=" O THR B 663 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU B 681 " --> pdb=" O VAL B 694 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 525 through 533 removed outlier: 4.447A pdb=" N SER B 529 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N SER B 515 " --> pdb=" O SER B 529 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR B 531 " --> pdb=" O THR B 513 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR B 513 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE B 533 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN B 511 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 547 " --> pdb=" O SER B 508 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS B 584 " --> pdb=" O THR B 620 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLY B 622 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE B 582 " --> pdb=" O GLY B 622 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 525 through 533 removed outlier: 4.447A pdb=" N SER B 529 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N SER B 515 " --> pdb=" O SER B 529 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR B 531 " --> pdb=" O THR B 513 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR B 513 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE B 533 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN B 511 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 547 " --> pdb=" O SER B 508 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LYS B 611 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLY B 602 " --> pdb=" O LYS B 611 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER B 562 " --> pdb=" O TYR B 603 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 746 through 748 Processing sheet with id=AC7, first strand: chain 'B' and resid 778 through 782 removed outlier: 4.589A pdb=" N LEU B1186 " --> pdb=" O ILE B1166 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 785 through 795 removed outlier: 3.815A pdb=" N PHE B1138 " --> pdb=" O THR B1153 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU B1155 " --> pdb=" O HIS B1136 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS B1136 " --> pdb=" O LEU B1155 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 801 through 803 Processing sheet with id=AD1, first strand: chain 'B' and resid 1217 through 1220 removed outlier: 4.416A pdb=" N ALA B1176 " --> pdb=" O ILE B1220 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B1230 " --> pdb=" O CYS B1170 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 46 through 51 removed outlier: 4.433A pdb=" N TYR C 223 " --> pdb=" O ASN C 213 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 177 through 181 Processing sheet with id=AD4, first strand: chain 'C' and resid 268 through 285 removed outlier: 5.538A pdb=" N LYS C 269 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 450 " --> pdb=" O LYS C 269 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL C 271 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE C 448 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ASN C 273 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ALA C 446 " --> pdb=" O ASN C 273 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 444 " --> pdb=" O PRO C 275 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER C 440 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU C 281 " --> pdb=" O ILE C 438 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE C 438 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ALA C 283 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TRP C 436 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL C 403 " --> pdb=" O TYR C 410 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 268 through 285 removed outlier: 5.538A pdb=" N LYS C 269 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 450 " --> pdb=" O LYS C 269 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL C 271 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE C 448 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ASN C 273 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ALA C 446 " --> pdb=" O ASN C 273 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 444 " --> pdb=" O PRO C 275 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER C 440 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU C 281 " --> pdb=" O ILE C 438 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE C 438 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ALA C 283 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TRP C 436 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ASP C 445 " --> pdb=" O TYR C 460 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N TYR C 460 " --> pdb=" O ASP C 445 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU C 447 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE C 458 " --> pdb=" O LEU C 447 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU C 449 " --> pdb=" O GLN C 456 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 290 through 295 removed outlier: 3.605A pdb=" N GLN C 292 " --> pdb=" O ILE C 421 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N HIS C 335 " --> pdb=" O ASP C 417 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL C 419 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL C 333 " --> pdb=" O VAL C 419 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE C 332 " --> pdb=" O PHE C 344 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TYR C 368 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL C 387 " --> pdb=" O TYR C 368 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N CYS C 370 " --> pdb=" O LEU C 385 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 480 through 485 removed outlier: 3.647A pdb=" N GLY C 712 " --> pdb=" O ALA C 704 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL C 706 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE C 710 " --> pdb=" O VAL C 706 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 496 through 499 removed outlier: 3.511A pdb=" N GLY C 656 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL C 691 " --> pdb=" O THR C 663 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LEU C 681 " --> pdb=" O VAL C 694 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR C 673 " --> pdb=" O LEU C 681 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 525 through 533 removed outlier: 5.440A pdb=" N LEU C 526 " --> pdb=" O GLY C 519 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY C 519 " --> pdb=" O LEU C 526 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ALA C 528 " --> pdb=" O ALA C 517 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA C 517 " --> pdb=" O ALA C 528 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C 510 " --> pdb=" O THR C 549 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N PHE C 551 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE C 512 " --> pdb=" O PHE C 551 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 538 through 540 removed outlier: 5.288A pdb=" N SER C 581 " --> pdb=" O GLY C 622 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY C 622 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR C 620 " --> pdb=" O SER C 583 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE C 585 " --> pdb=" O GLN C 618 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLN C 618 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL C 587 " --> pdb=" O TYR C 616 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR C 616 " --> pdb=" O VAL C 587 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 538 through 540 removed outlier: 5.288A pdb=" N SER C 581 " --> pdb=" O GLY C 622 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY C 622 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR C 620 " --> pdb=" O SER C 583 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE C 585 " --> pdb=" O GLN C 618 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLN C 618 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL C 587 " --> pdb=" O TYR C 616 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR C 616 " --> pdb=" O VAL C 587 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LYS C 611 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLY C 602 " --> pdb=" O LYS C 611 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER C 562 " --> pdb=" O TYR C 603 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 744 through 748 Processing sheet with id=AE4, first strand: chain 'C' and resid 778 through 782 Processing sheet with id=AE5, first strand: chain 'C' and resid 785 through 795 removed outlier: 7.010A pdb=" N GLY C1147 " --> pdb=" O ALA C1143 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ALA C1143 " --> pdb=" O GLY C1147 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU C1149 " --> pdb=" O VAL C1141 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL C1141 " --> pdb=" O LEU C1149 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU C1151 " --> pdb=" O SER C1139 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER C1139 " --> pdb=" O LEU C1151 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR C1153 " --> pdb=" O ILE C1137 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 801 through 803 Processing sheet with id=AE7, first strand: chain 'C' and resid 1217 through 1220 removed outlier: 4.425A pdb=" N ALA C1176 " --> pdb=" O ILE C1220 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2697 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: 6.45 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 183 1.21 - 1.36: 8094 1.36 - 1.51: 8447 1.51 - 1.67: 9151 1.67 - 1.82: 138 Bond restraints: 26013 Sorted by residual: bond pdb=" C ASN A 511 " pdb=" O ASN A 511 " ideal model delta sigma weight residual 1.236 1.056 0.180 1.24e-02 6.50e+03 2.11e+02 bond pdb=" C ASN C 422 " pdb=" O ASN C 422 " ideal model delta sigma weight residual 1.232 1.081 0.151 1.12e-02 7.97e+03 1.81e+02 bond pdb=" C ASN A 422 " pdb=" O ASN A 422 " ideal model delta sigma weight residual 1.232 1.103 0.128 1.01e-02 9.80e+03 1.61e+02 bond pdb=" CA ASN B 422 " pdb=" CB ASN B 422 " ideal model delta sigma weight residual 1.527 1.432 0.096 7.60e-03 1.73e+04 1.58e+02 bond pdb=" C ASN C 511 " pdb=" O ASN C 511 " ideal model delta sigma weight residual 1.235 1.102 0.132 1.18e-02 7.18e+03 1.26e+02 ... (remaining 26008 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.61: 34713 5.61 - 11.22: 629 11.22 - 16.83: 86 16.83 - 22.45: 13 22.45 - 28.06: 4 Bond angle restraints: 35445 Sorted by residual: angle pdb=" N ASN B 723 " pdb=" CA ASN B 723 " pdb=" C ASN B 723 " ideal model delta sigma weight residual 113.20 127.33 -14.13 1.21e+00 6.83e-01 1.36e+02 angle pdb=" N ASN C 723 " pdb=" CA ASN C 723 " pdb=" C ASN C 723 " ideal model delta sigma weight residual 113.18 126.88 -13.70 1.21e+00 6.83e-01 1.28e+02 angle pdb=" N ASN A 723 " pdb=" CA ASN A 723 " pdb=" C ASN A 723 " ideal model delta sigma weight residual 113.02 125.75 -12.73 1.20e+00 6.94e-01 1.13e+02 angle pdb=" N ASN B 348 " pdb=" CA ASN B 348 " pdb=" CB ASN B 348 " ideal model delta sigma weight residual 110.32 92.41 17.91 1.70e+00 3.46e-01 1.11e+02 angle pdb=" N ASN C 685 " pdb=" CA ASN C 685 " pdb=" C ASN C 685 " ideal model delta sigma weight residual 108.20 91.78 16.42 1.71e+00 3.42e-01 9.22e+01 ... (remaining 35440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.12: 15562 24.12 - 48.24: 666 48.24 - 72.35: 113 72.35 - 96.47: 44 96.47 - 120.59: 10 Dihedral angle restraints: 16395 sinusoidal: 7128 harmonic: 9267 Sorted by residual: dihedral pdb=" N ASN B 348 " pdb=" C ASN B 348 " pdb=" CA ASN B 348 " pdb=" CB ASN B 348 " ideal model delta harmonic sigma weight residual 122.80 99.57 23.23 0 2.50e+00 1.60e-01 8.64e+01 dihedral pdb=" N ASN A 213 " pdb=" C ASN A 213 " pdb=" CA ASN A 213 " pdb=" CB ASN A 213 " ideal model delta harmonic sigma weight residual 122.80 145.66 -22.86 0 2.50e+00 1.60e-01 8.36e+01 dihedral pdb=" C ASN A 213 " pdb=" N ASN A 213 " pdb=" CA ASN A 213 " pdb=" CB ASN A 213 " ideal model delta harmonic sigma weight residual -122.60 -145.02 22.42 0 2.50e+00 1.60e-01 8.04e+01 ... (remaining 16392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.868: 4364 0.868 - 1.736: 24 1.736 - 2.605: 14 2.605 - 3.473: 11 3.473 - 4.341: 3 Chirality restraints: 4416 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 0.80 -3.20 2.00e-02 2.50e+03 2.55e+04 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 0.35 -2.75 2.00e-02 2.50e+03 1.90e+04 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.12 -2.28 2.00e-02 2.50e+03 1.30e+04 ... (remaining 4413 not shown) Planarity restraints: 4473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1412 " -0.414 2.00e-02 2.50e+03 3.35e-01 1.40e+03 pdb=" C7 NAG A1412 " 0.119 2.00e-02 2.50e+03 pdb=" C8 NAG A1412 " -0.223 2.00e-02 2.50e+03 pdb=" N2 NAG A1412 " 0.568 2.00e-02 2.50e+03 pdb=" O7 NAG A1412 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1427 " 0.398 2.00e-02 2.50e+03 3.19e-01 1.28e+03 pdb=" C7 NAG B1427 " -0.117 2.00e-02 2.50e+03 pdb=" C8 NAG B1427 " 0.231 2.00e-02 2.50e+03 pdb=" N2 NAG B1427 " -0.533 2.00e-02 2.50e+03 pdb=" O7 NAG B1427 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1401 " 0.368 2.00e-02 2.50e+03 3.15e-01 1.24e+03 pdb=" C7 NAG B1401 " -0.090 2.00e-02 2.50e+03 pdb=" C8 NAG B1401 " 0.052 2.00e-02 2.50e+03 pdb=" N2 NAG B1401 " -0.549 2.00e-02 2.50e+03 pdb=" O7 NAG B1401 " 0.219 2.00e-02 2.50e+03 ... (remaining 4470 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 12 2.05 - 2.76: 2045 2.76 - 3.48: 34642 3.48 - 4.19: 58657 4.19 - 4.90: 103744 Nonbonded interactions: 199100 Sorted by model distance: nonbonded pdb=" OD2 ASP B 431 " pdb=" O6 NAG J 1 " model vdw 1.341 3.040 nonbonded pdb=" OD2 ASP B 431 " pdb=" C6 NAG J 1 " model vdw 1.602 3.440 nonbonded pdb=" OD2 ASP A 431 " pdb=" O6 NAG E 1 " model vdw 1.603 3.040 nonbonded pdb=" OD2 ASP A 431 " pdb=" C6 NAG E 1 " model vdw 1.743 3.440 nonbonded pdb=" OG SER C1139 " pdb=" ND1 HIS C1152 " model vdw 1.826 3.120 ... (remaining 199095 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 5.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.990 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 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 : 0.021 0.551 26136 Z= 1.280 Angle : 2.929 59.102 35766 Z= 1.509 Chirality : 0.273 4.341 4416 Planarity : 0.028 0.335 4419 Dihedral : 14.729 120.591 10344 Min Nonbonded Distance : 1.341 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.66 % Allowed : 5.65 % Favored : 91.68 % Cbeta Deviations : 2.09 % Peptide Plane: Cis-proline : 0.00 % 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: -1.38 (0.13), residues: 3150 helix: -2.24 (0.16), residues: 615 sheet: 0.71 (0.20), residues: 618 loop : -1.01 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG C1210 TYR 0.162 0.025 TYR C 950 PHE 0.074 0.015 PHE B 408 TRP 0.112 0.023 TRP B 165 HIS 0.011 0.004 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.01729 (26013) covalent geometry : angle 2.30103 (35445) SS BOND : bond 0.02131 ( 39) SS BOND : angle 3.18232 ( 78) hydrogen bonds : bond 0.18808 ( 949) hydrogen bonds : angle 8.44496 ( 2697) Misc. bond : bond 0.48420 ( 3) link_ALPHA1-2 : bond 0.01634 ( 3) link_ALPHA1-2 : angle 4.93180 ( 9) link_ALPHA1-3 : bond 0.00321 ( 3) link_ALPHA1-3 : angle 3.41045 ( 9) link_ALPHA1-6 : bond 0.01887 ( 3) link_ALPHA1-6 : angle 7.08211 ( 9) link_BETA1-4 : bond 0.02778 ( 18) link_BETA1-4 : angle 8.33417 ( 54) link_NAG-ASN : bond 0.22802 ( 54) link_NAG-ASN : angle 26.51914 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 489 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 HIS cc_start: 0.7496 (m-70) cc_final: 0.7011 (m-70) REVERT: A 290 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8326 (pt) REVERT: A 322 ASP cc_start: 0.7563 (t0) cc_final: 0.7268 (t0) REVERT: A 583 SER cc_start: 0.8680 (t) cc_final: 0.8257 (p) REVERT: A 679 GLN cc_start: 0.7546 (tt0) cc_final: 0.7182 (tp40) REVERT: A 737 ASP cc_start: 0.7684 (t0) cc_final: 0.7396 (t0) REVERT: A 745 VAL cc_start: 0.8814 (m) cc_final: 0.8586 (t) REVERT: A 867 ASP cc_start: 0.7338 (t70) cc_final: 0.6785 (t0) REVERT: A 933 SER cc_start: 0.8642 (m) cc_final: 0.8177 (p) REVERT: A 935 VAL cc_start: 0.9000 (p) cc_final: 0.8542 (m) REVERT: A 994 GLN cc_start: 0.7514 (mm-40) cc_final: 0.7140 (mm110) REVERT: A 1068 TYR cc_start: 0.8403 (m-80) cc_final: 0.7989 (m-80) REVERT: A 1135 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6776 (mm-30) REVERT: A 1175 ILE cc_start: 0.8031 (pt) cc_final: 0.6700 (pt) REVERT: B 209 TYR cc_start: 0.7811 (m-80) cc_final: 0.7534 (m-10) REVERT: B 234 TYR cc_start: 0.7574 (t80) cc_final: 0.7247 (t80) REVERT: B 450 VAL cc_start: 0.8433 (t) cc_final: 0.8200 (m) REVERT: B 566 ASP cc_start: 0.7464 (t0) cc_final: 0.7209 (t0) REVERT: B 578 ASP cc_start: 0.7790 (t0) cc_final: 0.7340 (t70) REVERT: B 583 SER cc_start: 0.8626 (t) cc_final: 0.8308 (p) REVERT: B 588 SER cc_start: 0.8505 (t) cc_final: 0.8130 (t) REVERT: B 599 ASP cc_start: 0.7441 (m-30) cc_final: 0.7223 (m-30) REVERT: B 635 ILE cc_start: 0.8855 (mm) cc_final: 0.8651 (mt) REVERT: B 641 MET cc_start: 0.8200 (mtm) cc_final: 0.7964 (mtt) REVERT: B 809 VAL cc_start: 0.8504 (t) cc_final: 0.8168 (m) REVERT: B 815 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8106 (tpp-160) REVERT: B 851 ILE cc_start: 0.8459 (mp) cc_final: 0.8234 (mm) REVERT: B 867 ASP cc_start: 0.7695 (t0) cc_final: 0.7212 (t0) REVERT: B 913 ASP cc_start: 0.7904 (p0) cc_final: 0.7589 (p0) REVERT: B 933 SER cc_start: 0.8617 (m) cc_final: 0.8262 (p) REVERT: B 994 GLN cc_start: 0.7592 (tm-30) cc_final: 0.7166 (tp40) REVERT: B 1135 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6782 (mm-30) REVERT: C 450 VAL cc_start: 0.8232 (t) cc_final: 0.8009 (m) REVERT: C 568 ASN cc_start: 0.7641 (t160) cc_final: 0.7410 (t0) REVERT: C 578 ASP cc_start: 0.7446 (t70) cc_final: 0.6998 (t0) REVERT: C 583 SER cc_start: 0.8809 (t) cc_final: 0.8608 (p) REVERT: C 867 ASP cc_start: 0.7435 (t70) cc_final: 0.6991 (t0) REVERT: C 994 GLN cc_start: 0.7062 (mm-40) cc_final: 0.6677 (mm-40) REVERT: C 1007 ILE cc_start: 0.7831 (pt) cc_final: 0.7599 (mm) REVERT: C 1041 SER cc_start: 0.8073 (m) cc_final: 0.7872 (t) REVERT: C 1065 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.7132 (t0) REVERT: C 1135 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6991 (mm-30) outliers start: 73 outliers final: 32 residues processed: 547 average time/residue: 0.1620 time to fit residues: 143.4589 Evaluate side-chains 351 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 316 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 1145 PRO Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 341 ASN Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 723 ASN Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 1145 PRO Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 723 ASN Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1065 ASP Chi-restraints excluded: chain C residue 1154 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 507 HIS A 707 ASN A 813 ASN A 873 ASN A 919 ASN A1040 ASN A1136 HIS B 292 GLN B 298 HIS B 507 HIS B 534 ASN B1136 HIS ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 HIS C 507 HIS C 568 ASN C 707 ASN C 822 GLN C1136 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.111060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.091352 restraints weight = 39214.467| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.49 r_work: 0.3052 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 26136 Z= 0.215 Angle : 1.040 22.741 35766 Z= 0.463 Chirality : 0.065 1.337 4416 Planarity : 0.005 0.063 4419 Dihedral : 11.332 172.084 5150 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.06 % Allowed : 9.23 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.64 (0.14), residues: 3150 helix: -0.28 (0.19), residues: 630 sheet: 0.37 (0.18), residues: 711 loop : -0.78 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 311 TYR 0.028 0.002 TYR B 369 PHE 0.025 0.002 PHE B 371 TRP 0.010 0.002 TRP B 256 HIS 0.004 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00495 (26013) covalent geometry : angle 0.92215 (35445) SS BOND : bond 0.00721 ( 39) SS BOND : angle 2.64639 ( 78) hydrogen bonds : bond 0.04529 ( 949) hydrogen bonds : angle 5.85352 ( 2697) Misc. bond : bond 0.00275 ( 3) link_ALPHA1-2 : bond 0.00494 ( 3) link_ALPHA1-2 : angle 1.63020 ( 9) link_ALPHA1-3 : bond 0.00476 ( 3) link_ALPHA1-3 : angle 2.36201 ( 9) link_ALPHA1-6 : bond 0.01299 ( 3) link_ALPHA1-6 : angle 1.33458 ( 9) link_BETA1-4 : bond 0.00506 ( 18) link_BETA1-4 : angle 2.82304 ( 54) link_NAG-ASN : bond 0.00950 ( 54) link_NAG-ASN : angle 6.80606 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 358 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7200 (m-80) cc_final: 0.6863 (m-80) REVERT: A 179 HIS cc_start: 0.7692 (m-70) cc_final: 0.7082 (m-70) REVERT: A 180 PHE cc_start: 0.7718 (m-80) cc_final: 0.7428 (m-80) REVERT: A 679 GLN cc_start: 0.8126 (tt0) cc_final: 0.7450 (mm110) REVERT: A 737 ASP cc_start: 0.8391 (t0) cc_final: 0.7821 (t0) REVERT: A 867 ASP cc_start: 0.8194 (t70) cc_final: 0.7598 (t0) REVERT: A 1027 THR cc_start: 0.8815 (t) cc_final: 0.8584 (t) REVERT: A 1037 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7664 (tp30) REVERT: A 1049 LEU cc_start: 0.8182 (tp) cc_final: 0.7970 (tt) REVERT: A 1068 TYR cc_start: 0.8717 (m-80) cc_final: 0.8258 (m-80) REVERT: A 1175 ILE cc_start: 0.7683 (pt) cc_final: 0.7434 (pt) REVERT: B 176 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6910 (mtpp) REVERT: B 178 TYR cc_start: 0.7460 (m-10) cc_final: 0.7223 (m-10) REVERT: B 179 HIS cc_start: 0.7739 (m-70) cc_final: 0.7475 (m-70) REVERT: B 201 MET cc_start: 0.8294 (mmp) cc_final: 0.7659 (mmm) REVERT: B 284 ILE cc_start: 0.8049 (mm) cc_final: 0.7528 (mt) REVERT: B 450 VAL cc_start: 0.8600 (t) cc_final: 0.8329 (m) REVERT: B 547 THR cc_start: 0.8621 (m) cc_final: 0.8380 (p) REVERT: B 566 ASP cc_start: 0.8176 (t0) cc_final: 0.7875 (t0) REVERT: B 578 ASP cc_start: 0.8330 (t0) cc_final: 0.7691 (t70) REVERT: B 581 SER cc_start: 0.8642 (m) cc_final: 0.8383 (p) REVERT: B 583 SER cc_start: 0.8840 (t) cc_final: 0.8446 (p) REVERT: B 588 SER cc_start: 0.8934 (t) cc_final: 0.8686 (t) REVERT: B 635 ILE cc_start: 0.9131 (mm) cc_final: 0.8865 (mt) REVERT: B 701 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7559 (mt-10) REVERT: B 737 ASP cc_start: 0.8169 (t0) cc_final: 0.7887 (t0) REVERT: B 756 SER cc_start: 0.8988 (m) cc_final: 0.8682 (t) REVERT: B 815 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.7207 (ttp-170) REVERT: B 867 ASP cc_start: 0.8462 (t0) cc_final: 0.7988 (t0) REVERT: B 913 ASP cc_start: 0.8390 (p0) cc_final: 0.7967 (p0) REVERT: B 933 SER cc_start: 0.8722 (m) cc_final: 0.8403 (p) REVERT: B 1041 SER cc_start: 0.8753 (m) cc_final: 0.8532 (t) REVERT: B 1068 TYR cc_start: 0.8723 (m-80) cc_final: 0.8469 (m-80) REVERT: B 1135 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7714 (mm-30) REVERT: C 179 HIS cc_start: 0.7928 (OUTLIER) cc_final: 0.7286 (p90) REVERT: C 211 MET cc_start: 0.7318 (mtp) cc_final: 0.7084 (mtt) REVERT: C 284 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7778 (mt) REVERT: C 578 ASP cc_start: 0.8092 (t70) cc_final: 0.7599 (t0) REVERT: C 588 SER cc_start: 0.8792 (t) cc_final: 0.8590 (t) REVERT: C 675 SER cc_start: 0.8676 (OUTLIER) cc_final: 0.8416 (p) REVERT: C 743 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7443 (pm20) REVERT: C 787 MET cc_start: 0.8952 (mtt) cc_final: 0.8380 (mtt) REVERT: C 867 ASP cc_start: 0.8377 (t70) cc_final: 0.7771 (t0) REVERT: C 922 SER cc_start: 0.9140 (t) cc_final: 0.8882 (p) REVERT: C 1023 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8218 (mtpt) REVERT: C 1065 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7614 (t0) outliers start: 84 outliers final: 45 residues processed: 427 average time/residue: 0.1601 time to fit residues: 111.6244 Evaluate side-chains 361 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 309 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 1203 SER Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 596 CYS Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 953 SER Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1023 LYS Chi-restraints excluded: chain C residue 1065 ASP Chi-restraints excluded: chain C residue 1222 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 30 optimal weight: 0.9990 chunk 273 optimal weight: 0.5980 chunk 314 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 267 optimal weight: 0.8980 chunk 306 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 275 optimal weight: 0.2980 chunk 213 optimal weight: 0.4980 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS A 426 HIS ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 813 ASN A1048 GLN A1162 ASN B 534 ASN B1146 GLN C 298 HIS C 534 ASN C 822 GLN C 994 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.111032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.091320 restraints weight = 39402.374| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.50 r_work: 0.3050 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 26136 Z= 0.171 Angle : 0.853 19.582 35766 Z= 0.388 Chirality : 0.056 0.770 4416 Planarity : 0.005 0.191 4419 Dihedral : 9.781 64.093 5115 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.65 % Allowed : 10.25 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.33 (0.14), residues: 3150 helix: 0.72 (0.21), residues: 612 sheet: 0.09 (0.19), residues: 648 loop : -0.62 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 311 TYR 0.015 0.001 TYR A 181 PHE 0.016 0.002 PHE A 344 TRP 0.007 0.001 TRP B 256 HIS 0.004 0.001 HIS B1136 Details of bonding type rmsd covalent geometry : bond 0.00396 (26013) covalent geometry : angle 0.75873 (35445) SS BOND : bond 0.00576 ( 39) SS BOND : angle 2.67996 ( 78) hydrogen bonds : bond 0.03976 ( 949) hydrogen bonds : angle 5.39910 ( 2697) Misc. bond : bond 0.00830 ( 3) link_ALPHA1-2 : bond 0.00472 ( 3) link_ALPHA1-2 : angle 2.09024 ( 9) link_ALPHA1-3 : bond 0.00572 ( 3) link_ALPHA1-3 : angle 2.10301 ( 9) link_ALPHA1-6 : bond 0.01083 ( 3) link_ALPHA1-6 : angle 1.31730 ( 9) link_BETA1-4 : bond 0.00421 ( 18) link_BETA1-4 : angle 1.99058 ( 54) link_NAG-ASN : bond 0.00664 ( 54) link_NAG-ASN : angle 5.42930 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 352 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7270 (m-80) cc_final: 0.6886 (m-80) REVERT: A 179 HIS cc_start: 0.7781 (m-70) cc_final: 0.7230 (m-70) REVERT: A 679 GLN cc_start: 0.8248 (tt0) cc_final: 0.7650 (mm110) REVERT: A 737 ASP cc_start: 0.8424 (t0) cc_final: 0.8020 (t0) REVERT: A 841 GLU cc_start: 0.8460 (tp30) cc_final: 0.8258 (mm-30) REVERT: A 867 ASP cc_start: 0.8233 (t70) cc_final: 0.7614 (t0) REVERT: A 911 ASP cc_start: 0.7459 (p0) cc_final: 0.7259 (p0) REVERT: A 1037 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7713 (tp30) REVERT: A 1049 LEU cc_start: 0.8213 (tp) cc_final: 0.7972 (tp) REVERT: A 1175 ILE cc_start: 0.7874 (pt) cc_final: 0.7661 (pt) REVERT: B 176 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6944 (mtpp) REVERT: B 178 TYR cc_start: 0.7568 (m-10) cc_final: 0.7296 (m-80) REVERT: B 180 PHE cc_start: 0.7632 (m-80) cc_final: 0.7299 (m-80) REVERT: B 181 TYR cc_start: 0.7740 (t80) cc_final: 0.7496 (t80) REVERT: B 244 ASN cc_start: 0.7929 (m-40) cc_final: 0.7308 (t0) REVERT: B 284 ILE cc_start: 0.8155 (mm) cc_final: 0.7756 (mt) REVERT: B 450 VAL cc_start: 0.8614 (t) cc_final: 0.8323 (m) REVERT: B 547 THR cc_start: 0.8614 (m) cc_final: 0.8245 (p) REVERT: B 566 ASP cc_start: 0.8182 (t0) cc_final: 0.7880 (t0) REVERT: B 578 ASP cc_start: 0.8385 (t0) cc_final: 0.7772 (t70) REVERT: B 581 SER cc_start: 0.8628 (m) cc_final: 0.8346 (p) REVERT: B 583 SER cc_start: 0.8883 (t) cc_final: 0.8503 (p) REVERT: B 588 SER cc_start: 0.8954 (t) cc_final: 0.8715 (t) REVERT: B 743 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7584 (pm20) REVERT: B 756 SER cc_start: 0.9129 (m) cc_final: 0.8816 (t) REVERT: B 815 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.7066 (ttp-170) REVERT: B 854 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8514 (pt0) REVERT: B 867 ASP cc_start: 0.8435 (t0) cc_final: 0.7959 (t0) REVERT: B 913 ASP cc_start: 0.8374 (p0) cc_final: 0.8068 (p0) REVERT: B 994 GLN cc_start: 0.7755 (tm-30) cc_final: 0.7151 (tp40) REVERT: B 1027 THR cc_start: 0.8906 (t) cc_final: 0.8660 (t) REVERT: B 1041 SER cc_start: 0.8756 (m) cc_final: 0.8544 (t) REVERT: B 1159 ASP cc_start: 0.8162 (m-30) cc_final: 0.7899 (m-30) REVERT: C 179 HIS cc_start: 0.7854 (OUTLIER) cc_final: 0.7308 (p90) REVERT: C 211 MET cc_start: 0.7443 (mtp) cc_final: 0.7193 (mtt) REVERT: C 284 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7913 (mt) REVERT: C 487 ARG cc_start: 0.8177 (mmm-85) cc_final: 0.7866 (mtm180) REVERT: C 578 ASP cc_start: 0.8215 (t70) cc_final: 0.7664 (t70) REVERT: C 737 ASP cc_start: 0.8356 (t0) cc_final: 0.8021 (t0) REVERT: C 743 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7448 (pm20) REVERT: C 787 MET cc_start: 0.8875 (mtt) cc_final: 0.8427 (mtt) REVERT: C 867 ASP cc_start: 0.8362 (t70) cc_final: 0.7821 (t0) REVERT: C 1027 THR cc_start: 0.8719 (t) cc_final: 0.8488 (t) outliers start: 100 outliers final: 61 residues processed: 432 average time/residue: 0.1548 time to fit residues: 110.2824 Evaluate side-chains 377 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 311 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain A residue 569 CYS Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 848 MET Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 596 CYS Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 936 MET Chi-restraints excluded: chain C residue 937 VAL Chi-restraints excluded: chain C residue 953 SER Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1222 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 54 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 188 optimal weight: 0.5980 chunk 279 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS A 319 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1146 GLN C 298 HIS C 305 ASN C 426 HIS C 822 GLN C 994 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.088684 restraints weight = 39383.307| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.52 r_work: 0.3010 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 26136 Z= 0.281 Angle : 0.859 18.006 35766 Z= 0.399 Chirality : 0.056 0.510 4416 Planarity : 0.004 0.049 4419 Dihedral : 9.725 176.997 5109 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.90 % Allowed : 11.67 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.49 (0.14), residues: 3150 helix: 0.83 (0.22), residues: 612 sheet: -0.46 (0.18), residues: 723 loop : -0.63 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 311 TYR 0.024 0.002 TYR B1068 PHE 0.029 0.002 PHE A 344 TRP 0.009 0.002 TRP B 256 HIS 0.006 0.001 HIS B1136 Details of bonding type rmsd covalent geometry : bond 0.00688 (26013) covalent geometry : angle 0.77937 (35445) SS BOND : bond 0.00642 ( 39) SS BOND : angle 2.75177 ( 78) hydrogen bonds : bond 0.04171 ( 949) hydrogen bonds : angle 5.36017 ( 2697) Misc. bond : bond 0.00335 ( 3) link_ALPHA1-2 : bond 0.01027 ( 3) link_ALPHA1-2 : angle 1.38610 ( 9) link_ALPHA1-3 : bond 0.00529 ( 3) link_ALPHA1-3 : angle 2.54517 ( 9) link_ALPHA1-6 : bond 0.01029 ( 3) link_ALPHA1-6 : angle 1.35132 ( 9) link_BETA1-4 : bond 0.00427 ( 18) link_BETA1-4 : angle 2.00611 ( 54) link_NAG-ASN : bond 0.00661 ( 54) link_NAG-ASN : angle 4.93956 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 334 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7439 (m-80) cc_final: 0.6982 (m-80) REVERT: A 179 HIS cc_start: 0.7871 (m-70) cc_final: 0.7302 (m-70) REVERT: A 180 PHE cc_start: 0.7792 (m-80) cc_final: 0.7575 (m-80) REVERT: A 476 ASP cc_start: 0.8570 (p0) cc_final: 0.8344 (p0) REVERT: A 679 GLN cc_start: 0.8168 (tt0) cc_final: 0.7568 (mm110) REVERT: A 737 ASP cc_start: 0.8465 (t0) cc_final: 0.8024 (t0) REVERT: A 867 ASP cc_start: 0.8224 (t70) cc_final: 0.7573 (t0) REVERT: A 922 SER cc_start: 0.9252 (t) cc_final: 0.8918 (p) REVERT: A 1049 LEU cc_start: 0.8188 (tp) cc_final: 0.7911 (tp) REVERT: B 176 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7123 (mtpp) REVERT: B 180 PHE cc_start: 0.7752 (m-80) cc_final: 0.7372 (m-80) REVERT: B 201 MET cc_start: 0.8160 (mmp) cc_final: 0.7695 (mmm) REVERT: B 210 TYR cc_start: 0.8355 (m-80) cc_final: 0.7820 (m-80) REVERT: B 244 ASN cc_start: 0.7847 (m-40) cc_final: 0.7257 (t0) REVERT: B 450 VAL cc_start: 0.8644 (t) cc_final: 0.8410 (m) REVERT: B 566 ASP cc_start: 0.8172 (t0) cc_final: 0.7863 (t0) REVERT: B 578 ASP cc_start: 0.8378 (t0) cc_final: 0.7762 (t70) REVERT: B 581 SER cc_start: 0.8694 (m) cc_final: 0.8429 (p) REVERT: B 583 SER cc_start: 0.8839 (t) cc_final: 0.8361 (p) REVERT: B 588 SER cc_start: 0.8963 (t) cc_final: 0.8716 (t) REVERT: B 599 ASP cc_start: 0.8022 (m-30) cc_final: 0.7796 (m-30) REVERT: B 756 SER cc_start: 0.9112 (m) cc_final: 0.8876 (t) REVERT: B 854 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8511 (pt0) REVERT: B 867 ASP cc_start: 0.8431 (t0) cc_final: 0.7896 (t0) REVERT: B 913 ASP cc_start: 0.8475 (p0) cc_final: 0.8091 (p0) REVERT: B 994 GLN cc_start: 0.7721 (tm-30) cc_final: 0.7150 (tp40) REVERT: B 1027 THR cc_start: 0.8763 (t) cc_final: 0.8562 (t) REVERT: B 1159 ASP cc_start: 0.8196 (m-30) cc_final: 0.7892 (m-30) REVERT: C 179 HIS cc_start: 0.7907 (OUTLIER) cc_final: 0.7377 (p90) REVERT: C 182 LEU cc_start: 0.7044 (mt) cc_final: 0.6832 (mt) REVERT: C 211 MET cc_start: 0.7466 (mtp) cc_final: 0.7090 (mtp) REVERT: C 263 SER cc_start: 0.8859 (p) cc_final: 0.8630 (t) REVERT: C 383 LYS cc_start: 0.8061 (mttt) cc_final: 0.7834 (mtpt) REVERT: C 487 ARG cc_start: 0.8173 (mmm-85) cc_final: 0.7875 (mtm180) REVERT: C 567 SER cc_start: 0.8609 (m) cc_final: 0.8379 (p) REVERT: C 574 GLN cc_start: 0.8400 (pm20) cc_final: 0.8177 (pm20) REVERT: C 578 ASP cc_start: 0.8293 (t70) cc_final: 0.7687 (t70) REVERT: C 737 ASP cc_start: 0.8472 (t0) cc_final: 0.8105 (t0) REVERT: C 743 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7455 (pm20) REVERT: C 867 ASP cc_start: 0.8334 (t70) cc_final: 0.7765 (t0) REVERT: C 922 SER cc_start: 0.9227 (t) cc_final: 0.8954 (p) REVERT: C 1041 SER cc_start: 0.8238 (t) cc_final: 0.7898 (p) outliers start: 107 outliers final: 83 residues processed: 422 average time/residue: 0.1563 time to fit residues: 108.7357 Evaluate side-chains 394 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 308 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain A residue 569 CYS Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 848 MET Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1034 LYS Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1203 SER Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 596 CYS Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 936 MET Chi-restraints excluded: chain C residue 937 VAL Chi-restraints excluded: chain C residue 953 SER Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1137 ILE Chi-restraints excluded: chain C residue 1222 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 29 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 315 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 211 optimal weight: 0.7980 chunk 162 optimal weight: 0.6980 chunk 238 optimal weight: 0.5980 chunk 237 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1146 GLN B1162 ASN C 298 HIS C 305 ASN C 822 GLN C 873 ASN C 992 ASN C1146 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.110129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.090357 restraints weight = 39134.513| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.51 r_work: 0.3035 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 26136 Z= 0.183 Angle : 0.760 18.219 35766 Z= 0.354 Chirality : 0.052 0.504 4416 Planarity : 0.004 0.095 4419 Dihedral : 8.762 59.441 5100 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.79 % Allowed : 12.98 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.15), residues: 3150 helix: 1.04 (0.22), residues: 615 sheet: -0.54 (0.19), residues: 684 loop : -0.62 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 311 TYR 0.018 0.001 TYR B1068 PHE 0.018 0.002 PHE A 344 TRP 0.006 0.001 TRP C 436 HIS 0.003 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00440 (26013) covalent geometry : angle 0.68526 (35445) SS BOND : bond 0.00640 ( 39) SS BOND : angle 2.57992 ( 78) hydrogen bonds : bond 0.03688 ( 949) hydrogen bonds : angle 5.18898 ( 2697) Misc. bond : bond 0.00316 ( 3) link_ALPHA1-2 : bond 0.00970 ( 3) link_ALPHA1-2 : angle 2.57908 ( 9) link_ALPHA1-3 : bond 0.00646 ( 3) link_ALPHA1-3 : angle 1.90043 ( 9) link_ALPHA1-6 : bond 0.01040 ( 3) link_ALPHA1-6 : angle 1.41127 ( 9) link_BETA1-4 : bond 0.00359 ( 18) link_BETA1-4 : angle 1.88676 ( 54) link_NAG-ASN : bond 0.00597 ( 54) link_NAG-ASN : angle 4.44927 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 337 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7358 (m-80) cc_final: 0.6967 (m-80) REVERT: A 179 HIS cc_start: 0.7829 (m-70) cc_final: 0.7288 (m-70) REVERT: A 476 ASP cc_start: 0.8559 (p0) cc_final: 0.8312 (p0) REVERT: A 599 ASP cc_start: 0.8047 (m-30) cc_final: 0.7798 (m-30) REVERT: A 642 THR cc_start: 0.8880 (m) cc_final: 0.8608 (p) REVERT: A 679 GLN cc_start: 0.8258 (tt0) cc_final: 0.7673 (mm110) REVERT: A 805 CYS cc_start: 0.8046 (t) cc_final: 0.7753 (t) REVERT: A 867 ASP cc_start: 0.8244 (t70) cc_final: 0.7585 (t0) REVERT: A 922 SER cc_start: 0.9247 (t) cc_final: 0.8935 (p) REVERT: A 1049 LEU cc_start: 0.8173 (tp) cc_final: 0.7910 (tp) REVERT: B 176 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.7144 (mtpp) REVERT: B 180 PHE cc_start: 0.7793 (m-80) cc_final: 0.7574 (m-80) REVERT: B 181 TYR cc_start: 0.8052 (t80) cc_final: 0.7769 (t80) REVERT: B 201 MET cc_start: 0.8174 (mmp) cc_final: 0.7704 (mmm) REVERT: B 210 TYR cc_start: 0.8344 (m-80) cc_final: 0.7648 (m-80) REVERT: B 244 ASN cc_start: 0.7843 (m-40) cc_final: 0.7273 (t0) REVERT: B 284 ILE cc_start: 0.8212 (mm) cc_final: 0.7923 (mt) REVERT: B 450 VAL cc_start: 0.8644 (t) cc_final: 0.8412 (m) REVERT: B 566 ASP cc_start: 0.8167 (t0) cc_final: 0.7878 (t0) REVERT: B 578 ASP cc_start: 0.8411 (t0) cc_final: 0.7762 (t70) REVERT: B 581 SER cc_start: 0.8620 (m) cc_final: 0.8331 (p) REVERT: B 583 SER cc_start: 0.8867 (t) cc_final: 0.8418 (p) REVERT: B 588 SER cc_start: 0.8958 (t) cc_final: 0.8728 (t) REVERT: B 599 ASP cc_start: 0.8000 (m-30) cc_final: 0.7766 (m-30) REVERT: B 638 VAL cc_start: 0.8658 (OUTLIER) cc_final: 0.8457 (p) REVERT: B 641 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8360 (mtp) REVERT: B 756 SER cc_start: 0.9188 (m) cc_final: 0.8924 (t) REVERT: B 854 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8486 (pt0) REVERT: B 867 ASP cc_start: 0.8423 (t0) cc_final: 0.7907 (t0) REVERT: B 913 ASP cc_start: 0.8427 (p0) cc_final: 0.8110 (p0) REVERT: B 994 GLN cc_start: 0.7747 (tm-30) cc_final: 0.7193 (tp40) REVERT: B 1159 ASP cc_start: 0.8170 (m-30) cc_final: 0.7857 (m-30) REVERT: C 182 LEU cc_start: 0.7130 (mt) cc_final: 0.6926 (mt) REVERT: C 211 MET cc_start: 0.7423 (mtp) cc_final: 0.7109 (mtp) REVERT: C 263 SER cc_start: 0.8829 (p) cc_final: 0.8623 (t) REVERT: C 383 LYS cc_start: 0.8085 (mttt) cc_final: 0.7879 (mtpt) REVERT: C 487 ARG cc_start: 0.8155 (mmm-85) cc_final: 0.7891 (mtm180) REVERT: C 566 ASP cc_start: 0.8366 (t0) cc_final: 0.8101 (t0) REVERT: C 578 ASP cc_start: 0.8302 (t70) cc_final: 0.7679 (t70) REVERT: C 586 CYS cc_start: 0.7409 (m) cc_final: 0.7175 (m) REVERT: C 737 ASP cc_start: 0.8511 (t0) cc_final: 0.8218 (t0) REVERT: C 743 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7380 (pm20) REVERT: C 787 MET cc_start: 0.8852 (mtt) cc_final: 0.8369 (mtt) REVERT: C 867 ASP cc_start: 0.8252 (t70) cc_final: 0.7657 (t0) REVERT: C 922 SER cc_start: 0.9147 (t) cc_final: 0.8876 (p) REVERT: C 1041 SER cc_start: 0.8251 (t) cc_final: 0.7940 (p) outliers start: 104 outliers final: 72 residues processed: 421 average time/residue: 0.1580 time to fit residues: 109.8581 Evaluate side-chains 385 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 309 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain A residue 569 CYS Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 641 MET Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1034 LYS Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1154 VAL Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 540 CYS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 936 MET Chi-restraints excluded: chain C residue 937 VAL Chi-restraints excluded: chain C residue 953 SER Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1222 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 304 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 292 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 238 optimal weight: 1.9990 chunk 254 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 256 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 813 ASN B 707 ASN B1146 GLN C 298 HIS C 822 GLN C1048 GLN C1146 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.110162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.090295 restraints weight = 39216.480| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.53 r_work: 0.3036 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 26136 Z= 0.188 Angle : 0.747 17.693 35766 Z= 0.350 Chirality : 0.051 0.492 4416 Planarity : 0.004 0.044 4419 Dihedral : 8.333 59.774 5100 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.70 % Rotamer: Outliers : 3.98 % Allowed : 13.64 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.15), residues: 3150 helix: 1.19 (0.22), residues: 615 sheet: -0.63 (0.19), residues: 684 loop : -0.61 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1109 TYR 0.022 0.001 TYR A 400 PHE 0.019 0.002 PHE A 344 TRP 0.005 0.001 TRP C 436 HIS 0.004 0.001 HIS B1136 Details of bonding type rmsd covalent geometry : bond 0.00455 (26013) covalent geometry : angle 0.67932 (35445) SS BOND : bond 0.00661 ( 39) SS BOND : angle 2.46931 ( 78) hydrogen bonds : bond 0.03616 ( 949) hydrogen bonds : angle 5.13912 ( 2697) Misc. bond : bond 0.00631 ( 3) link_ALPHA1-2 : bond 0.01283 ( 3) link_ALPHA1-2 : angle 1.49217 ( 9) link_ALPHA1-3 : bond 0.00805 ( 3) link_ALPHA1-3 : angle 1.66802 ( 9) link_ALPHA1-6 : bond 0.01037 ( 3) link_ALPHA1-6 : angle 1.28150 ( 9) link_BETA1-4 : bond 0.00342 ( 18) link_BETA1-4 : angle 1.89369 ( 54) link_NAG-ASN : bond 0.00606 ( 54) link_NAG-ASN : angle 4.21353 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 322 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7361 (m-80) cc_final: 0.6933 (m-80) REVERT: A 179 HIS cc_start: 0.7885 (OUTLIER) cc_final: 0.7316 (m-70) REVERT: A 599 ASP cc_start: 0.8096 (m-30) cc_final: 0.7862 (m-30) REVERT: A 679 GLN cc_start: 0.8154 (tt0) cc_final: 0.7544 (mm110) REVERT: A 867 ASP cc_start: 0.8240 (t70) cc_final: 0.7547 (t0) REVERT: A 922 SER cc_start: 0.9248 (t) cc_final: 0.8930 (p) REVERT: A 1049 LEU cc_start: 0.8124 (tp) cc_final: 0.7870 (tp) REVERT: A 1066 ASP cc_start: 0.8383 (t0) cc_final: 0.8011 (t0) REVERT: B 176 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6958 (mtpp) REVERT: B 180 PHE cc_start: 0.7755 (m-80) cc_final: 0.7553 (m-80) REVERT: B 244 ASN cc_start: 0.7825 (m-40) cc_final: 0.7253 (t0) REVERT: B 284 ILE cc_start: 0.8145 (mm) cc_final: 0.7867 (mt) REVERT: B 450 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8339 (m) REVERT: B 566 ASP cc_start: 0.8174 (t0) cc_final: 0.7886 (t0) REVERT: B 578 ASP cc_start: 0.8476 (t0) cc_final: 0.7761 (t70) REVERT: B 581 SER cc_start: 0.8625 (m) cc_final: 0.8311 (p) REVERT: B 588 SER cc_start: 0.8965 (t) cc_final: 0.8733 (t) REVERT: B 599 ASP cc_start: 0.7984 (m-30) cc_final: 0.7741 (m-30) REVERT: B 641 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8470 (mtp) REVERT: B 756 SER cc_start: 0.9208 (m) cc_final: 0.8917 (t) REVERT: B 854 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8502 (pt0) REVERT: B 867 ASP cc_start: 0.8451 (t0) cc_final: 0.7911 (t0) REVERT: B 913 ASP cc_start: 0.8416 (p0) cc_final: 0.8076 (p0) REVERT: B 994 GLN cc_start: 0.7712 (tm-30) cc_final: 0.7156 (tp40) REVERT: B 1159 ASP cc_start: 0.8190 (m-30) cc_final: 0.7838 (m-30) REVERT: C 263 SER cc_start: 0.8809 (p) cc_final: 0.8593 (t) REVERT: C 277 LEU cc_start: 0.8501 (tp) cc_final: 0.8299 (tp) REVERT: C 487 ARG cc_start: 0.8134 (mmm-85) cc_final: 0.7868 (mtm180) REVERT: C 566 ASP cc_start: 0.8355 (t0) cc_final: 0.8088 (t0) REVERT: C 574 GLN cc_start: 0.8614 (pm20) cc_final: 0.8222 (mp10) REVERT: C 578 ASP cc_start: 0.8294 (t70) cc_final: 0.7601 (t70) REVERT: C 737 ASP cc_start: 0.8523 (t0) cc_final: 0.8195 (t0) REVERT: C 743 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7319 (pm20) REVERT: C 867 ASP cc_start: 0.8256 (t70) cc_final: 0.7637 (t0) REVERT: C 922 SER cc_start: 0.9256 (t) cc_final: 0.8993 (p) REVERT: C 1041 SER cc_start: 0.8300 (t) cc_final: 0.7935 (p) outliers start: 109 outliers final: 85 residues processed: 410 average time/residue: 0.1523 time to fit residues: 103.4721 Evaluate side-chains 397 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 307 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1034 LYS Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 641 MET Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1034 LYS Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1203 SER Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 540 CYS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 596 CYS Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 936 MET Chi-restraints excluded: chain C residue 937 VAL Chi-restraints excluded: chain C residue 953 SER Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1137 ILE Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1222 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 134 optimal weight: 0.4980 chunk 254 optimal weight: 0.5980 chunk 303 optimal weight: 0.8980 chunk 308 optimal weight: 0.9980 chunk 295 optimal weight: 0.4980 chunk 160 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 211 optimal weight: 0.7980 chunk 228 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 813 ASN A1048 GLN B1146 GLN C 298 HIS C 822 GLN C1042 GLN C1048 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.110754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.091408 restraints weight = 38973.569| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.41 r_work: 0.3056 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 26136 Z= 0.169 Angle : 0.704 17.352 35766 Z= 0.333 Chirality : 0.049 0.486 4416 Planarity : 0.004 0.046 4419 Dihedral : 7.808 58.881 5100 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.89 % Favored : 97.08 % Rotamer: Outliers : 3.87 % Allowed : 14.55 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.15), residues: 3150 helix: 1.19 (0.22), residues: 630 sheet: -0.55 (0.19), residues: 675 loop : -0.56 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 393 TYR 0.020 0.001 TYR A 400 PHE 0.023 0.001 PHE C 344 TRP 0.005 0.001 TRP B 165 HIS 0.003 0.001 HIS C 298 Details of bonding type rmsd covalent geometry : bond 0.00406 (26013) covalent geometry : angle 0.63952 (35445) SS BOND : bond 0.00647 ( 39) SS BOND : angle 2.33820 ( 78) hydrogen bonds : bond 0.03433 ( 949) hydrogen bonds : angle 5.04400 ( 2697) Misc. bond : bond 0.00235 ( 3) link_ALPHA1-2 : bond 0.00874 ( 3) link_ALPHA1-2 : angle 1.53088 ( 9) link_ALPHA1-3 : bond 0.00786 ( 3) link_ALPHA1-3 : angle 1.78649 ( 9) link_ALPHA1-6 : bond 0.01088 ( 3) link_ALPHA1-6 : angle 1.24310 ( 9) link_BETA1-4 : bond 0.00340 ( 18) link_BETA1-4 : angle 1.80543 ( 54) link_NAG-ASN : bond 0.00666 ( 54) link_NAG-ASN : angle 3.99209 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 329 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7435 (m-80) cc_final: 0.7063 (m-80) REVERT: A 179 HIS cc_start: 0.7778 (OUTLIER) cc_final: 0.7240 (m-70) REVERT: A 244 ASN cc_start: 0.7765 (m-40) cc_final: 0.7056 (t0) REVERT: A 297 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7616 (t0) REVERT: A 599 ASP cc_start: 0.8026 (m-30) cc_final: 0.7772 (m-30) REVERT: A 679 GLN cc_start: 0.8184 (tt0) cc_final: 0.7618 (mm110) REVERT: A 867 ASP cc_start: 0.8212 (t70) cc_final: 0.7533 (t0) REVERT: A 922 SER cc_start: 0.9219 (t) cc_final: 0.8919 (p) REVERT: A 1049 LEU cc_start: 0.8203 (tp) cc_final: 0.7960 (tp) REVERT: A 1066 ASP cc_start: 0.8400 (t0) cc_final: 0.8016 (t0) REVERT: B 176 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.7075 (mtpp) REVERT: B 180 PHE cc_start: 0.7722 (m-80) cc_final: 0.7521 (m-80) REVERT: B 201 MET cc_start: 0.8082 (mmp) cc_final: 0.7623 (mmm) REVERT: B 244 ASN cc_start: 0.7754 (m-40) cc_final: 0.7304 (t160) REVERT: B 284 ILE cc_start: 0.8199 (mm) cc_final: 0.7943 (mt) REVERT: B 450 VAL cc_start: 0.8628 (t) cc_final: 0.8391 (m) REVERT: B 566 ASP cc_start: 0.8179 (t0) cc_final: 0.7902 (t0) REVERT: B 578 ASP cc_start: 0.8465 (t0) cc_final: 0.7760 (t70) REVERT: B 581 SER cc_start: 0.8623 (m) cc_final: 0.8337 (p) REVERT: B 588 SER cc_start: 0.8944 (t) cc_final: 0.8725 (t) REVERT: B 591 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8566 (tt) REVERT: B 599 ASP cc_start: 0.7948 (m-30) cc_final: 0.7708 (m-30) REVERT: B 638 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.8485 (p) REVERT: B 641 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8422 (mtp) REVERT: B 756 SER cc_start: 0.9246 (m) cc_final: 0.9036 (t) REVERT: B 854 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8471 (pt0) REVERT: B 867 ASP cc_start: 0.8391 (t0) cc_final: 0.7853 (t0) REVERT: B 913 ASP cc_start: 0.8333 (p0) cc_final: 0.8029 (p0) REVERT: B 994 GLN cc_start: 0.7700 (tm-30) cc_final: 0.7129 (tp40) REVERT: B 1174 GLU cc_start: 0.8269 (tp30) cc_final: 0.7968 (tt0) REVERT: C 211 MET cc_start: 0.7311 (mtp) cc_final: 0.7100 (mtp) REVERT: C 263 SER cc_start: 0.8737 (p) cc_final: 0.8434 (t) REVERT: C 277 LEU cc_start: 0.8589 (tp) cc_final: 0.8379 (tp) REVERT: C 487 ARG cc_start: 0.8139 (mmm-85) cc_final: 0.7860 (mtm180) REVERT: C 566 ASP cc_start: 0.8335 (t0) cc_final: 0.8099 (t0) REVERT: C 574 GLN cc_start: 0.8668 (pm20) cc_final: 0.8465 (mp10) REVERT: C 578 ASP cc_start: 0.8288 (t70) cc_final: 0.7584 (t70) REVERT: C 737 ASP cc_start: 0.8530 (t0) cc_final: 0.8235 (t0) REVERT: C 743 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7385 (pm20) REVERT: C 867 ASP cc_start: 0.8225 (t70) cc_final: 0.7617 (t0) REVERT: C 922 SER cc_start: 0.9244 (t) cc_final: 0.8969 (p) REVERT: C 1037 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7279 (tt0) REVERT: C 1041 SER cc_start: 0.8317 (t) cc_final: 0.8037 (p) outliers start: 106 outliers final: 78 residues processed: 415 average time/residue: 0.1459 time to fit residues: 100.8135 Evaluate side-chains 389 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 304 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 641 MET Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1154 VAL Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 540 CYS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 641 MET Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 936 MET Chi-restraints excluded: chain C residue 953 SER Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1137 ILE Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1222 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 97 optimal weight: 0.6980 chunk 205 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 148 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 250 optimal weight: 0.9980 chunk 297 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 272 optimal weight: 0.8980 chunk 280 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 813 ASN B 873 ASN B1146 GLN C 298 HIS C 822 GLN C1125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.110048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.090407 restraints weight = 39159.287| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.47 r_work: 0.3046 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 26136 Z= 0.203 Angle : 0.722 16.932 35766 Z= 0.342 Chirality : 0.051 0.511 4416 Planarity : 0.004 0.049 4419 Dihedral : 7.740 59.607 5100 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.30 % Favored : 96.67 % Rotamer: Outliers : 3.87 % Allowed : 14.73 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.15), residues: 3150 helix: 1.17 (0.22), residues: 624 sheet: -0.62 (0.19), residues: 693 loop : -0.61 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 393 TYR 0.020 0.001 TYR B1068 PHE 0.022 0.002 PHE B 344 TRP 0.005 0.001 TRP A 436 HIS 0.005 0.001 HIS B1136 Details of bonding type rmsd covalent geometry : bond 0.00495 (26013) covalent geometry : angle 0.65557 (35445) SS BOND : bond 0.00595 ( 39) SS BOND : angle 2.54428 ( 78) hydrogen bonds : bond 0.03559 ( 949) hydrogen bonds : angle 5.05758 ( 2697) Misc. bond : bond 0.00230 ( 3) link_ALPHA1-2 : bond 0.00814 ( 3) link_ALPHA1-2 : angle 1.51261 ( 9) link_ALPHA1-3 : bond 0.00728 ( 3) link_ALPHA1-3 : angle 1.87609 ( 9) link_ALPHA1-6 : bond 0.01030 ( 3) link_ALPHA1-6 : angle 1.24379 ( 9) link_BETA1-4 : bond 0.00346 ( 18) link_BETA1-4 : angle 1.82138 ( 54) link_NAG-ASN : bond 0.00552 ( 54) link_NAG-ASN : angle 4.04357 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 308 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7437 (m-80) cc_final: 0.7052 (m-80) REVERT: A 179 HIS cc_start: 0.7787 (OUTLIER) cc_final: 0.7312 (m-70) REVERT: A 244 ASN cc_start: 0.7800 (m-40) cc_final: 0.7080 (t0) REVERT: A 297 ASN cc_start: 0.8084 (OUTLIER) cc_final: 0.7619 (t0) REVERT: A 679 GLN cc_start: 0.8178 (tt0) cc_final: 0.7610 (mm110) REVERT: A 867 ASP cc_start: 0.8203 (t70) cc_final: 0.7511 (t0) REVERT: A 922 SER cc_start: 0.9221 (t) cc_final: 0.8911 (p) REVERT: A 1023 LYS cc_start: 0.8469 (mtpt) cc_final: 0.8175 (mttm) REVERT: A 1049 LEU cc_start: 0.8196 (tp) cc_final: 0.7944 (tp) REVERT: A 1066 ASP cc_start: 0.8394 (t0) cc_final: 0.8040 (t0) REVERT: B 201 MET cc_start: 0.8065 (mmp) cc_final: 0.7623 (mmm) REVERT: B 244 ASN cc_start: 0.7784 (m-40) cc_final: 0.7292 (t0) REVERT: B 284 ILE cc_start: 0.8198 (mm) cc_final: 0.7945 (mt) REVERT: B 450 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8394 (m) REVERT: B 566 ASP cc_start: 0.8185 (t0) cc_final: 0.7919 (t0) REVERT: B 578 ASP cc_start: 0.8471 (t0) cc_final: 0.7749 (t70) REVERT: B 581 SER cc_start: 0.8634 (m) cc_final: 0.8343 (p) REVERT: B 588 SER cc_start: 0.8945 (t) cc_final: 0.8734 (t) REVERT: B 599 ASP cc_start: 0.7973 (m-30) cc_final: 0.7725 (m-30) REVERT: B 638 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8498 (p) REVERT: B 641 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8480 (mtp) REVERT: B 743 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7411 (pm20) REVERT: B 756 SER cc_start: 0.9233 (m) cc_final: 0.9005 (t) REVERT: B 854 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8489 (pt0) REVERT: B 867 ASP cc_start: 0.8398 (t0) cc_final: 0.7867 (t0) REVERT: B 913 ASP cc_start: 0.8367 (p0) cc_final: 0.8052 (p0) REVERT: B 994 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7194 (tp40) REVERT: B 1174 GLU cc_start: 0.8296 (tp30) cc_final: 0.8024 (tt0) REVERT: C 263 SER cc_start: 0.8602 (p) cc_final: 0.8362 (t) REVERT: C 277 LEU cc_start: 0.8592 (tp) cc_final: 0.8379 (tp) REVERT: C 487 ARG cc_start: 0.8141 (mmm-85) cc_final: 0.7899 (mtm180) REVERT: C 566 ASP cc_start: 0.8374 (t0) cc_final: 0.8131 (t0) REVERT: C 574 GLN cc_start: 0.8683 (pm20) cc_final: 0.8468 (mp10) REVERT: C 578 ASP cc_start: 0.8320 (t70) cc_final: 0.7594 (t70) REVERT: C 737 ASP cc_start: 0.8539 (t0) cc_final: 0.8227 (t0) REVERT: C 743 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7282 (pm20) REVERT: C 867 ASP cc_start: 0.8233 (t70) cc_final: 0.7616 (t0) REVERT: C 922 SER cc_start: 0.9257 (t) cc_final: 0.8966 (p) REVERT: C 1041 SER cc_start: 0.8319 (t) cc_final: 0.7948 (p) outliers start: 106 outliers final: 87 residues processed: 392 average time/residue: 0.1443 time to fit residues: 94.4265 Evaluate side-chains 394 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 301 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1034 LYS Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 641 MET Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1034 LYS Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1154 VAL Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1203 SER Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 298 HIS Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 641 MET Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 936 MET Chi-restraints excluded: chain C residue 953 SER Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1137 ILE Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1222 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 188 optimal weight: 0.7980 chunk 282 optimal weight: 0.0980 chunk 64 optimal weight: 0.9980 chunk 288 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 59 optimal weight: 0.2980 chunk 119 optimal weight: 0.9980 chunk 139 optimal weight: 0.0870 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 813 ASN B 426 HIS B1146 GLN C 822 GLN C1125 GLN C1146 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.111517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.091640 restraints weight = 38954.152| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.52 r_work: 0.3061 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 26136 Z= 0.143 Angle : 0.689 17.072 35766 Z= 0.326 Chirality : 0.049 0.595 4416 Planarity : 0.004 0.046 4419 Dihedral : 7.538 58.400 5100 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 3.28 % Allowed : 15.43 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.15), residues: 3150 helix: 1.22 (0.22), residues: 636 sheet: -0.58 (0.19), residues: 723 loop : -0.53 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 393 TYR 0.019 0.001 TYR A 400 PHE 0.016 0.001 PHE C 251 TRP 0.004 0.001 TRP B 165 HIS 0.034 0.001 HIS C 298 Details of bonding type rmsd covalent geometry : bond 0.00344 (26013) covalent geometry : angle 0.62155 (35445) SS BOND : bond 0.00672 ( 39) SS BOND : angle 2.45507 ( 78) hydrogen bonds : bond 0.03296 ( 949) hydrogen bonds : angle 5.02074 ( 2697) Misc. bond : bond 0.00269 ( 3) link_ALPHA1-2 : bond 0.00647 ( 3) link_ALPHA1-2 : angle 1.53413 ( 9) link_ALPHA1-3 : bond 0.00818 ( 3) link_ALPHA1-3 : angle 1.80930 ( 9) link_ALPHA1-6 : bond 0.01070 ( 3) link_ALPHA1-6 : angle 1.24358 ( 9) link_BETA1-4 : bond 0.00367 ( 18) link_BETA1-4 : angle 1.80687 ( 54) link_NAG-ASN : bond 0.00589 ( 54) link_NAG-ASN : angle 4.00250 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 310 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7321 (m-80) cc_final: 0.6928 (m-80) REVERT: A 179 HIS cc_start: 0.7774 (OUTLIER) cc_final: 0.7313 (m-70) REVERT: A 244 ASN cc_start: 0.7818 (m-40) cc_final: 0.7084 (t0) REVERT: A 297 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7641 (t0) REVERT: A 679 GLN cc_start: 0.8160 (tt0) cc_final: 0.7483 (mm-40) REVERT: A 867 ASP cc_start: 0.8212 (t70) cc_final: 0.7506 (t0) REVERT: A 922 SER cc_start: 0.9228 (t) cc_final: 0.8919 (p) REVERT: A 1023 LYS cc_start: 0.8392 (mtpt) cc_final: 0.8078 (mttm) REVERT: A 1049 LEU cc_start: 0.8154 (tp) cc_final: 0.7901 (tp) REVERT: A 1066 ASP cc_start: 0.8379 (t0) cc_final: 0.7979 (t0) REVERT: B 201 MET cc_start: 0.8076 (mmp) cc_final: 0.7655 (mmm) REVERT: B 244 ASN cc_start: 0.7786 (m-40) cc_final: 0.7283 (t0) REVERT: B 284 ILE cc_start: 0.8159 (mm) cc_final: 0.7916 (mt) REVERT: B 450 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8342 (m) REVERT: B 566 ASP cc_start: 0.8187 (t0) cc_final: 0.7923 (t0) REVERT: B 578 ASP cc_start: 0.8472 (t0) cc_final: 0.7700 (t70) REVERT: B 581 SER cc_start: 0.8643 (m) cc_final: 0.8341 (p) REVERT: B 588 SER cc_start: 0.8965 (t) cc_final: 0.8757 (t) REVERT: B 599 ASP cc_start: 0.7956 (m-30) cc_final: 0.7704 (m-30) REVERT: B 638 VAL cc_start: 0.8680 (OUTLIER) cc_final: 0.8466 (p) REVERT: B 641 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8476 (mtp) REVERT: B 756 SER cc_start: 0.9259 (m) cc_final: 0.9041 (t) REVERT: B 867 ASP cc_start: 0.8415 (t0) cc_final: 0.7870 (t0) REVERT: B 913 ASP cc_start: 0.8286 (p0) cc_final: 0.7984 (p0) REVERT: B 994 GLN cc_start: 0.7656 (tm-30) cc_final: 0.7164 (tp40) REVERT: B 1054 GLN cc_start: 0.8533 (pt0) cc_final: 0.8330 (pt0) REVERT: B 1174 GLU cc_start: 0.8325 (tp30) cc_final: 0.8035 (tt0) REVERT: C 487 ARG cc_start: 0.8138 (mmm-85) cc_final: 0.7905 (mtm180) REVERT: C 578 ASP cc_start: 0.8287 (t70) cc_final: 0.7547 (t70) REVERT: C 737 ASP cc_start: 0.8525 (t0) cc_final: 0.8211 (t0) REVERT: C 743 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7184 (pm20) REVERT: C 867 ASP cc_start: 0.8232 (t70) cc_final: 0.7605 (t0) REVERT: C 922 SER cc_start: 0.9247 (t) cc_final: 0.8958 (p) REVERT: C 1037 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7214 (tt0) REVERT: C 1041 SER cc_start: 0.8334 (t) cc_final: 0.8045 (p) outliers start: 90 outliers final: 75 residues processed: 381 average time/residue: 0.1446 time to fit residues: 91.2056 Evaluate side-chains 377 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 297 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1034 LYS Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 641 MET Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1034 LYS Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1154 VAL Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 540 CYS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 936 MET Chi-restraints excluded: chain C residue 953 SER Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1137 ILE Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1222 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 272 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 192 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 164 optimal weight: 0.5980 chunk 209 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 813 ASN B1146 GLN C 298 HIS C1125 GLN C1146 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.109854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.090288 restraints weight = 39141.730| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.44 r_work: 0.3042 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 26136 Z= 0.215 Angle : 0.724 16.567 35766 Z= 0.344 Chirality : 0.051 0.578 4416 Planarity : 0.004 0.049 4419 Dihedral : 7.630 59.566 5098 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.30 % Favored : 96.60 % Rotamer: Outliers : 3.46 % Allowed : 15.46 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.39 (0.15), residues: 3150 helix: 1.19 (0.22), residues: 627 sheet: -0.60 (0.18), residues: 735 loop : -0.58 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1205 TYR 0.022 0.002 TYR B1068 PHE 0.029 0.002 PHE C 344 TRP 0.005 0.001 TRP A 436 HIS 0.005 0.001 HIS B1136 Details of bonding type rmsd covalent geometry : bond 0.00526 (26013) covalent geometry : angle 0.65647 (35445) SS BOND : bond 0.00628 ( 39) SS BOND : angle 2.79037 ( 78) hydrogen bonds : bond 0.03580 ( 949) hydrogen bonds : angle 5.04665 ( 2697) Misc. bond : bond 0.00194 ( 3) link_ALPHA1-2 : bond 0.00734 ( 3) link_ALPHA1-2 : angle 1.47579 ( 9) link_ALPHA1-3 : bond 0.00684 ( 3) link_ALPHA1-3 : angle 1.92176 ( 9) link_ALPHA1-6 : bond 0.01009 ( 3) link_ALPHA1-6 : angle 1.23961 ( 9) link_BETA1-4 : bond 0.00264 ( 18) link_BETA1-4 : angle 1.79972 ( 54) link_NAG-ASN : bond 0.00542 ( 54) link_NAG-ASN : angle 4.02624 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 305 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7462 (m-80) cc_final: 0.7080 (m-80) REVERT: A 179 HIS cc_start: 0.7788 (OUTLIER) cc_final: 0.7323 (m-70) REVERT: A 201 MET cc_start: 0.7799 (mmp) cc_final: 0.7586 (mmm) REVERT: A 244 ASN cc_start: 0.7809 (m-40) cc_final: 0.7121 (t0) REVERT: A 297 ASN cc_start: 0.8141 (OUTLIER) cc_final: 0.7679 (t0) REVERT: A 679 GLN cc_start: 0.8181 (tt0) cc_final: 0.7610 (mm110) REVERT: A 867 ASP cc_start: 0.8211 (t70) cc_final: 0.7519 (t0) REVERT: A 922 SER cc_start: 0.9220 (t) cc_final: 0.8906 (p) REVERT: A 1023 LYS cc_start: 0.8485 (mtpt) cc_final: 0.8171 (mttm) REVERT: A 1049 LEU cc_start: 0.8213 (tp) cc_final: 0.7961 (tp) REVERT: A 1066 ASP cc_start: 0.8391 (t0) cc_final: 0.8021 (t0) REVERT: B 201 MET cc_start: 0.8064 (mmp) cc_final: 0.7629 (mmm) REVERT: B 211 MET cc_start: 0.7320 (mmt) cc_final: 0.7076 (mmt) REVERT: B 244 ASN cc_start: 0.7780 (m-40) cc_final: 0.7507 (t0) REVERT: B 284 ILE cc_start: 0.8201 (mm) cc_final: 0.7987 (mt) REVERT: B 450 VAL cc_start: 0.8633 (OUTLIER) cc_final: 0.8402 (m) REVERT: B 566 ASP cc_start: 0.8156 (t0) cc_final: 0.7897 (t0) REVERT: B 568 ASN cc_start: 0.8151 (t0) cc_final: 0.7881 (t0) REVERT: B 578 ASP cc_start: 0.8474 (t0) cc_final: 0.7757 (t70) REVERT: B 581 SER cc_start: 0.8637 (m) cc_final: 0.8362 (p) REVERT: B 588 SER cc_start: 0.8954 (t) cc_final: 0.8750 (t) REVERT: B 599 ASP cc_start: 0.7962 (m-30) cc_final: 0.7714 (m-30) REVERT: B 743 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7500 (pm20) REVERT: B 756 SER cc_start: 0.9269 (m) cc_final: 0.9001 (t) REVERT: B 867 ASP cc_start: 0.8400 (t0) cc_final: 0.7874 (t0) REVERT: B 913 ASP cc_start: 0.8342 (p0) cc_final: 0.8122 (p0) REVERT: B 994 GLN cc_start: 0.7664 (tm-30) cc_final: 0.7160 (tp40) REVERT: B 1174 GLU cc_start: 0.8340 (tp30) cc_final: 0.8071 (tt0) REVERT: C 487 ARG cc_start: 0.8115 (mmm-85) cc_final: 0.7884 (mtm180) REVERT: C 566 ASP cc_start: 0.8366 (t0) cc_final: 0.8135 (t0) REVERT: C 578 ASP cc_start: 0.8315 (t70) cc_final: 0.7634 (t70) REVERT: C 737 ASP cc_start: 0.8540 (t0) cc_final: 0.8239 (t0) REVERT: C 743 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7252 (pm20) REVERT: C 867 ASP cc_start: 0.8224 (t70) cc_final: 0.7608 (t0) REVERT: C 922 SER cc_start: 0.9236 (t) cc_final: 0.8948 (p) REVERT: C 1037 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7298 (tt0) outliers start: 95 outliers final: 82 residues processed: 380 average time/residue: 0.1477 time to fit residues: 93.6485 Evaluate side-chains 384 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 299 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1034 LYS Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 641 MET Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1034 LYS Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1154 VAL Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1203 SER Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 540 CYS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 641 MET Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 848 MET Chi-restraints excluded: chain C residue 936 MET Chi-restraints excluded: chain C residue 953 SER Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1137 ILE Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1222 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 174 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 274 optimal weight: 0.7980 chunk 91 optimal weight: 0.2980 chunk 46 optimal weight: 0.6980 chunk 193 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 253 optimal weight: 0.7980 chunk 201 optimal weight: 0.5980 chunk 304 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 813 ASN B1146 GLN C 298 HIS C1125 GLN C1146 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.110865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.091327 restraints weight = 38688.831| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.41 r_work: 0.3058 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 26136 Z= 0.171 Angle : 0.693 16.774 35766 Z= 0.330 Chirality : 0.049 0.505 4416 Planarity : 0.004 0.047 4419 Dihedral : 7.513 57.335 5098 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 3.36 % Allowed : 15.54 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.15), residues: 3150 helix: 1.28 (0.22), residues: 627 sheet: -0.61 (0.18), residues: 735 loop : -0.58 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 393 TYR 0.019 0.001 TYR A 400 PHE 0.021 0.001 PHE A 344 TRP 0.004 0.001 TRP C 256 HIS 0.003 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00417 (26013) covalent geometry : angle 0.62678 (35445) SS BOND : bond 0.00631 ( 39) SS BOND : angle 2.69361 ( 78) hydrogen bonds : bond 0.03377 ( 949) hydrogen bonds : angle 5.01529 ( 2697) Misc. bond : bond 0.00151 ( 3) link_ALPHA1-2 : bond 0.00743 ( 3) link_ALPHA1-2 : angle 1.49763 ( 9) link_ALPHA1-3 : bond 0.00764 ( 3) link_ALPHA1-3 : angle 1.84626 ( 9) link_ALPHA1-6 : bond 0.01042 ( 3) link_ALPHA1-6 : angle 1.23753 ( 9) link_BETA1-4 : bond 0.00283 ( 18) link_BETA1-4 : angle 1.76420 ( 54) link_NAG-ASN : bond 0.00542 ( 54) link_NAG-ASN : angle 3.88886 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6548.73 seconds wall clock time: 112 minutes 56.48 seconds (6776.48 seconds total)