Starting phenix.real_space_refine on Thu May 29 08:02:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oyt_17295/05_2025/8oyt_17295.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oyt_17295/05_2025/8oyt_17295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oyt_17295/05_2025/8oyt_17295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oyt_17295/05_2025/8oyt_17295.map" model { file = "/net/cci-nas-00/data/ceres_data/8oyt_17295/05_2025/8oyt_17295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oyt_17295/05_2025/8oyt_17295.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2886 atoms to isotropic. 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 135 5.16 5 C 18576 2.51 5 N 4845 2.21 5 O 5622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29178 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8610 Classifications: {'peptide': 1099} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 60, 'TRANS': 1038} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 8610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8610 Classifications: {'peptide': 1099} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 60, 'TRANS': 1038} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 8610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8610 Classifications: {'peptide': 1099} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 60, 'TRANS': 1038} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 962 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 126, 955 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Conformer: "B" Number of residues, atoms: 126, 955 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} bond proxies already assigned to first conformer: 968 Chain: "G" Number of atoms: 962 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 126, 955 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Conformer: "B" Number of residues, atoms: 126, 955 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} bond proxies already assigned to first conformer: 968 Chain: "F" Number of atoms: 962 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 126, 955 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Conformer: "B" Number of residues, atoms: 126, 955 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} bond proxies already assigned to first conformer: 968 Chain: "D" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: 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: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 17.60, per 1000 atoms: 0.60 Number of scatterers: 29178 At special positions: 0 Unit cell: (174, 172.8, 144, 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 135 16.00 O 5622 8.00 N 4845 7.00 C 18576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.02 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.02 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.02 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.02 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.02 Simple disulfide: pdb=" SG CYS B 837 " - pdb=" SG CYS B 848 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.02 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C 837 " - pdb=" SG CYS C 848 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.02 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 51 " - pdb=" SG CYS E 107 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 99 " distance=2.03 Simple disulfide: pdb=" SG CYS G 51 " - pdb=" SG CYS G 107 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 99 " distance=2.03 Simple disulfide: pdb=" SG CYS F 51 " - pdb=" SG CYS F 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " 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 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 A1301 " - " ASN A 706 " " NAG A1302 " - " ASN A1071 " " NAG B1301 " - " ASN B1071 " " NAG B1302 " - " ASN B1131 " " NAG B1303 " - " ASN B 706 " " NAG B1304 " - " ASN B 279 " " NAG C1301 " - " ASN C 279 " " NAG C1302 " - " ASN C 706 " " NAG C1303 " - " ASN C1071 " " NAG D 1 " - " ASN A 279 " " NAG H 1 " - " ASN A1131 " " NAG I 1 " - " ASN A1095 " " NAG J 1 " - " ASN A 714 " " NAG K 1 " - " ASN A 798 " " NAG L 1 " - " ASN B 798 " " NAG M 1 " - " ASN B 714 " " NAG N 1 " - " ASN B1095 " " NAG O 1 " - " ASN C1131 " " NAG P 1 " - " ASN C1095 " " NAG Q 1 " - " ASN C 798 " " NAG R 1 " - " ASN C 714 " Time building additional restraints: 7.28 Conformation dependent library (CDL) restraints added in 4.0 seconds 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6876 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 57 sheets defined 21.7% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.92 Creating SS restraints... Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.968A pdb=" N ASN A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 4.350A pdb=" N PHE A 152 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 153 " --> pdb=" O SER A 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 149 through 153' Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 362 through 368 Processing helix chain 'A' and resid 380 through 385 Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.518A pdb=" N ALA A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 495 through 499 removed outlier: 3.546A pdb=" N TYR A 498 " --> pdb=" O ARG A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 543 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.753A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 780 Processing helix chain 'A' and resid 813 through 824 Processing helix chain 'A' and resid 846 through 852 removed outlier: 3.512A pdb=" N PHE A 852 " --> pdb=" O CYS A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 881 Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 909 through 937 removed outlier: 4.203A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS A 918 " --> pdb=" O TYR A 914 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU A 919 " --> pdb=" O GLU A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.502A pdb=" N GLN A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.757A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 removed outlier: 4.309A pdb=" N PHE B 339 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 368 Processing helix chain 'B' and resid 380 through 384 removed outlier: 3.830A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.519A pdb=" N ALA B 408 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 618 through 622 removed outlier: 4.001A pdb=" N ILE B 621 " --> pdb=" O PRO B 618 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS B 622 " --> pdb=" O VAL B 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 622' Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 752 removed outlier: 3.566A pdb=" N SER B 747 " --> pdb=" O SER B 743 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 780 Processing helix chain 'B' and resid 813 through 824 Processing helix chain 'B' and resid 846 through 853 removed outlier: 3.817A pdb=" N LYS B 853 " --> pdb=" O ALA B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.521A pdb=" N ALA B 887 " --> pdb=" O THR B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 909 through 937 removed outlier: 4.469A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LYS B 918 " --> pdb=" O TYR B 914 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU B 919 " --> pdb=" O GLU B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.838A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 980 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.875A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 removed outlier: 3.914A pdb=" N PHE C 339 " --> pdb=" O PHE C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 368 Processing helix chain 'C' and resid 403 through 408 removed outlier: 4.281A pdb=" N ALA C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 539 through 543 Processing helix chain 'C' and resid 620 through 624 removed outlier: 4.065A pdb=" N ALA C 623 " --> pdb=" O ALA C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 752 Processing helix chain 'C' and resid 757 through 780 Processing helix chain 'C' and resid 813 through 824 Processing helix chain 'C' and resid 846 through 852 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 887 Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 909 through 937 removed outlier: 4.291A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS C 918 " --> pdb=" O TYR C 914 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU C 919 " --> pdb=" O GLU C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.653A pdb=" N GLN C 946 " --> pdb=" O LEU C 942 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 980 Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.671A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 68 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'G' and resid 65 through 68 Processing helix chain 'G' and resid 90 through 94 Processing helix chain 'F' and resid 65 through 68 Processing helix chain 'F' and resid 90 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.189A pdb=" N VAL A 36 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 221 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE A 198 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP A 225 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N PHE A 196 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A 201 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.598A pdb=" N GLN A 268 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A 275 " --> pdb=" O ASP A 284 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA5, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA6, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.585A pdb=" N ARG A 100 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 104 through 105 removed outlier: 3.521A pdb=" N PHE A 104 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER A 114 " --> pdb=" O CYS A 129 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS A 129 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU A 116 " --> pdb=" O LYS A 127 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS A 127 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE A 163 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLU A 130 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N CYS A 161 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N GLN A 132 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N ASN A 159 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 308 through 316 removed outlier: 7.106A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 355 removed outlier: 3.536A pdb=" N ILE A 355 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL A 392 " --> pdb=" O ILE A 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 398 through 399 removed outlier: 3.861A pdb=" N ILE A 399 " --> pdb=" O TYR A 505 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 535 through 537 removed outlier: 5.185A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY A 563 " --> pdb=" O ASP A 571 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.248A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR A 692 " --> pdb=" O CYS A 668 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N CYS A 668 " --> pdb=" O TYR A 692 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 698 through 699 removed outlier: 6.951A pdb=" N ALA A 698 " --> pdb=" O ILE B 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.708A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.708A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A1093 " --> pdb=" O PHE A1100 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A1100 " --> pdb=" O VAL A1093 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 730 through 732 removed outlier: 4.404A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 732 " --> pdb=" O THR A 856 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 784 through 785 Processing sheet with id=AB9, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AC1, first strand: chain 'B' and resid 29 through 30 Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.544A pdb=" N ASP B 53 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AC4, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.625A pdb=" N LEU B 82 " --> pdb=" O PHE B 235 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.970A pdb=" N LYS B 127 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE B 163 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N GLU B 130 " --> pdb=" O CYS B 161 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N CYS B 161 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N GLN B 132 " --> pdb=" O ASN B 159 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N ASN B 159 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 186 through 192 removed outlier: 6.217A pdb=" N PHE B 196 " --> pdb=" O ASP B 225 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP B 225 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE B 198 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU B 221 " --> pdb=" O SER B 200 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 308 through 316 removed outlier: 7.185A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 353 through 354 removed outlier: 3.741A pdb=" N LYS B 353 " --> pdb=" O ALA B 394 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA B 394 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP B 395 " --> pdb=" O VAL B 509 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL B 509 " --> pdb=" O ASP B 395 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE B 397 " --> pdb=" O VAL B 507 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B 507 " --> pdb=" O PHE B 397 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 535 through 540 removed outlier: 4.072A pdb=" N PHE B 540 " --> pdb=" O LEU B 543 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 651 through 652 removed outlier: 5.890A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR B 692 " --> pdb=" O CYS B 668 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS B 668 " --> pdb=" O TYR B 692 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 698 through 699 removed outlier: 6.398A pdb=" N ALA B 698 " --> pdb=" O ILE C 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 709 through 725 removed outlier: 6.553A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 709 through 725 removed outlier: 6.553A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR B1073 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 730 through 732 removed outlier: 4.616A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER B 732 " --> pdb=" O THR B 856 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR B 856 " --> pdb=" O SER B 732 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1117 through 1119 removed outlier: 3.518A pdb=" N PHE B1118 " --> pdb=" O PHE B1086 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 29 through 30 Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.690A pdb=" N GLN C 268 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 66 through 67 removed outlier: 3.501A pdb=" N TYR C 263 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 113 through 114 removed outlier: 3.702A pdb=" N CYS C 129 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE C 163 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N GLU C 130 " --> pdb=" O CYS C 161 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N CYS C 161 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N GLN C 132 " --> pdb=" O ASN C 159 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N ASN C 159 " --> pdb=" O GLN C 132 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 186 through 192 removed outlier: 3.510A pdb=" N LYS C 201 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N PHE C 196 " --> pdb=" O ASP C 225 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP C 225 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE C 198 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.328A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER C 313 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 353 through 355 removed outlier: 4.086A pdb=" N LYS C 353 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU C 513 " --> pdb=" O THR C 390 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL C 392 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N SER C 511 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ALA C 394 " --> pdb=" O VAL C 509 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL C 509 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL C 507 " --> pdb=" O PHE C 397 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE C 397 " --> pdb=" O VAL C 507 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 353 through 355 removed outlier: 4.086A pdb=" N LYS C 353 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU C 513 " --> pdb=" O THR C 390 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL C 392 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N SER C 511 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ALA C 394 " --> pdb=" O VAL C 509 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL C 509 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU C 510 " --> pdb=" O CYS C 429 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS C 429 " --> pdb=" O LEU C 510 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 535 through 537 removed outlier: 3.647A pdb=" N GLY C 547 " --> pdb=" O VAL C 536 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 651 through 652 removed outlier: 5.935A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 709 through 725 removed outlier: 6.919A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 709 through 725 removed outlier: 6.919A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.137A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1117 through 1119 Processing sheet with id=AF3, first strand: chain 'E' and resid 4 through 8 removed outlier: 4.111A pdb=" N GLN E 4 " --> pdb=" O SER E 26 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 4 through 8 removed outlier: 4.111A pdb=" N GLN E 4 " --> pdb=" O SER E 26 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 12 through 13 removed outlier: 5.644A pdb=" N ARG E 39 " --> pdb=" O GLY E 48 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLY E 48 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 12 through 13 removed outlier: 3.530A pdb=" N THR E 101 " --> pdb=" O TRP E 116 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 4 through 8 removed outlier: 3.932A pdb=" N GLN G 4 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLY G 17 " --> pdb=" O SER G 88 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL G 82 " --> pdb=" O CYS G 23 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR G 81 " --> pdb=" O ASP G 76 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER G 74 " --> pdb=" O TYR G 83 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 12 through 13 removed outlier: 6.246A pdb=" N ARG G 39 " --> pdb=" O GLY G 48 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLY G 48 " --> pdb=" O ARG G 39 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AG1, first strand: chain 'F' and resid 4 through 8 removed outlier: 3.854A pdb=" N GLN F 4 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL F 82 " --> pdb=" O CYS F 23 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR F 81 " --> pdb=" O ASP F 76 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 12 through 13 removed outlier: 5.366A pdb=" N ARG F 39 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLY F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 12 through 13 974 hydrogen bonds defined for protein. 2609 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: 11.75 Time building geometry restraints manager: 8.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9321 1.34 - 1.47: 7495 1.47 - 1.59: 12890 1.59 - 1.71: 0 1.71 - 1.83: 171 Bond restraints: 29877 Sorted by residual: bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 9.82e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.05e+00 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.11e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.01e+00 ... (remaining 29872 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 40177 3.40 - 6.79: 416 6.79 - 10.19: 59 10.19 - 13.58: 13 13.58 - 16.98: 3 Bond angle restraints: 40668 Sorted by residual: angle pdb=" CA MET A1026 " pdb=" CB MET A1026 " pdb=" CG MET A1026 " ideal model delta sigma weight residual 114.10 127.91 -13.81 2.00e+00 2.50e-01 4.77e+01 angle pdb=" C LYS A 526 " pdb=" CA LYS A 526 " pdb=" CB LYS A 526 " ideal model delta sigma weight residual 116.54 109.54 7.00 1.15e+00 7.56e-01 3.71e+01 angle pdb=" CA MET A1047 " pdb=" CB MET A1047 " pdb=" CG MET A1047 " ideal model delta sigma weight residual 114.10 125.77 -11.67 2.00e+00 2.50e-01 3.41e+01 angle pdb=" CA TYR A 393 " pdb=" CB TYR A 393 " pdb=" CG TYR A 393 " ideal model delta sigma weight residual 113.90 124.32 -10.42 1.80e+00 3.09e-01 3.35e+01 angle pdb=" N GLY A 501 " pdb=" CA GLY A 501 " pdb=" C GLY A 501 " ideal model delta sigma weight residual 113.18 126.30 -13.12 2.37e+00 1.78e-01 3.06e+01 ... (remaining 40663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.26: 16946 24.26 - 48.51: 1093 48.51 - 72.77: 136 72.77 - 97.03: 51 97.03 - 121.28: 50 Dihedral angle restraints: 18276 sinusoidal: 7560 harmonic: 10716 Sorted by residual: dihedral pdb=" CB CYS C 837 " pdb=" SG CYS C 837 " pdb=" SG CYS C 848 " pdb=" CB CYS C 848 " ideal model delta sinusoidal sigma weight residual -86.00 -174.19 88.19 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS B 837 " pdb=" SG CYS B 837 " pdb=" SG CYS B 848 " pdb=" CB CYS B 848 " ideal model delta sinusoidal sigma weight residual -86.00 -170.41 84.41 1 1.00e+01 1.00e-02 8.66e+01 dihedral pdb=" CB CYS B 333 " pdb=" SG CYS B 333 " pdb=" SG CYS B 358 " pdb=" CB CYS B 358 " ideal model delta sinusoidal sigma weight residual -86.00 -14.38 -71.62 1 1.00e+01 1.00e-02 6.57e+01 ... (remaining 18273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 4436 0.109 - 0.218: 197 0.218 - 0.328: 16 0.328 - 0.437: 4 0.437 - 0.546: 3 Chirality restraints: 4656 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B 714 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.46e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A1095 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.00e+00 chirality pdb=" CB VAL A 324 " pdb=" CA VAL A 324 " pdb=" CG1 VAL A 324 " pdb=" CG2 VAL A 324 " both_signs ideal model delta sigma weight residual False -2.63 -2.12 -0.51 2.00e-01 2.50e+01 6.42e+00 ... (remaining 4653 not shown) Planarity restraints: 5247 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 389 " 0.025 2.00e-02 2.50e+03 4.99e-02 4.36e+01 pdb=" CG PHE A 389 " -0.107 2.00e-02 2.50e+03 pdb=" CD1 PHE A 389 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 PHE A 389 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 PHE A 389 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE A 389 " 0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 389 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 865 " 0.023 2.00e-02 2.50e+03 4.63e-02 2.14e+01 pdb=" C GLU A 865 " -0.080 2.00e-02 2.50e+03 pdb=" O GLU A 865 " 0.030 2.00e-02 2.50e+03 pdb=" N MET A 866 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 627 " -0.064 5.00e-02 4.00e+02 9.50e-02 1.45e+01 pdb=" N PRO A 628 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO A 628 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 628 " -0.051 5.00e-02 4.00e+02 ... (remaining 5244 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 624 2.65 - 3.21: 28254 3.21 - 3.77: 45949 3.77 - 4.34: 62022 4.34 - 4.90: 99151 Nonbonded interactions: 236000 Sorted by model distance: nonbonded pdb=" OG SER A 346 " pdb=" O LEU A 449 " model vdw 2.086 3.040 nonbonded pdb=" OG1 THR A 29 " pdb=" OD1 ASP A 212 " model vdw 2.088 3.040 nonbonded pdb=" OE1 GLN A 52 " pdb=" OG1 THR A 271 " model vdw 2.103 3.040 nonbonded pdb=" O HIS B 66 " pdb=" NH2 ARG B 76 " model vdw 2.107 3.120 nonbonded pdb=" OG1 THR B1113 " pdb=" OD1 ASP B1115 " model vdw 2.130 3.040 ... (remaining 235995 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 19 through 1144 or resid 1301 through 1302)) selection = (chain 'C' and (resid 19 through 1144 or resid 1301 through 1302)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = (chain 'E' and (resid 2 through 25 or resid 27 through 63 or resid 65 through 12 \ 7)) selection = (chain 'F' and (resid 2 through 25 or resid 27 through 63 or resid 65 through 12 \ 7)) selection = (chain 'G' and (resid 2 through 25 or resid 27 through 63 or resid 65 through 12 \ 7)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.030 Extract box with map and model: 0.970 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 64.840 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.160 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5685 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 29958 Z= 0.196 Angle : 0.949 16.977 40863 Z= 0.492 Chirality : 0.055 0.546 4656 Planarity : 0.005 0.095 5226 Dihedral : 16.958 121.283 11256 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.87 % Favored : 92.64 % Rotamer: Outliers : 0.25 % Allowed : 11.72 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.14), residues: 3645 helix: 1.43 (0.21), residues: 732 sheet: -0.36 (0.22), residues: 621 loop : -1.41 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 630 HIS 0.007 0.001 HIS C1045 PHE 0.107 0.002 PHE A 389 TYR 0.052 0.002 TYR A 393 ARG 0.020 0.001 ARG A 980 Details of bonding type rmsd link_NAG-ASN : bond 0.00696 ( 21) link_NAG-ASN : angle 4.42146 ( 63) link_BETA1-4 : bond 0.01417 ( 12) link_BETA1-4 : angle 5.42579 ( 36) hydrogen bonds : bond 0.20121 ( 909) hydrogen bonds : angle 8.45569 ( 2609) SS BOND : bond 0.00461 ( 48) SS BOND : angle 2.60816 ( 96) covalent geometry : bond 0.00417 (29877) covalent geometry : angle 0.91242 (40668) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 731 time to evaluate : 3.073 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 28 TYR cc_start: 0.5022 (m-80) cc_final: 0.4720 (m-80) REVERT: A 38 TYR cc_start: 0.5885 (m-80) cc_final: 0.5255 (m-80) REVERT: A 40 ASP cc_start: 0.6835 (t70) cc_final: 0.5983 (p0) REVERT: A 79 ASN cc_start: 0.6190 (m110) cc_final: 0.5970 (m110) REVERT: A 98 ILE cc_start: 0.5730 (mp) cc_final: 0.5377 (mm) REVERT: A 136 ASP cc_start: 0.5084 (t70) cc_final: 0.4512 (m-30) REVERT: A 213 LEU cc_start: 0.6381 (mp) cc_final: 0.6031 (mm) REVERT: A 294 SER cc_start: 0.7843 (m) cc_final: 0.7631 (p) REVERT: A 312 THR cc_start: 0.6085 (p) cc_final: 0.5550 (p) REVERT: A 549 LEU cc_start: 0.6397 (mt) cc_final: 0.6030 (mt) REVERT: A 589 PHE cc_start: 0.6225 (p90) cc_final: 0.5640 (p90) REVERT: A 630 TRP cc_start: 0.1657 (m100) cc_final: 0.0905 (m100) REVERT: A 631 ARG cc_start: 0.4434 (pmt170) cc_final: 0.4076 (ptp90) REVERT: A 632 VAL cc_start: 0.5878 (t) cc_final: 0.5442 (t) REVERT: A 643 ARG cc_start: 0.5326 (mtp180) cc_final: 0.4764 (ttm-80) REVERT: A 704 TYR cc_start: 0.5878 (t80) cc_final: 0.5439 (t80) REVERT: A 711 ILE cc_start: 0.4508 (tt) cc_final: 0.3776 (mm) REVERT: A 816 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7322 (mt-10) REVERT: A 864 ASP cc_start: 0.7095 (m-30) cc_final: 0.6082 (t0) REVERT: A 865 GLU cc_start: 0.7167 (mp0) cc_final: 0.6710 (mm-30) REVERT: A 975 ASN cc_start: 0.6326 (m-40) cc_final: 0.6072 (p0) REVERT: A 976 ASP cc_start: 0.6400 (m-30) cc_final: 0.5955 (m-30) REVERT: A 987 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7180 (tt0) REVERT: A 1005 VAL cc_start: 0.8969 (p) cc_final: 0.8544 (p) REVERT: A 1008 GLN cc_start: 0.8106 (mm110) cc_final: 0.7085 (mm110) REVERT: A 1122 ASN cc_start: 0.7424 (p0) cc_final: 0.7140 (p0) REVERT: B 64 TRP cc_start: 0.6284 (p-90) cc_final: 0.5400 (t60) REVERT: B 155 TYR cc_start: 0.4276 (p90) cc_final: 0.4002 (p90) REVERT: B 200 SER cc_start: 0.6905 (t) cc_final: 0.6660 (t) REVERT: B 276 TYR cc_start: 0.5718 (m-80) cc_final: 0.4865 (m-80) REVERT: B 294 SER cc_start: 0.7886 (m) cc_final: 0.7639 (p) REVERT: B 314 ASN cc_start: 0.5847 (m110) cc_final: 0.5560 (p0) REVERT: B 431 ILE cc_start: 0.5362 (mm) cc_final: 0.5117 (mm) REVERT: B 534 LYS cc_start: 0.3896 (mmtm) cc_final: 0.3606 (tptt) REVERT: B 538 PHE cc_start: 0.7002 (p90) cc_final: 0.6711 (p90) REVERT: B 544 LYS cc_start: 0.5708 (tmtt) cc_final: 0.5371 (tptp) REVERT: B 571 ASP cc_start: 0.6779 (t0) cc_final: 0.6464 (p0) REVERT: B 631 ARG cc_start: 0.4481 (pmt170) cc_final: 0.4055 (ptt90) REVERT: B 655 ASN cc_start: 0.6603 (m-40) cc_final: 0.5929 (p0) REVERT: B 770 GLU cc_start: 0.7651 (tt0) cc_final: 0.7335 (tt0) REVERT: B 773 LYS cc_start: 0.8223 (ttpt) cc_final: 0.7994 (ttpp) REVERT: B 791 ILE cc_start: 0.6999 (mp) cc_final: 0.6773 (tp) REVERT: B 793 TYR cc_start: 0.7488 (t80) cc_final: 0.7222 (t80) REVERT: B 861 LEU cc_start: 0.6122 (mm) cc_final: 0.5781 (tp) REVERT: B 915 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8073 (pp20) REVERT: B 957 ASN cc_start: 0.8577 (t0) cc_final: 0.8289 (m110) REVERT: B 1064 TYR cc_start: 0.6881 (t80) cc_final: 0.6393 (t80) REVERT: C 65 PHE cc_start: 0.6737 (m-80) cc_final: 0.6367 (m-80) REVERT: C 79 ASN cc_start: 0.2084 (m110) cc_final: 0.1816 (m-40) REVERT: C 144 ASN cc_start: 0.2452 (m110) cc_final: 0.2208 (t0) REVERT: C 148 MET cc_start: 0.1136 (tpt) cc_final: -0.0435 (mmm) REVERT: C 294 SER cc_start: 0.6891 (m) cc_final: 0.6678 (p) REVERT: C 297 LYS cc_start: 0.7860 (mttt) cc_final: 0.7478 (mtpt) REVERT: C 494 PHE cc_start: 0.1529 (m-10) cc_final: 0.1237 (m-80) REVERT: C 539 ASN cc_start: 0.6809 (t0) cc_final: 0.6593 (m-40) REVERT: C 540 PHE cc_start: 0.5290 (m-10) cc_final: 0.4971 (m-10) REVERT: C 655 ASN cc_start: 0.6753 (m-40) cc_final: 0.6470 (p0) REVERT: C 657 TYR cc_start: 0.7296 (m-10) cc_final: 0.6561 (m-10) REVERT: C 717 ILE cc_start: 0.8312 (mm) cc_final: 0.7457 (mt) REVERT: C 728 MET cc_start: 0.7103 (ppp) cc_final: 0.6891 (ptm) REVERT: C 756 PHE cc_start: 0.6292 (p90) cc_final: 0.5989 (p90) REVERT: C 770 GLU cc_start: 0.8156 (tt0) cc_final: 0.7940 (mt-10) REVERT: C 773 LYS cc_start: 0.8091 (ttpt) cc_final: 0.7788 (pttp) REVERT: C 792 LYS cc_start: 0.5588 (mmtm) cc_final: 0.5274 (mmtm) REVERT: C 974 LEU cc_start: 0.4684 (pt) cc_final: 0.4448 (mp) REVERT: C 1001 LEU cc_start: 0.8117 (mm) cc_final: 0.7856 (tp) REVERT: C 1130 VAL cc_start: 0.6631 (t) cc_final: 0.6423 (m) REVERT: E 4 GLN cc_start: 0.3863 (pm20) cc_final: 0.3476 (tm-30) outliers start: 7 outliers final: 3 residues processed: 736 average time/residue: 0.4118 time to fit residues: 472.7777 Evaluate side-chains 313 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 310 time to evaluate : 3.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 798 ASN Chi-restraints excluded: chain C residue 694 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 306 optimal weight: 0.9990 chunk 275 optimal weight: 3.9990 chunk 152 optimal weight: 0.0040 chunk 93 optimal weight: 4.9990 chunk 185 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 284 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 173 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 chunk 329 optimal weight: 10.0000 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 ASN A 577 GLN A 748 ASN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN A1007 GLN ** A1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 GLN B 801 GLN ** B 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 989 GLN B1020 ASN ** B1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1116 ASN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN ** C 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 GLN ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 GLN ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 ASN G 2 GLN F 122 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.087661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.067453 restraints weight = 328687.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.069656 restraints weight = 165960.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.069490 restraints weight = 96018.740| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6053 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.155 29958 Z= 0.262 Angle : 0.928 11.869 40863 Z= 0.465 Chirality : 0.055 0.448 4656 Planarity : 0.007 0.079 5226 Dihedral : 12.323 118.102 4675 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.42 % Favored : 92.28 % Rotamer: Outliers : 4.61 % Allowed : 16.95 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.13), residues: 3645 helix: 0.55 (0.19), residues: 726 sheet: -0.41 (0.22), residues: 597 loop : -1.81 (0.12), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 630 HIS 0.012 0.003 HIS B 66 PHE 0.033 0.004 PHE C 978 TYR 0.025 0.003 TYR A 786 ARG 0.011 0.001 ARG A 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00874 ( 21) link_NAG-ASN : angle 3.59467 ( 63) link_BETA1-4 : bond 0.01580 ( 12) link_BETA1-4 : angle 4.53940 ( 36) hydrogen bonds : bond 0.04790 ( 909) hydrogen bonds : angle 6.73772 ( 2609) SS BOND : bond 0.01400 ( 48) SS BOND : angle 1.55537 ( 96) covalent geometry : bond 0.00593 (29877) covalent geometry : angle 0.90626 (40668) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 341 time to evaluate : 3.296 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 98 ILE cc_start: 0.5049 (OUTLIER) cc_final: 0.4518 (mm) REVERT: A 136 ASP cc_start: 0.5123 (t70) cc_final: 0.4494 (m-30) REVERT: A 383 LYS cc_start: 0.5036 (tptp) cc_final: 0.4644 (mtpt) REVERT: A 555 LYS cc_start: 0.6016 (mppt) cc_final: 0.5066 (mtpp) REVERT: A 582 LEU cc_start: 0.5937 (mt) cc_final: 0.5069 (mt) REVERT: A 630 TRP cc_start: 0.2032 (m100) cc_final: 0.1669 (m-10) REVERT: A 643 ARG cc_start: 0.5520 (mtp180) cc_final: 0.5161 (ttm-80) REVERT: A 855 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6447 (mp) REVERT: A 933 ASP cc_start: 0.6131 (m-30) cc_final: 0.5620 (m-30) REVERT: A 1008 GLN cc_start: 0.7612 (mm110) cc_final: 0.7397 (mm110) REVERT: B 54 LEU cc_start: 0.7628 (mp) cc_final: 0.7304 (pp) REVERT: B 64 TRP cc_start: 0.5460 (p-90) cc_final: 0.4744 (t60) REVERT: B 190 LYS cc_start: 0.6337 (OUTLIER) cc_final: 0.6100 (tptp) REVERT: B 208 ARG cc_start: 0.3270 (OUTLIER) cc_final: 0.1954 (mmp80) REVERT: B 294 SER cc_start: 0.7772 (m) cc_final: 0.7325 (p) REVERT: B 314 ASN cc_start: 0.5966 (m110) cc_final: 0.5382 (p0) REVERT: B 347 VAL cc_start: 0.2010 (OUTLIER) cc_final: 0.1788 (t) REVERT: B 374 PHE cc_start: 0.3027 (OUTLIER) cc_final: 0.2328 (p90) REVERT: B 448 TYR cc_start: 0.2964 (m-80) cc_final: 0.2732 (m-80) REVERT: B 506 ARG cc_start: 0.3230 (OUTLIER) cc_final: 0.2803 (ptp90) REVERT: B 534 LYS cc_start: 0.4983 (mmtm) cc_final: 0.4654 (ptpt) REVERT: B 540 PHE cc_start: 0.2404 (OUTLIER) cc_final: 0.1448 (m-80) REVERT: B 544 LYS cc_start: 0.6273 (tmtt) cc_final: 0.5952 (tppt) REVERT: B 555 LYS cc_start: 0.4773 (OUTLIER) cc_final: 0.3450 (mmtt) REVERT: B 797 PHE cc_start: 0.5927 (m-80) cc_final: 0.5614 (m-80) REVERT: B 935 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6693 (mm) REVERT: B 981 LEU cc_start: 0.6582 (mt) cc_final: 0.6178 (tp) REVERT: C 148 MET cc_start: -0.0556 (tpt) cc_final: -0.1693 (mmm) REVERT: C 243 ARG cc_start: 0.4103 (tpp-160) cc_final: 0.3844 (tpp-160) REVERT: C 323 ILE cc_start: 0.6561 (tt) cc_final: 0.6349 (tt) REVERT: C 717 ILE cc_start: 0.7602 (mm) cc_final: 0.7354 (mt) REVERT: C 852 PHE cc_start: 0.6271 (m-80) cc_final: 0.6062 (m-80) REVERT: C 1001 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7543 (mt) REVERT: C 1002 GLN cc_start: 0.7190 (mm-40) cc_final: 0.6918 (mm-40) REVERT: G 37 TRP cc_start: 0.1063 (m100) cc_final: 0.0527 (m100) REVERT: F 71 PHE cc_start: 0.2514 (m-10) cc_final: 0.2260 (m-10) outliers start: 145 outliers final: 81 residues processed: 462 average time/residue: 0.3670 time to fit residues: 278.4007 Evaluate side-chains 314 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 222 time to evaluate : 2.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 433 TRP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 506 ARG Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 785 ILE Chi-restraints excluded: chain B residue 800 SER Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 903 PHE Chi-restraints excluded: chain C residue 942 LEU Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 24 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 125 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 259 optimal weight: 0.9980 chunk 172 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 279 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 338 optimal weight: 0.6980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 ASN ** B1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 ASN ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1139 GLN G 2 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.086766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.066891 restraints weight = 314630.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.068440 restraints weight = 162618.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.068599 restraints weight = 105400.394| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.132 29958 Z= 0.207 Angle : 0.787 13.996 40863 Z= 0.394 Chirality : 0.049 0.341 4656 Planarity : 0.006 0.059 5226 Dihedral : 10.922 117.586 4670 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.54 % Favored : 93.16 % Rotamer: Outliers : 4.73 % Allowed : 19.14 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.13), residues: 3645 helix: 0.86 (0.20), residues: 690 sheet: -0.54 (0.21), residues: 600 loop : -1.92 (0.11), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 64 HIS 0.009 0.002 HIS B 622 PHE 0.036 0.003 PHE C1092 TYR 0.027 0.002 TYR G 112 ARG 0.009 0.001 ARG A 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 21) link_NAG-ASN : angle 3.17558 ( 63) link_BETA1-4 : bond 0.01744 ( 12) link_BETA1-4 : angle 4.50860 ( 36) hydrogen bonds : bond 0.04481 ( 909) hydrogen bonds : angle 6.45352 ( 2609) SS BOND : bond 0.00456 ( 48) SS BOND : angle 2.20919 ( 96) covalent geometry : bond 0.00463 (29877) covalent geometry : angle 0.75924 (40668) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 257 time to evaluate : 3.258 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 98 ILE cc_start: 0.5359 (mp) cc_final: 0.4936 (mm) REVERT: A 383 LYS cc_start: 0.5157 (tptp) cc_final: 0.4879 (mtpt) REVERT: A 555 LYS cc_start: 0.6064 (mppt) cc_final: 0.5332 (ptmt) REVERT: A 582 LEU cc_start: 0.6283 (mt) cc_final: 0.5489 (mp) REVERT: A 630 TRP cc_start: 0.2347 (m100) cc_final: 0.2135 (m-10) REVERT: A 811 LYS cc_start: 0.7014 (mmtt) cc_final: 0.6768 (mmtp) REVERT: B 54 LEU cc_start: 0.8089 (mp) cc_final: 0.7422 (pt) REVERT: B 64 TRP cc_start: 0.5363 (p-90) cc_final: 0.4741 (t60) REVERT: B 88 VAL cc_start: 0.5967 (m) cc_final: 0.5742 (p) REVERT: B 115 LEU cc_start: 0.5434 (mm) cc_final: 0.5135 (mp) REVERT: B 208 ARG cc_start: 0.4184 (OUTLIER) cc_final: 0.3895 (mmp-170) REVERT: B 314 ASN cc_start: 0.6172 (m110) cc_final: 0.5519 (p0) REVERT: B 326 PHE cc_start: 0.5160 (t80) cc_final: 0.4947 (t80) REVERT: B 424 ASP cc_start: 0.2185 (OUTLIER) cc_final: 0.1935 (t70) REVERT: B 433 TRP cc_start: 0.1686 (p90) cc_final: 0.1411 (p90) REVERT: B 526 LYS cc_start: 0.2909 (ptpp) cc_final: 0.2646 (ptpp) REVERT: B 534 LYS cc_start: 0.5470 (mmtm) cc_final: 0.4997 (ptpt) REVERT: B 540 PHE cc_start: 0.3073 (OUTLIER) cc_final: 0.2127 (m-10) REVERT: B 544 LYS cc_start: 0.6132 (tmtt) cc_final: 0.5864 (tptp) REVERT: B 748 ASN cc_start: 0.7261 (OUTLIER) cc_final: 0.7014 (m-40) REVERT: B 797 PHE cc_start: 0.6188 (m-80) cc_final: 0.5858 (m-10) REVERT: C 88 VAL cc_start: 0.7014 (t) cc_final: 0.6806 (m) REVERT: C 148 MET cc_start: -0.0682 (tpt) cc_final: -0.1928 (ppp) REVERT: C 243 ARG cc_start: 0.4368 (tpp-160) cc_final: 0.4159 (tpp-160) REVERT: C 717 ILE cc_start: 0.7640 (mm) cc_final: 0.7398 (mt) REVERT: C 852 PHE cc_start: 0.6517 (m-80) cc_final: 0.6189 (m-80) REVERT: C 1002 GLN cc_start: 0.7373 (mm-40) cc_final: 0.7061 (mm-40) REVERT: C 1064 TYR cc_start: 0.6543 (OUTLIER) cc_final: 0.6011 (t80) REVERT: E 47 GLU cc_start: 0.4105 (tm-30) cc_final: 0.3848 (pp20) REVERT: G 37 TRP cc_start: 0.1106 (m100) cc_final: -0.0168 (m100) outliers start: 149 outliers final: 93 residues processed: 391 average time/residue: 0.3487 time to fit residues: 228.4064 Evaluate side-chains 317 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 219 time to evaluate : 2.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 350 TRP Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 527 SER Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 800 SER Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 739 ILE Chi-restraints excluded: chain C residue 740 CYS Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 746 CYS Chi-restraints excluded: chain C residue 755 SER Chi-restraints excluded: chain C residue 758 THR Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 942 LEU Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1064 TYR Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1139 GLN Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain F residue 24 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 212 optimal weight: 9.9990 chunk 205 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 340 optimal weight: 6.9990 chunk 170 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 270 optimal weight: 7.9990 chunk 355 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 GLN A 311 GLN A 419 ASN A 457 ASN A 471 GLN A 478 ASN ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 GLN ** A1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN B 529 ASN ** B 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1103 GLN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 ASN C 641 GLN ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 946 GLN ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 ASN G 2 GLN G 57 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.085242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.066150 restraints weight = 289058.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.066257 restraints weight = 213346.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.066244 restraints weight = 160172.184| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.6115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.192 29958 Z= 0.288 Angle : 0.923 11.693 40863 Z= 0.469 Chirality : 0.054 0.373 4656 Planarity : 0.007 0.074 5226 Dihedral : 10.907 117.489 4670 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.07 % Favored : 90.63 % Rotamer: Outliers : 6.92 % Allowed : 20.27 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.13), residues: 3645 helix: 0.08 (0.19), residues: 690 sheet: -0.80 (0.20), residues: 615 loop : -2.34 (0.11), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 64 HIS 0.015 0.002 HIS B 622 PHE 0.039 0.004 PHE G 71 TYR 0.023 0.003 TYR E 83 ARG 0.007 0.001 ARG B 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 21) link_NAG-ASN : angle 3.99682 ( 63) link_BETA1-4 : bond 0.01588 ( 12) link_BETA1-4 : angle 4.56892 ( 36) hydrogen bonds : bond 0.05079 ( 909) hydrogen bonds : angle 6.89282 ( 2609) SS BOND : bond 0.00755 ( 48) SS BOND : angle 1.71851 ( 96) covalent geometry : bond 0.00656 (29877) covalent geometry : angle 0.89811 (40668) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 256 time to evaluate : 3.116 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 82 LEU cc_start: 0.5215 (OUTLIER) cc_final: 0.5009 (tp) REVERT: A 295 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6413 (tp30) REVERT: A 383 LYS cc_start: 0.5459 (tptp) cc_final: 0.5062 (mttt) REVERT: A 585 THR cc_start: 0.8177 (p) cc_final: 0.7898 (t) REVERT: A 631 ARG cc_start: 0.3284 (OUTLIER) cc_final: 0.2652 (ptp90) REVERT: A 935 LEU cc_start: 0.7174 (mm) cc_final: 0.6746 (mt) REVERT: A 965 SER cc_start: 0.6214 (OUTLIER) cc_final: 0.5878 (t) REVERT: A 978 PHE cc_start: 0.4559 (OUTLIER) cc_final: 0.3956 (t80) REVERT: B 102 TRP cc_start: 0.5896 (m-90) cc_final: 0.4855 (m-90) REVERT: B 103 ILE cc_start: 0.5537 (OUTLIER) cc_final: 0.5333 (pt) REVERT: B 115 LEU cc_start: 0.5606 (OUTLIER) cc_final: 0.5104 (mt) REVERT: B 208 ARG cc_start: 0.3816 (OUTLIER) cc_final: 0.3588 (mmp-170) REVERT: B 371 PHE cc_start: 0.0669 (OUTLIER) cc_final: 0.0300 (m-80) REVERT: B 374 PHE cc_start: 0.2515 (OUTLIER) cc_final: 0.1928 (p90) REVERT: B 487 PHE cc_start: 0.1458 (OUTLIER) cc_final: 0.1254 (t80) REVERT: B 495 ARG cc_start: 0.3423 (mpt180) cc_final: 0.3074 (ptp-170) REVERT: B 506 ARG cc_start: 0.3333 (OUTLIER) cc_final: 0.2227 (ptp90) REVERT: B 514 LEU cc_start: 0.2333 (OUTLIER) cc_final: 0.2051 (tp) REVERT: B 525 LYS cc_start: 0.2514 (OUTLIER) cc_final: 0.2173 (mptt) REVERT: B 532 LYS cc_start: 0.5522 (OUTLIER) cc_final: 0.5153 (tttp) REVERT: B 534 LYS cc_start: 0.5568 (mmtm) cc_final: 0.5077 (ptpt) REVERT: B 540 PHE cc_start: 0.3278 (OUTLIER) cc_final: 0.2550 (m-10) REVERT: B 748 ASN cc_start: 0.7271 (OUTLIER) cc_final: 0.6988 (m-40) REVERT: B 797 PHE cc_start: 0.6577 (m-80) cc_final: 0.6198 (m-80) REVERT: B 963 LEU cc_start: 0.6599 (mt) cc_final: 0.6203 (pp) REVERT: B 1085 HIS cc_start: 0.4793 (OUTLIER) cc_final: 0.4508 (m170) REVERT: B 1086 PHE cc_start: 0.4435 (OUTLIER) cc_final: 0.4213 (t80) REVERT: C 123 ASN cc_start: 0.4406 (m110) cc_final: 0.4089 (t0) REVERT: C 127 LYS cc_start: 0.3400 (tptt) cc_final: 0.2206 (mtpt) REVERT: C 148 MET cc_start: -0.0834 (tpt) cc_final: -0.2281 (ptt) REVERT: C 245 TYR cc_start: 0.3008 (OUTLIER) cc_final: 0.2752 (t80) REVERT: C 266 TYR cc_start: 0.5643 (OUTLIER) cc_final: 0.5376 (m-80) REVERT: C 287 ASP cc_start: 0.5413 (OUTLIER) cc_final: 0.5144 (p0) REVERT: C 353 LYS cc_start: 0.4439 (tptt) cc_final: 0.3900 (mptt) REVERT: C 405 ARG cc_start: 0.2256 (tpp-160) cc_final: 0.1612 (tpp80) REVERT: C 445 ASN cc_start: 0.4242 (m-40) cc_final: 0.3929 (t0) REVERT: C 544 LYS cc_start: 0.6769 (OUTLIER) cc_final: 0.5587 (mtmt) REVERT: C 742 ASP cc_start: 0.5129 (m-30) cc_final: 0.4802 (t0) REVERT: C 852 PHE cc_start: 0.6520 (m-80) cc_final: 0.6082 (m-80) REVERT: C 976 ASP cc_start: 0.6205 (m-30) cc_final: 0.5760 (t0) REVERT: C 1064 TYR cc_start: 0.6653 (OUTLIER) cc_final: 0.6182 (t80) REVERT: C 1104 ARG cc_start: 0.6447 (OUTLIER) cc_final: 0.5654 (ptp-110) REVERT: E 4 GLN cc_start: 0.4217 (mp10) cc_final: 0.3908 (mm-40) REVERT: E 47 GLU cc_start: 0.4006 (tm-30) cc_final: 0.3712 (tm-30) REVERT: F 73 MET cc_start: 0.3872 (ptt) cc_final: 0.3610 (ptt) outliers start: 219 outliers final: 127 residues processed: 456 average time/residue: 0.3990 time to fit residues: 299.6408 Evaluate side-chains 348 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 196 time to evaluate : 3.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 978 PHE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 350 TRP Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain B residue 487 PHE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 506 ARG Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 800 SER Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1085 HIS Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1112 ILE Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 350 TRP Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 544 LYS Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 746 CYS Chi-restraints excluded: chain C residue 755 SER Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1064 TYR Chi-restraints excluded: chain C residue 1104 ARG Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 33 TYR Chi-restraints excluded: chain F residue 67 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 49 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 239 optimal weight: 0.7980 chunk 211 optimal weight: 5.9990 chunk 256 optimal weight: 8.9990 chunk 330 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 577 GLN ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN A 954 GLN ** A1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1132 ASN ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 HIS ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN B 904 ASN ** B 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** B1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 ASN ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.085844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.065472 restraints weight = 322530.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.067321 restraints weight = 162069.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.067508 restraints weight = 95416.761| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.6178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 29958 Z= 0.143 Angle : 0.704 9.328 40863 Z= 0.353 Chirality : 0.047 0.312 4656 Planarity : 0.005 0.053 5226 Dihedral : 9.587 116.117 4670 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.02 % Favored : 93.71 % Rotamer: Outliers : 4.26 % Allowed : 22.74 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.13), residues: 3645 helix: 0.81 (0.20), residues: 690 sheet: -0.73 (0.21), residues: 588 loop : -2.13 (0.11), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 630 HIS 0.005 0.001 HIS C 141 PHE 0.027 0.002 PHE B 715 TYR 0.023 0.002 TYR B 262 ARG 0.006 0.001 ARG C1104 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 21) link_NAG-ASN : angle 2.81309 ( 63) link_BETA1-4 : bond 0.01460 ( 12) link_BETA1-4 : angle 4.46744 ( 36) hydrogen bonds : bond 0.03862 ( 909) hydrogen bonds : angle 6.16742 ( 2609) SS BOND : bond 0.00657 ( 48) SS BOND : angle 1.39029 ( 96) covalent geometry : bond 0.00325 (29877) covalent geometry : angle 0.68062 (40668) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 251 time to evaluate : 3.057 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 196 PHE cc_start: 0.7735 (t80) cc_final: 0.7190 (t80) REVERT: A 383 LYS cc_start: 0.5173 (tptp) cc_final: 0.4933 (mttt) REVERT: A 520 THR cc_start: 0.2315 (OUTLIER) cc_final: 0.2039 (m) REVERT: A 555 LYS cc_start: 0.5934 (mppt) cc_final: 0.5011 (mtpp) REVERT: A 582 LEU cc_start: 0.5865 (mt) cc_final: 0.4939 (mt) REVERT: A 585 THR cc_start: 0.8178 (p) cc_final: 0.7973 (t) REVERT: A 723 ILE cc_start: 0.7514 (mp) cc_final: 0.7210 (mt) REVERT: A 879 ILE cc_start: 0.8673 (pt) cc_final: 0.8363 (mt) REVERT: A 978 PHE cc_start: 0.4580 (OUTLIER) cc_final: 0.3964 (t80) REVERT: A 1132 ASN cc_start: 0.7314 (OUTLIER) cc_final: 0.7031 (m-40) REVERT: B 102 TRP cc_start: 0.6062 (m-90) cc_final: 0.5017 (m-90) REVERT: B 115 LEU cc_start: 0.5676 (OUTLIER) cc_final: 0.5217 (mt) REVERT: B 424 ASP cc_start: 0.1646 (OUTLIER) cc_final: 0.1336 (t70) REVERT: B 433 TRP cc_start: 0.1316 (p90) cc_final: 0.0868 (p90) REVERT: B 487 PHE cc_start: 0.1640 (OUTLIER) cc_final: 0.1425 (t80) REVERT: B 506 ARG cc_start: 0.3531 (OUTLIER) cc_final: 0.2785 (ptp90) REVERT: B 532 LYS cc_start: 0.5622 (OUTLIER) cc_final: 0.5182 (tttp) REVERT: B 540 PHE cc_start: 0.3402 (OUTLIER) cc_final: 0.2676 (m-10) REVERT: B 603 ASN cc_start: 0.7434 (m-40) cc_final: 0.7042 (t0) REVERT: B 748 ASN cc_start: 0.7386 (OUTLIER) cc_final: 0.6503 (m-40) REVERT: B 797 PHE cc_start: 0.6505 (m-80) cc_final: 0.5738 (m-10) REVERT: B 963 LEU cc_start: 0.6847 (mt) cc_final: 0.6326 (pp) REVERT: B 975 ASN cc_start: 0.4294 (p0) cc_final: 0.4075 (p0) REVERT: C 123 ASN cc_start: 0.3657 (m110) cc_final: 0.3183 (t0) REVERT: C 127 LYS cc_start: 0.3062 (tptt) cc_final: 0.1833 (mtmt) REVERT: C 143 ASN cc_start: 0.3611 (m-40) cc_final: 0.3120 (p0) REVERT: C 148 MET cc_start: -0.0296 (tpt) cc_final: -0.1700 (ppp) REVERT: C 238 LEU cc_start: 0.7200 (mt) cc_final: 0.6985 (mm) REVERT: C 287 ASP cc_start: 0.5372 (OUTLIER) cc_final: 0.5144 (p0) REVERT: C 544 LYS cc_start: 0.6604 (OUTLIER) cc_final: 0.5654 (mmmt) REVERT: C 562 PHE cc_start: 0.5344 (OUTLIER) cc_final: 0.4960 (m-10) REVERT: C 852 PHE cc_start: 0.6361 (m-80) cc_final: 0.6056 (m-80) REVERT: C 1104 ARG cc_start: 0.6527 (OUTLIER) cc_final: 0.6178 (ptp-110) REVERT: C 1133 THR cc_start: 0.7045 (OUTLIER) cc_final: 0.6812 (p) REVERT: F 73 MET cc_start: 0.3567 (ptt) cc_final: 0.3285 (ptt) outliers start: 133 outliers final: 72 residues processed: 369 average time/residue: 0.3999 time to fit residues: 243.8534 Evaluate side-chains 287 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 200 time to evaluate : 3.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 978 PHE Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1132 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 487 PHE Chi-restraints excluded: chain B residue 506 ARG Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain B residue 800 SER Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 350 TRP Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 544 LYS Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 589 PHE Chi-restraints excluded: chain C residue 739 ILE Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 746 CYS Chi-restraints excluded: chain C residue 755 SER Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain C residue 1104 ARG Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain F residue 33 TYR Chi-restraints excluded: chain F residue 67 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 150 optimal weight: 10.0000 chunk 315 optimal weight: 0.9980 chunk 171 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 324 optimal weight: 0.0060 chunk 72 optimal weight: 5.9990 chunk 290 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1008 GLN ** A1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 ASN ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1085 HIS ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 ASN ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 687 GLN ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.086094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.065808 restraints weight = 319882.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.067496 restraints weight = 162222.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.067821 restraints weight = 96351.230| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 moved from start: 0.6294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 29958 Z= 0.130 Angle : 0.680 14.186 40863 Z= 0.339 Chirality : 0.047 0.335 4656 Planarity : 0.005 0.057 5226 Dihedral : 8.949 113.019 4670 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.65 % Favored : 93.10 % Rotamer: Outliers : 3.98 % Allowed : 23.68 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.13), residues: 3645 helix: 1.17 (0.20), residues: 690 sheet: -0.82 (0.20), residues: 639 loop : -1.99 (0.12), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 630 HIS 0.005 0.001 HIS C 141 PHE 0.025 0.002 PHE B 756 TYR 0.022 0.002 TYR B 262 ARG 0.009 0.000 ARG C1104 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 21) link_NAG-ASN : angle 2.58563 ( 63) link_BETA1-4 : bond 0.01523 ( 12) link_BETA1-4 : angle 4.37173 ( 36) hydrogen bonds : bond 0.03613 ( 909) hydrogen bonds : angle 5.88722 ( 2609) SS BOND : bond 0.00328 ( 48) SS BOND : angle 1.14533 ( 96) covalent geometry : bond 0.00295 (29877) covalent geometry : angle 0.65868 (40668) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 223 time to evaluate : 3.042 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 173 ASP cc_start: 0.1053 (OUTLIER) cc_final: 0.0355 (p0) REVERT: A 196 PHE cc_start: 0.7575 (t80) cc_final: 0.7148 (t80) REVERT: A 295 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6660 (tp30) REVERT: A 383 LYS cc_start: 0.5126 (tptp) cc_final: 0.4904 (mttt) REVERT: A 555 LYS cc_start: 0.5881 (mppt) cc_final: 0.5024 (mtpp) REVERT: A 582 LEU cc_start: 0.5884 (mt) cc_final: 0.4952 (mt) REVERT: A 702 VAL cc_start: 0.7216 (OUTLIER) cc_final: 0.7002 (m) REVERT: A 723 ILE cc_start: 0.7700 (mp) cc_final: 0.7388 (mt) REVERT: A 879 ILE cc_start: 0.8685 (pt) cc_final: 0.8344 (mt) REVERT: A 935 LEU cc_start: 0.7542 (mm) cc_final: 0.7079 (mt) REVERT: A 978 PHE cc_start: 0.4537 (OUTLIER) cc_final: 0.3940 (t80) REVERT: B 102 TRP cc_start: 0.6199 (m-90) cc_final: 0.5171 (m-90) REVERT: B 115 LEU cc_start: 0.5645 (OUTLIER) cc_final: 0.5209 (mt) REVERT: B 433 TRP cc_start: 0.1350 (p90) cc_final: 0.1045 (p90) REVERT: B 487 PHE cc_start: 0.1673 (OUTLIER) cc_final: 0.1458 (t80) REVERT: B 506 ARG cc_start: 0.3637 (OUTLIER) cc_final: 0.2760 (ptp90) REVERT: B 532 LYS cc_start: 0.5379 (OUTLIER) cc_final: 0.4936 (tttp) REVERT: B 540 PHE cc_start: 0.3497 (OUTLIER) cc_final: 0.2823 (m-10) REVERT: B 748 ASN cc_start: 0.7500 (OUTLIER) cc_final: 0.6653 (m-40) REVERT: B 797 PHE cc_start: 0.6503 (m-80) cc_final: 0.5700 (m-10) REVERT: B 818 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8279 (tt) REVERT: B 963 LEU cc_start: 0.6835 (mt) cc_final: 0.6311 (pp) REVERT: C 127 LYS cc_start: 0.3418 (tptt) cc_final: 0.2179 (mtpt) REVERT: C 148 MET cc_start: -0.0258 (tpt) cc_final: -0.1667 (ppp) REVERT: C 236 GLN cc_start: 0.4649 (mp10) cc_final: 0.4210 (tt0) REVERT: C 238 LEU cc_start: 0.7310 (mt) cc_final: 0.7058 (mm) REVERT: C 287 ASP cc_start: 0.5420 (OUTLIER) cc_final: 0.5209 (p0) REVERT: C 544 LYS cc_start: 0.6483 (OUTLIER) cc_final: 0.5521 (mmmt) REVERT: C 562 PHE cc_start: 0.4908 (OUTLIER) cc_final: 0.4649 (m-10) REVERT: C 852 PHE cc_start: 0.6329 (m-80) cc_final: 0.6021 (m-80) REVERT: C 1104 ARG cc_start: 0.6327 (OUTLIER) cc_final: 0.5175 (ptt-90) REVERT: E 73 MET cc_start: 0.1881 (ttp) cc_final: 0.1586 (ttt) REVERT: F 73 MET cc_start: 0.3401 (ptt) cc_final: 0.3078 (ptt) outliers start: 124 outliers final: 82 residues processed: 335 average time/residue: 0.3867 time to fit residues: 216.7230 Evaluate side-chains 294 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 197 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 978 PHE Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1116 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 487 PHE Chi-restraints excluded: chain B residue 506 ARG Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain B residue 800 SER Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1085 HIS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 350 TRP Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 544 LYS Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 589 PHE Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 709 ILE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 746 CYS Chi-restraints excluded: chain C residue 755 SER Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain C residue 1104 ARG Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain G residue 71 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 165 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 335 optimal weight: 6.9990 chunk 199 optimal weight: 0.9990 chunk 203 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 330 optimal weight: 7.9990 chunk 302 optimal weight: 0.0670 chunk 293 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1132 ASN ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN ** B 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1098 HIS ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.085747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.064343 restraints weight = 321340.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.067208 restraints weight = 165952.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.067181 restraints weight = 89118.334| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3670 r_free = 0.3670 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3670 r_free = 0.3670 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6163 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 29958 Z= 0.146 Angle : 0.685 9.531 40863 Z= 0.342 Chirality : 0.047 0.295 4656 Planarity : 0.005 0.054 5226 Dihedral : 8.794 113.892 4670 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.45 % Favored : 92.31 % Rotamer: Outliers : 4.70 % Allowed : 22.90 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.13), residues: 3645 helix: 1.08 (0.20), residues: 690 sheet: -0.74 (0.20), residues: 669 loop : -2.00 (0.12), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 630 HIS 0.026 0.001 HIS B1085 PHE 0.034 0.002 PHE C 303 TYR 0.022 0.002 TYR B 418 ARG 0.018 0.001 ARG C1104 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 21) link_NAG-ASN : angle 2.64333 ( 63) link_BETA1-4 : bond 0.01422 ( 12) link_BETA1-4 : angle 4.40475 ( 36) hydrogen bonds : bond 0.03700 ( 909) hydrogen bonds : angle 5.85879 ( 2609) SS BOND : bond 0.00388 ( 48) SS BOND : angle 1.27656 ( 96) covalent geometry : bond 0.00336 (29877) covalent geometry : angle 0.66280 (40668) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 210 time to evaluate : 3.270 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 173 ASP cc_start: 0.0556 (OUTLIER) cc_final: 0.0091 (p0) REVERT: A 196 PHE cc_start: 0.7658 (t80) cc_final: 0.7215 (t80) REVERT: A 295 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6748 (tp30) REVERT: A 383 LYS cc_start: 0.5341 (tptp) cc_final: 0.5028 (mttt) REVERT: A 470 TYR cc_start: 0.1015 (t80) cc_final: 0.0799 (t80) REVERT: A 555 LYS cc_start: 0.5866 (mppt) cc_final: 0.5485 (ptpt) REVERT: A 582 LEU cc_start: 0.5735 (mt) cc_final: 0.4814 (mt) REVERT: A 631 ARG cc_start: 0.3041 (OUTLIER) cc_final: 0.2508 (ptp90) REVERT: A 702 VAL cc_start: 0.7261 (OUTLIER) cc_final: 0.6993 (m) REVERT: A 723 ILE cc_start: 0.7634 (mp) cc_final: 0.7332 (mt) REVERT: A 879 ILE cc_start: 0.8649 (pt) cc_final: 0.8338 (mt) REVERT: A 935 LEU cc_start: 0.7441 (mm) cc_final: 0.6994 (mt) REVERT: A 978 PHE cc_start: 0.4610 (OUTLIER) cc_final: 0.3993 (t80) REVERT: B 102 TRP cc_start: 0.6132 (m-90) cc_final: 0.5115 (m-90) REVERT: B 115 LEU cc_start: 0.5700 (OUTLIER) cc_final: 0.5243 (mt) REVERT: B 464 ASP cc_start: 0.1985 (OUTLIER) cc_final: -0.0347 (t70) REVERT: B 506 ARG cc_start: 0.3702 (OUTLIER) cc_final: 0.2719 (ptp90) REVERT: B 532 LYS cc_start: 0.5364 (OUTLIER) cc_final: 0.4925 (tttp) REVERT: B 540 PHE cc_start: 0.3500 (OUTLIER) cc_final: 0.2772 (m-10) REVERT: B 748 ASN cc_start: 0.7384 (m-40) cc_final: 0.6584 (m-40) REVERT: B 797 PHE cc_start: 0.6552 (m-80) cc_final: 0.5710 (m-10) REVERT: B 963 LEU cc_start: 0.6952 (mt) cc_final: 0.6393 (pp) REVERT: C 52 GLN cc_start: 0.5953 (OUTLIER) cc_final: 0.5663 (mm-40) REVERT: C 127 LYS cc_start: 0.3319 (tptt) cc_final: 0.2145 (mtmt) REVERT: C 148 MET cc_start: -0.0435 (tpt) cc_final: -0.1819 (ppp) REVERT: C 238 LEU cc_start: 0.7450 (mt) cc_final: 0.7221 (mm) REVERT: C 272 PHE cc_start: 0.6426 (m-10) cc_final: 0.6154 (m-10) REVERT: C 287 ASP cc_start: 0.5830 (OUTLIER) cc_final: 0.5577 (p0) REVERT: C 562 PHE cc_start: 0.5329 (OUTLIER) cc_final: 0.5100 (m-10) REVERT: C 852 PHE cc_start: 0.6414 (m-80) cc_final: 0.6129 (m-80) REVERT: C 1104 ARG cc_start: 0.6279 (OUTLIER) cc_final: 0.5879 (ptt-90) REVERT: F 73 MET cc_start: 0.3645 (ptt) cc_final: 0.3420 (ptt) outliers start: 147 outliers final: 103 residues processed: 342 average time/residue: 0.3687 time to fit residues: 212.2652 Evaluate side-chains 305 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 188 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 978 PHE Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 350 TRP Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 506 ARG Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 800 SER Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 350 TRP Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 589 PHE Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 709 ILE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 755 SER Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 942 LEU Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain C residue 1104 ARG Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain G residue 51 CYS Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain G residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 347 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 326 optimal weight: 6.9990 chunk 195 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 153 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 ASN ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 989 GLN ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.084752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.065516 restraints weight = 289367.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.065823 restraints weight = 189147.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.065792 restraints weight = 141991.356| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.7165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.155 29958 Z= 0.220 Angle : 0.806 10.193 40863 Z= 0.407 Chirality : 0.051 0.320 4656 Planarity : 0.006 0.056 5226 Dihedral : 9.372 121.466 4670 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.12 % Favored : 90.60 % Rotamer: Outliers : 5.14 % Allowed : 23.09 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.13), residues: 3645 helix: 0.59 (0.20), residues: 672 sheet: -0.71 (0.21), residues: 540 loop : -2.24 (0.11), residues: 2433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 630 HIS 0.011 0.002 HIS B 622 PHE 0.034 0.003 PHE G 71 TYR 0.022 0.003 TYR C 165 ARG 0.007 0.001 ARG B 153 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 21) link_NAG-ASN : angle 3.28320 ( 63) link_BETA1-4 : bond 0.01472 ( 12) link_BETA1-4 : angle 4.38008 ( 36) hydrogen bonds : bond 0.04400 ( 909) hydrogen bonds : angle 6.32036 ( 2609) SS BOND : bond 0.00419 ( 48) SS BOND : angle 1.43962 ( 96) covalent geometry : bond 0.00502 (29877) covalent geometry : angle 0.78335 (40668) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 199 time to evaluate : 2.976 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 173 ASP cc_start: 0.0907 (OUTLIER) cc_final: 0.0429 (p0) REVERT: A 196 PHE cc_start: 0.7791 (t80) cc_final: 0.7338 (t80) REVERT: A 295 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6565 (tp30) REVERT: A 631 ARG cc_start: 0.3217 (OUTLIER) cc_final: 0.2619 (ptp90) REVERT: A 702 VAL cc_start: 0.7305 (OUTLIER) cc_final: 0.7100 (m) REVERT: A 935 LEU cc_start: 0.7541 (mm) cc_final: 0.7150 (mt) REVERT: A 978 PHE cc_start: 0.4449 (OUTLIER) cc_final: 0.3860 (t80) REVERT: B 102 TRP cc_start: 0.6075 (m-90) cc_final: 0.5275 (m-90) REVERT: B 115 LEU cc_start: 0.5806 (OUTLIER) cc_final: 0.5291 (mt) REVERT: B 253 SER cc_start: 0.3251 (m) cc_final: 0.3022 (p) REVERT: B 464 ASP cc_start: 0.2271 (OUTLIER) cc_final: -0.0039 (t70) REVERT: B 506 ARG cc_start: 0.3795 (OUTLIER) cc_final: 0.2623 (ptp90) REVERT: B 532 LYS cc_start: 0.5383 (OUTLIER) cc_final: 0.4952 (tttp) REVERT: B 540 PHE cc_start: 0.3417 (OUTLIER) cc_final: 0.2759 (m-10) REVERT: B 748 ASN cc_start: 0.7434 (OUTLIER) cc_final: 0.7200 (m-40) REVERT: B 963 LEU cc_start: 0.6617 (mt) cc_final: 0.6333 (mt) REVERT: C 123 ASN cc_start: 0.3475 (m110) cc_final: 0.3169 (t0) REVERT: C 127 LYS cc_start: 0.3315 (tptt) cc_final: 0.2279 (mtmt) REVERT: C 148 MET cc_start: -0.0080 (tpt) cc_final: -0.1715 (ppp) REVERT: C 245 TYR cc_start: 0.3250 (OUTLIER) cc_final: 0.2665 (t80) REVERT: C 287 ASP cc_start: 0.6089 (OUTLIER) cc_final: 0.5320 (p0) REVERT: C 562 PHE cc_start: 0.5576 (OUTLIER) cc_final: 0.5268 (m-10) REVERT: C 852 PHE cc_start: 0.6391 (m-80) cc_final: 0.5936 (m-80) REVERT: C 976 ASP cc_start: 0.6546 (m-30) cc_final: 0.6202 (t0) REVERT: E 71 PHE cc_start: 0.0607 (m-80) cc_final: -0.0222 (m-10) REVERT: G 47 GLU cc_start: 0.3866 (pp20) cc_final: 0.2453 (pm20) REVERT: F 73 MET cc_start: 0.3538 (ptt) cc_final: 0.3209 (ptt) outliers start: 161 outliers final: 117 residues processed: 342 average time/residue: 0.3436 time to fit residues: 196.0582 Evaluate side-chains 317 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 186 time to evaluate : 2.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 978 PHE Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1116 ASN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 350 TRP Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 506 ARG Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 800 SER Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 350 TRP Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 709 ILE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 746 CYS Chi-restraints excluded: chain C residue 755 SER Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 942 LEU Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain G residue 51 CYS Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 33 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 222 optimal weight: 7.9990 chunk 226 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 190 optimal weight: 0.0870 chunk 79 optimal weight: 0.0020 chunk 101 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 overall best weight: 1.8172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 ASN ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.085121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.065426 restraints weight = 250597.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.066065 restraints weight = 167846.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.066256 restraints weight = 114692.572| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.7264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 29958 Z= 0.165 Angle : 0.731 11.253 40863 Z= 0.368 Chirality : 0.048 0.355 4656 Planarity : 0.005 0.064 5226 Dihedral : 8.897 119.134 4670 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.75 % Favored : 91.98 % Rotamer: Outliers : 4.67 % Allowed : 24.12 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.13), residues: 3645 helix: 0.57 (0.20), residues: 708 sheet: -0.74 (0.21), residues: 570 loop : -2.18 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 630 HIS 0.008 0.001 HIS C 141 PHE 0.030 0.002 PHE G 71 TYR 0.023 0.002 TYR B 418 ARG 0.011 0.001 ARG B 980 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 21) link_NAG-ASN : angle 2.89702 ( 63) link_BETA1-4 : bond 0.01501 ( 12) link_BETA1-4 : angle 4.36505 ( 36) hydrogen bonds : bond 0.03880 ( 909) hydrogen bonds : angle 6.03282 ( 2609) SS BOND : bond 0.00325 ( 48) SS BOND : angle 1.55515 ( 96) covalent geometry : bond 0.00382 (29877) covalent geometry : angle 0.70823 (40668) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 216 time to evaluate : 3.788 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 173 ASP cc_start: 0.0861 (OUTLIER) cc_final: 0.0377 (p0) REVERT: A 196 PHE cc_start: 0.7615 (t80) cc_final: 0.7265 (t80) REVERT: A 295 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6689 (tp30) REVERT: A 631 ARG cc_start: 0.3081 (OUTLIER) cc_final: 0.2384 (ptp90) REVERT: A 702 VAL cc_start: 0.7340 (OUTLIER) cc_final: 0.7119 (m) REVERT: A 935 LEU cc_start: 0.7367 (mm) cc_final: 0.6944 (mt) REVERT: A 978 PHE cc_start: 0.4419 (OUTLIER) cc_final: 0.3808 (t80) REVERT: B 102 TRP cc_start: 0.6152 (m-90) cc_final: 0.5266 (m-90) REVERT: B 103 ILE cc_start: 0.4532 (OUTLIER) cc_final: 0.4286 (pt) REVERT: B 115 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5501 (mt) REVERT: B 464 ASP cc_start: 0.2091 (OUTLIER) cc_final: -0.0295 (t70) REVERT: B 506 ARG cc_start: 0.3588 (OUTLIER) cc_final: 0.2805 (ptp90) REVERT: B 532 LYS cc_start: 0.5506 (OUTLIER) cc_final: 0.5056 (tttp) REVERT: B 540 PHE cc_start: 0.3309 (OUTLIER) cc_final: 0.2701 (m-10) REVERT: B 549 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6838 (tp) REVERT: B 748 ASN cc_start: 0.7389 (OUTLIER) cc_final: 0.6633 (m-40) REVERT: B 963 LEU cc_start: 0.6742 (mt) cc_final: 0.6458 (mt) REVERT: C 123 ASN cc_start: 0.3123 (m110) cc_final: 0.2701 (t0) REVERT: C 127 LYS cc_start: 0.3928 (tptt) cc_final: 0.2766 (mtmt) REVERT: C 148 MET cc_start: -0.0100 (tpt) cc_final: -0.1729 (ppp) REVERT: C 287 ASP cc_start: 0.6018 (OUTLIER) cc_final: 0.5192 (p0) REVERT: C 494 PHE cc_start: 0.3805 (OUTLIER) cc_final: 0.3404 (t80) REVERT: C 539 ASN cc_start: 0.5667 (t0) cc_final: 0.5402 (m-40) REVERT: C 562 PHE cc_start: 0.5510 (OUTLIER) cc_final: 0.5196 (m-10) REVERT: C 694 MET cc_start: 0.7219 (tpt) cc_final: 0.6618 (mmm) REVERT: C 852 PHE cc_start: 0.6399 (m-80) cc_final: 0.5994 (m-80) REVERT: C 976 ASP cc_start: 0.6480 (m-30) cc_final: 0.6176 (t0) REVERT: G 47 GLU cc_start: 0.3324 (pp20) cc_final: 0.2140 (pm20) REVERT: F 73 MET cc_start: 0.3528 (ptt) cc_final: 0.3210 (ptt) outliers start: 146 outliers final: 111 residues processed: 343 average time/residue: 0.3725 time to fit residues: 213.4865 Evaluate side-chains 318 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 191 time to evaluate : 3.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 978 PHE Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1116 ASN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 506 ARG Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 800 SER Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 350 TRP Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 709 ILE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 746 CYS Chi-restraints excluded: chain C residue 755 SER Chi-restraints excluded: chain C residue 942 LEU Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain G residue 51 CYS Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 33 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 143 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 198 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 104 optimal weight: 0.0970 chunk 18 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 53 optimal weight: 0.4980 chunk 124 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 GLN A1116 ASN ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 923 GLN ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.085695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.065526 restraints weight = 233318.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.066677 restraints weight = 148382.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.067547 restraints weight = 90757.065| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.7221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 29958 Z= 0.128 Angle : 0.691 11.533 40863 Z= 0.344 Chirality : 0.047 0.361 4656 Planarity : 0.005 0.057 5226 Dihedral : 8.152 116.084 4670 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.95 % Favored : 92.77 % Rotamer: Outliers : 3.16 % Allowed : 25.88 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.13), residues: 3645 helix: 0.89 (0.20), residues: 711 sheet: -0.73 (0.20), residues: 669 loop : -2.02 (0.12), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 630 HIS 0.006 0.001 HIS C 141 PHE 0.028 0.002 PHE A 895 TYR 0.023 0.001 TYR B 262 ARG 0.013 0.001 ARG A 405 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 21) link_NAG-ASN : angle 2.60431 ( 63) link_BETA1-4 : bond 0.01445 ( 12) link_BETA1-4 : angle 4.37701 ( 36) hydrogen bonds : bond 0.03519 ( 909) hydrogen bonds : angle 5.64898 ( 2609) SS BOND : bond 0.00311 ( 48) SS BOND : angle 1.40937 ( 96) covalent geometry : bond 0.00290 (29877) covalent geometry : angle 0.66955 (40668) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 236 time to evaluate : 3.322 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 138 PHE cc_start: 0.3216 (p90) cc_final: 0.2632 (p90) REVERT: A 148 MET cc_start: 0.0031 (tpt) cc_final: -0.0212 (tpp) REVERT: A 173 ASP cc_start: 0.1102 (OUTLIER) cc_final: 0.0526 (p0) REVERT: A 196 PHE cc_start: 0.7491 (t80) cc_final: 0.7148 (t80) REVERT: A 295 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6886 (tp30) REVERT: A 492 TYR cc_start: 0.0361 (OUTLIER) cc_final: 0.0137 (m-80) REVERT: A 555 LYS cc_start: 0.5944 (mppt) cc_final: 0.5180 (mtpp) REVERT: A 631 ARG cc_start: 0.2806 (OUTLIER) cc_final: 0.2302 (ptp90) REVERT: A 728 MET cc_start: 0.6935 (ptm) cc_final: 0.6636 (ptt) REVERT: A 935 LEU cc_start: 0.7245 (mm) cc_final: 0.6845 (mt) REVERT: A 974 LEU cc_start: 0.5815 (OUTLIER) cc_final: 0.5025 (tp) REVERT: B 102 TRP cc_start: 0.6198 (m-90) cc_final: 0.5397 (m-90) REVERT: B 115 LEU cc_start: 0.5925 (OUTLIER) cc_final: 0.5449 (mt) REVERT: B 464 ASP cc_start: 0.1938 (OUTLIER) cc_final: -0.0452 (t70) REVERT: B 506 ARG cc_start: 0.3675 (OUTLIER) cc_final: 0.3098 (ptp90) REVERT: B 532 LYS cc_start: 0.5407 (OUTLIER) cc_final: 0.4984 (tttp) REVERT: B 540 PHE cc_start: 0.3180 (OUTLIER) cc_final: 0.2513 (m-10) REVERT: B 742 ASP cc_start: 0.5056 (m-30) cc_final: 0.4608 (t0) REVERT: B 963 LEU cc_start: 0.6828 (mt) cc_final: 0.6304 (pp) REVERT: C 123 ASN cc_start: 0.3042 (m110) cc_final: 0.2659 (t0) REVERT: C 127 LYS cc_start: 0.3763 (tptt) cc_final: 0.2580 (mtmt) REVERT: C 148 MET cc_start: -0.0084 (tpt) cc_final: -0.1667 (ppp) REVERT: C 287 ASP cc_start: 0.5979 (OUTLIER) cc_final: 0.5116 (p0) REVERT: C 494 PHE cc_start: 0.3665 (OUTLIER) cc_final: 0.3345 (t80) REVERT: C 539 ASN cc_start: 0.5422 (t0) cc_final: 0.5190 (m-40) REVERT: C 562 PHE cc_start: 0.5299 (OUTLIER) cc_final: 0.5019 (m-10) REVERT: C 694 MET cc_start: 0.7231 (tpt) cc_final: 0.6637 (mmm) REVERT: C 852 PHE cc_start: 0.6557 (m-80) cc_final: 0.6213 (m-80) REVERT: E 33 TYR cc_start: 0.2272 (m-10) cc_final: 0.2010 (m-10) REVERT: E 75 ARG cc_start: 0.4346 (OUTLIER) cc_final: 0.2934 (tpt-90) REVERT: G 47 GLU cc_start: 0.2957 (pp20) cc_final: 0.2016 (pm20) REVERT: F 73 MET cc_start: 0.3560 (ptt) cc_final: 0.3275 (ptt) outliers start: 98 outliers final: 71 residues processed: 324 average time/residue: 0.3738 time to fit residues: 198.8875 Evaluate side-chains 280 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 195 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 506 ARG Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 800 SER Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 350 TRP Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 709 ILE Chi-restraints excluded: chain C residue 942 LEU Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain G residue 51 CYS Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 33 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 8 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 38 optimal weight: 0.2980 chunk 78 optimal weight: 4.9990 chunk 191 optimal weight: 0.9980 chunk 326 optimal weight: 5.9990 chunk 181 optimal weight: 0.9980 chunk 349 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 230 optimal weight: 9.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 923 GLN ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1116 ASN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1098 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.084875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.065040 restraints weight = 278593.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.065763 restraints weight = 168567.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.065954 restraints weight = 123073.132| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.7482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 29958 Z= 0.173 Angle : 0.753 16.641 40863 Z= 0.377 Chirality : 0.049 0.334 4656 Planarity : 0.006 0.056 5226 Dihedral : 8.434 118.519 4670 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.30 % Favored : 91.40 % Rotamer: Outliers : 3.48 % Allowed : 25.72 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.13), residues: 3645 helix: 0.38 (0.20), residues: 747 sheet: -0.72 (0.21), residues: 591 loop : -2.08 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 630 HIS 0.008 0.001 HIS C 141 PHE 0.035 0.002 PHE A 978 TYR 0.019 0.002 TYR C 165 ARG 0.006 0.001 ARG A 405 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 21) link_NAG-ASN : angle 2.85645 ( 63) link_BETA1-4 : bond 0.01511 ( 12) link_BETA1-4 : angle 4.33528 ( 36) hydrogen bonds : bond 0.03941 ( 909) hydrogen bonds : angle 5.91788 ( 2609) SS BOND : bond 0.00522 ( 48) SS BOND : angle 2.06995 ( 96) covalent geometry : bond 0.00398 (29877) covalent geometry : angle 0.72830 (40668) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10876.00 seconds wall clock time: 190 minutes 56.95 seconds (11456.95 seconds total)