Starting phenix.real_space_refine on Tue Aug 26 00:08:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oyt_17295/08_2025/8oyt_17295.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oyt_17295/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8oyt_17295/08_2025/8oyt_17295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oyt_17295/08_2025/8oyt_17295.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oyt_17295/08_2025/8oyt_17295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oyt_17295/08_2025/8oyt_17295.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 7.53, per 1000 atoms: 0.26 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: 2.58 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.24 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: 6.81 Time building geometry restraints manager: 3.40 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 1302) selection = (chain 'C' and resid 19 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 28.260 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.700 ------------------------------------------------------------------------------- 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 : 19.26 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (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 ARG 0.020 0.001 ARG A 980 TYR 0.052 0.002 TYR A 393 PHE 0.107 0.002 PHE A 389 TRP 0.057 0.002 TRP A 630 HIS 0.007 0.001 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00417 (29877) covalent geometry : angle 0.91242 (40668) SS BOND : bond 0.00461 ( 48) SS BOND : angle 2.60816 ( 96) hydrogen bonds : bond 0.20121 ( 909) hydrogen bonds : angle 8.45569 ( 2609) link_BETA1-4 : bond 0.01417 ( 12) link_BETA1-4 : angle 5.42579 ( 36) link_NAG-ASN : bond 0.00696 ( 21) link_NAG-ASN : angle 4.42146 ( 63) *********************** 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 : 1.118 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: 0.4712 (m-80) REVERT: A 38 TYR cc_start: 0.5885 (m-80) cc_final: 0.5254 (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 86 ASP cc_start: 0.6318 (m-30) cc_final: 0.6118 (t0) 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: 0.5551 (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: 0.5639 (p90) REVERT: A 630 TRP cc_start: 0.1657 (m100) cc_final: 0.0906 (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: 0.6083 (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: 0.5954 (m-30) REVERT: A 987 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7175 (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 195 TYR cc_start: 0.7722 (m-80) cc_final: 0.7442 (m-80) REVERT: B 200 SER cc_start: 0.6905 (t) cc_final: 0.6631 (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: 0.6712 (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: 0.6477 (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: 0.7336 (tt0) REVERT: B 773 LYS cc_start: 0.8223 (ttpt) cc_final: 0.7995 (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: 0.6394 (t80) REVERT: C 44 ARG cc_start: 0.6202 (ptp-170) cc_final: 0.5613 (mpp80) REVERT: C 65 PHE cc_start: 0.6737 (m-80) cc_final: 0.6307 (m-80) REVERT: C 79 ASN cc_start: 0.2084 (m110) cc_final: 0.1839 (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: 0.6677 (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: 0.6590 (m-40) REVERT: C 540 PHE cc_start: 0.5290 (m-10) cc_final: 0.4957 (m-10) REVERT: C 655 ASN cc_start: 0.6753 (m-40) cc_final: 0.6468 (p0) REVERT: C 657 TYR cc_start: 0.7296 (m-10) cc_final: 0.6565 (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: 0.7949 (mt-10) REVERT: C 773 LYS cc_start: 0.8091 (ttpt) cc_final: 0.7783 (pttp) REVERT: C 792 LYS cc_start: 0.5588 (mmtm) cc_final: 0.5274 (mmtm) REVERT: C 967 PHE cc_start: 0.6403 (m-80) cc_final: 0.6015 (m-10) REVERT: C 974 LEU cc_start: 0.4684 (pt) cc_final: 0.4446 (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: 0.1831 time to fit residues: 212.3413 Evaluate side-chains 312 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 309 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 311 GLN ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 ASN A 577 GLN A 748 ASN A 904 ASN A 999 GLN A1007 GLN B 79 ASN ** B 141 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** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 GLN ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 GLN C 952 ASN G 2 GLN F 122 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.091024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.074305 restraints weight = 239591.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.073662 restraints weight = 196557.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.073876 restraints weight = 145506.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.074163 restraints weight = 128426.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.074229 restraints weight = 113659.262| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3800 r_free = 0.3800 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3800 r_free = 0.3800 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5965 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 29958 Z= 0.181 Angle : 0.783 10.573 40863 Z= 0.388 Chirality : 0.050 0.462 4656 Planarity : 0.006 0.057 5226 Dihedral : 11.982 113.980 4675 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.29 % Favored : 93.40 % Rotamer: Outliers : 3.16 % Allowed : 16.20 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.13), residues: 3645 helix: 1.33 (0.21), residues: 690 sheet: -0.40 (0.22), residues: 600 loop : -1.57 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 76 TYR 0.023 0.002 TYR B 362 PHE 0.030 0.002 PHE C 978 TRP 0.022 0.003 TRP A 630 HIS 0.007 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00408 (29877) covalent geometry : angle 0.75947 (40668) SS BOND : bond 0.00363 ( 48) SS BOND : angle 1.38341 ( 96) hydrogen bonds : bond 0.04309 ( 909) hydrogen bonds : angle 6.47587 ( 2609) link_BETA1-4 : bond 0.01540 ( 12) link_BETA1-4 : angle 4.53626 ( 36) link_NAG-ASN : bond 0.00570 ( 21) link_NAG-ASN : angle 3.24061 ( 63) *********************** 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 450 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 349 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.6060 (t70) cc_final: 0.5719 (p0) REVERT: A 98 ILE cc_start: 0.4957 (OUTLIER) cc_final: 0.4550 (mm) REVERT: A 136 ASP cc_start: 0.5282 (t70) cc_final: 0.4549 (m-30) REVERT: A 213 LEU cc_start: 0.5703 (OUTLIER) cc_final: 0.5467 (mt) REVERT: A 582 LEU cc_start: 0.5854 (mt) cc_final: 0.4942 (mt) REVERT: A 583 ASP cc_start: 0.3896 (OUTLIER) cc_final: 0.3651 (t0) REVERT: A 630 TRP cc_start: 0.1941 (m100) cc_final: 0.1530 (m-10) REVERT: A 632 VAL cc_start: 0.6053 (t) cc_final: 0.5757 (t) REVERT: B 64 TRP cc_start: 0.5602 (p-90) cc_final: 0.4920 (t60) REVERT: B 95 LYS cc_start: 0.3213 (tptp) cc_final: 0.2964 (pttt) REVERT: B 208 ARG cc_start: 0.4193 (OUTLIER) cc_final: 0.2955 (mmp80) REVERT: B 294 SER cc_start: 0.7767 (m) cc_final: 0.7300 (p) REVERT: B 314 ASN cc_start: 0.5984 (m110) cc_final: 0.5495 (p0) REVERT: B 411 GLN cc_start: 0.3004 (OUTLIER) cc_final: 0.2795 (pp30) REVERT: B 534 LYS cc_start: 0.4949 (mmtm) cc_final: 0.4559 (ptpt) REVERT: B 544 LYS cc_start: 0.6059 (tmtt) cc_final: 0.5703 (tptp) REVERT: B 555 LYS cc_start: 0.4756 (OUTLIER) cc_final: 0.3613 (mmtt) REVERT: B 935 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6780 (mm) REVERT: B 981 LEU cc_start: 0.6401 (mt) cc_final: 0.6047 (tp) REVERT: C 64 TRP cc_start: 0.7276 (p-90) cc_final: 0.7043 (p-90) REVERT: C 144 ASN cc_start: 0.2601 (m110) cc_final: 0.1711 (t0) REVERT: C 148 MET cc_start: -0.0990 (tpt) cc_final: -0.1928 (mmm) REVERT: C 243 ARG cc_start: 0.3960 (tpp-160) cc_final: 0.3759 (tpp-160) REVERT: C 540 PHE cc_start: 0.4895 (m-10) cc_final: 0.4392 (m-10) REVERT: C 543 LEU cc_start: 0.6998 (mm) cc_final: 0.6788 (mp) REVERT: C 544 LYS cc_start: 0.6135 (OUTLIER) cc_final: 0.5027 (mmmt) REVERT: C 1100 PHE cc_start: 0.5476 (m-80) cc_final: 0.5168 (m-10) REVERT: C 1103 GLN cc_start: 0.5922 (tp-100) cc_final: 0.5368 (tt0) REVERT: E 47 GLU cc_start: 0.4016 (tm-30) cc_final: 0.3781 (pp20) REVERT: G 37 TRP cc_start: 0.0970 (m100) cc_final: 0.0404 (m100) outliers start: 101 outliers final: 54 residues processed: 430 average time/residue: 0.1700 time to fit residues: 119.3469 Evaluate side-chains 277 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 215 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 213 LEU 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 492 TYR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 733 VAL 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 942 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 585 THR 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 785 ILE Chi-restraints excluded: chain B residue 800 SER 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 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 172 MET Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 544 LYS Chi-restraints excluded: chain C residue 548 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 739 ILE Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 945 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 334 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 275 optimal weight: 0.2980 chunk 66 optimal weight: 3.9990 chunk 254 optimal weight: 9.9990 chunk 167 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 268 optimal weight: 3.9990 chunk 242 optimal weight: 1.9990 chunk 351 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 311 GLN ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1008 GLN ** 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 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 ASN B 975 ASN B1116 ASN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.087414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.068422 restraints weight = 307730.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.068671 restraints weight = 197510.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.068876 restraints weight = 142592.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.069088 restraints weight = 145314.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.069270 restraints weight = 123549.024| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 29958 Z= 0.207 Angle : 0.791 13.708 40863 Z= 0.395 Chirality : 0.050 0.338 4656 Planarity : 0.006 0.067 5226 Dihedral : 10.615 116.158 4670 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.51 % Favored : 93.21 % Rotamer: Outliers : 4.39 % Allowed : 18.08 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.13), residues: 3645 helix: 0.88 (0.20), residues: 690 sheet: -0.50 (0.20), residues: 654 loop : -1.78 (0.12), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 185 TYR 0.026 0.002 TYR C 914 PHE 0.021 0.003 PHE F 71 TRP 0.024 0.003 TRP A 630 HIS 0.009 0.002 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00466 (29877) covalent geometry : angle 0.76760 (40668) SS BOND : bond 0.00546 ( 48) SS BOND : angle 1.67964 ( 96) hydrogen bonds : bond 0.04472 ( 909) hydrogen bonds : angle 6.43638 ( 2609) link_BETA1-4 : bond 0.01736 ( 12) link_BETA1-4 : angle 4.43035 ( 36) link_NAG-ASN : bond 0.00481 ( 21) link_NAG-ASN : angle 3.12148 ( 63) *********************** 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 407 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 269 time to evaluate : 1.055 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 98 ILE cc_start: 0.5341 (mp) cc_final: 0.4918 (mm) REVERT: A 136 ASP cc_start: 0.5102 (t70) cc_final: 0.4477 (m-30) REVERT: A 582 LEU cc_start: 0.6223 (mt) cc_final: 0.5326 (mp) REVERT: A 694 MET cc_start: 0.5995 (ptm) cc_final: 0.5415 (ttp) REVERT: A 899 MET cc_start: 0.7190 (tpp) cc_final: 0.6939 (tpp) REVERT: B 64 TRP cc_start: 0.5294 (p-90) cc_final: 0.4733 (t60) REVERT: B 115 LEU cc_start: 0.5421 (mm) cc_final: 0.5127 (mp) REVERT: B 195 TYR cc_start: 0.6571 (OUTLIER) cc_final: 0.6281 (m-10) REVERT: B 208 ARG cc_start: 0.3830 (OUTLIER) cc_final: 0.3111 (mmp80) REVERT: B 231 ASN cc_start: 0.4186 (t0) cc_final: 0.3278 (m110) REVERT: B 314 ASN cc_start: 0.5984 (m110) cc_final: 0.5450 (p0) REVERT: B 366 TYR cc_start: 0.3530 (m-80) cc_final: 0.3288 (m-80) REVERT: B 374 PHE cc_start: 0.2548 (OUTLIER) cc_final: 0.1900 (p90) REVERT: B 506 ARG cc_start: 0.3459 (OUTLIER) cc_final: 0.2880 (ptp90) REVERT: B 534 LYS cc_start: 0.5588 (mmtm) cc_final: 0.4997 (ptpt) REVERT: B 540 PHE cc_start: 0.2904 (OUTLIER) cc_final: 0.1945 (m-10) REVERT: B 633 TYR cc_start: 0.3384 (p90) cc_final: 0.3125 (p90) REVERT: B 1001 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7879 (tp) REVERT: B 1038 ASP cc_start: 0.7094 (t0) cc_final: 0.6449 (t0) REVERT: C 144 ASN cc_start: 0.3309 (m-40) cc_final: 0.2675 (t0) REVERT: C 148 MET cc_start: -0.0309 (tpt) cc_final: -0.1521 (mmm) REVERT: C 243 ARG cc_start: 0.4117 (tpp-160) cc_final: 0.3835 (tpp-160) REVERT: C 540 PHE cc_start: 0.5229 (m-10) cc_final: 0.4852 (m-80) REVERT: C 544 LYS cc_start: 0.6583 (OUTLIER) cc_final: 0.5879 (mmmt) REVERT: C 1001 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7617 (tp) REVERT: C 1117 THR cc_start: 0.6662 (p) cc_final: 0.6411 (t) REVERT: E 47 GLU cc_start: 0.3961 (tm-30) cc_final: 0.3641 (pp20) REVERT: G 37 TRP cc_start: 0.1137 (m100) cc_final: -0.0093 (m100) outliers start: 138 outliers final: 80 residues processed: 396 average time/residue: 0.1609 time to fit residues: 106.3676 Evaluate side-chains 294 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 206 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 112 THR 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 384 LEU 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 537 ASN Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 816 GLU 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 942 LEU 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 62 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 195 TYR 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 264 VAL 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 374 PHE Chi-restraints excluded: chain B residue 506 ARG 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 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 749 LEU Chi-restraints excluded: chain B residue 800 SER Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 959 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 C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU 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 544 LYS Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 729 THR 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 788 THR Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1007 GLN 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 71 PHE Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 67 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 53 optimal weight: 4.9990 chunk 262 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 293 optimal weight: 0.6980 chunk 250 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 13 optimal weight: 0.0870 overall best weight: 1.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN A 311 GLN A 419 ASN A 457 ASN A 478 ASN ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** A1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 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 411 GLN B 529 ASN ** B 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 ASN C 946 GLN ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1103 GLN ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 GLN G 57 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.087122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.066839 restraints weight = 270794.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.068147 restraints weight = 175887.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.069105 restraints weight = 114872.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.069105 restraints weight = 106520.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.069231 restraints weight = 80776.858| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6092 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 29958 Z= 0.171 Angle : 0.736 11.345 40863 Z= 0.365 Chirality : 0.048 0.304 4656 Planarity : 0.005 0.053 5226 Dihedral : 9.821 109.838 4670 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.65 % Favored : 93.08 % Rotamer: Outliers : 4.39 % Allowed : 19.42 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.13), residues: 3645 helix: 0.92 (0.20), residues: 690 sheet: -0.48 (0.20), residues: 681 loop : -1.90 (0.12), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 34 TYR 0.019 0.002 TYR E 98 PHE 0.028 0.002 PHE B 967 TRP 0.045 0.002 TRP A 630 HIS 0.009 0.002 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00391 (29877) covalent geometry : angle 0.71146 (40668) SS BOND : bond 0.00347 ( 48) SS BOND : angle 1.62284 ( 96) hydrogen bonds : bond 0.03992 ( 909) hydrogen bonds : angle 6.19149 ( 2609) link_BETA1-4 : bond 0.01595 ( 12) link_BETA1-4 : angle 4.40838 ( 36) link_NAG-ASN : bond 0.00421 ( 21) link_NAG-ASN : angle 3.07817 ( 63) *********************** 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 387 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 249 time to evaluate : 0.764 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 320 THR cc_start: 0.6446 (p) cc_final: 0.6227 (t) REVERT: A 555 LYS cc_start: 0.6126 (mppt) cc_final: 0.5135 (mtpp) REVERT: A 694 MET cc_start: 0.6039 (ptm) cc_final: 0.5466 (ttp) REVERT: A 739 ILE cc_start: 0.6791 (mm) cc_final: 0.6570 (tt) REVERT: B 64 TRP cc_start: 0.5050 (p-90) cc_final: 0.4579 (t60) REVERT: B 88 VAL cc_start: 0.5966 (m) cc_final: 0.5744 (p) REVERT: B 115 LEU cc_start: 0.5412 (OUTLIER) cc_final: 0.5144 (mp) REVERT: B 195 TYR cc_start: 0.6679 (OUTLIER) cc_final: 0.6288 (m-80) REVERT: B 208 ARG cc_start: 0.3690 (OUTLIER) cc_final: 0.3457 (mmp-170) REVERT: B 231 ASN cc_start: 0.4668 (t0) cc_final: 0.4265 (m110) REVERT: B 314 ASN cc_start: 0.6186 (m110) cc_final: 0.5582 (p0) REVERT: B 424 ASP cc_start: 0.2056 (OUTLIER) cc_final: 0.1843 (t70) REVERT: B 433 TRP cc_start: 0.1196 (p90) cc_final: 0.0700 (p90) REVERT: B 506 ARG cc_start: 0.3544 (OUTLIER) cc_final: 0.2868 (ptp90) REVERT: B 531 VAL cc_start: 0.5495 (p) cc_final: 0.5141 (p) REVERT: B 532 LYS cc_start: 0.5295 (OUTLIER) cc_final: 0.4935 (tttp) REVERT: B 534 LYS cc_start: 0.5676 (mmtm) cc_final: 0.5043 (ptpt) REVERT: B 540 PHE cc_start: 0.3501 (OUTLIER) cc_final: 0.2452 (m-10) REVERT: B 748 ASN cc_start: 0.7065 (m-40) cc_final: 0.6468 (m-40) REVERT: B 1001 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7916 (tp) REVERT: C 123 ASN cc_start: 0.4310 (m110) cc_final: 0.3986 (t0) REVERT: C 148 MET cc_start: -0.0530 (tpt) cc_final: -0.1657 (ppp) REVERT: C 323 ILE cc_start: 0.6389 (tt) cc_final: 0.6039 (tt) REVERT: C 540 PHE cc_start: 0.5291 (m-10) cc_final: 0.4908 (m-10) REVERT: C 544 LYS cc_start: 0.6503 (OUTLIER) cc_final: 0.5784 (mmmt) REVERT: C 694 MET cc_start: 0.6150 (tpt) cc_final: 0.5927 (tpt) REVERT: C 1001 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7812 (mm) REVERT: C 1002 GLN cc_start: 0.7588 (mm-40) cc_final: 0.7279 (mm-40) REVERT: C 1117 THR cc_start: 0.6691 (p) cc_final: 0.6429 (t) REVERT: G 37 TRP cc_start: 0.1182 (m100) cc_final: -0.0078 (m100) REVERT: F 38 PHE cc_start: 0.1518 (OUTLIER) cc_final: 0.0656 (m-80) outliers start: 138 outliers final: 82 residues processed: 373 average time/residue: 0.1783 time to fit residues: 110.3064 Evaluate side-chains 290 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 197 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 118 VAL Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 309 ILE 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 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 537 ASN Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 816 GLU 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 990 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 424 ASP 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 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 769 VAL Chi-restraints excluded: chain B residue 800 SER Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 959 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 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 171 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 359 VAL 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 469 ILE Chi-restraints excluded: chain C residue 544 LYS Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 717 ILE 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 755 SER Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 942 LEU Chi-restraints excluded: chain C residue 992 ARG Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1007 GLN 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 G residue 71 PHE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 38 PHE 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 307 optimal weight: 0.5980 chunk 266 optimal weight: 0.6980 chunk 191 optimal weight: 3.9990 chunk 320 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 202 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 199 optimal weight: 8.9990 chunk 153 optimal weight: 0.0170 chunk 196 optimal weight: 0.4980 chunk 125 optimal weight: 0.0980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN 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 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 ASN ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 GLN ** G 57 HIS ** 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 = 0.4181 r_free = 0.4181 target = 0.087804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.067773 restraints weight = 280652.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.069098 restraints weight = 174197.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.069047 restraints weight = 120958.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.069342 restraints weight = 112588.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.069530 restraints weight = 90426.558| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29958 Z= 0.125 Angle : 0.666 10.149 40863 Z= 0.328 Chirality : 0.046 0.316 4656 Planarity : 0.005 0.048 5226 Dihedral : 8.808 106.680 4670 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.05 % Favored : 93.71 % Rotamer: Outliers : 3.04 % Allowed : 21.37 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.13), residues: 3645 helix: 1.40 (0.21), residues: 672 sheet: -0.35 (0.20), residues: 666 loop : -1.82 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 185 TYR 0.023 0.001 TYR B 262 PHE 0.020 0.002 PHE B 715 TRP 0.026 0.002 TRP A 630 HIS 0.006 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00279 (29877) covalent geometry : angle 0.64297 (40668) SS BOND : bond 0.00229 ( 48) SS BOND : angle 1.41401 ( 96) hydrogen bonds : bond 0.03585 ( 909) hydrogen bonds : angle 5.79242 ( 2609) link_BETA1-4 : bond 0.01509 ( 12) link_BETA1-4 : angle 4.47913 ( 36) link_NAG-ASN : bond 0.00390 ( 21) link_NAG-ASN : angle 2.47503 ( 63) *********************** 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 338 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 244 time to evaluate : 1.157 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 424 ASP cc_start: 0.5613 (t0) cc_final: 0.5298 (p0) REVERT: A 694 MET cc_start: 0.6242 (ptm) cc_final: 0.5722 (ttp) REVERT: A 739 ILE cc_start: 0.6802 (mm) cc_final: 0.6584 (tt) REVERT: A 742 ASP cc_start: 0.5483 (OUTLIER) cc_final: 0.5230 (t0) REVERT: A 832 LYS cc_start: 0.3724 (mptt) cc_final: 0.3491 (mmtp) REVERT: A 878 THR cc_start: 0.8395 (m) cc_final: 0.8107 (p) REVERT: A 879 ILE cc_start: 0.8757 (pt) cc_final: 0.8511 (mt) REVERT: B 64 TRP cc_start: 0.5030 (p-90) cc_final: 0.4535 (t60) REVERT: B 115 LEU cc_start: 0.5365 (mm) cc_final: 0.5093 (mp) REVERT: B 195 TYR cc_start: 0.6757 (OUTLIER) cc_final: 0.6425 (m-80) REVERT: B 208 ARG cc_start: 0.3715 (OUTLIER) cc_final: 0.3007 (mmp80) REVERT: B 314 ASN cc_start: 0.6045 (m110) cc_final: 0.5368 (p0) REVERT: B 506 ARG cc_start: 0.3491 (OUTLIER) cc_final: 0.3085 (ptp90) REVERT: B 531 VAL cc_start: 0.5464 (p) cc_final: 0.5130 (p) REVERT: B 532 LYS cc_start: 0.5482 (OUTLIER) cc_final: 0.5148 (tttp) REVERT: B 534 LYS cc_start: 0.5656 (mmtm) cc_final: 0.4999 (ptpt) REVERT: B 540 PHE cc_start: 0.3430 (OUTLIER) cc_final: 0.2512 (m-10) REVERT: C 123 ASN cc_start: 0.2662 (m110) cc_final: 0.2299 (t0) REVERT: C 127 LYS cc_start: 0.3040 (tptt) cc_final: 0.1960 (mtpt) REVERT: C 148 MET cc_start: -0.0505 (tpt) cc_final: -0.1863 (ptt) REVERT: C 323 ILE cc_start: 0.6692 (tt) cc_final: 0.6394 (tt) REVERT: C 469 ILE cc_start: 0.0755 (OUTLIER) cc_final: 0.0429 (mp) REVERT: C 503 GLN cc_start: 0.4913 (OUTLIER) cc_final: 0.4415 (pm20) REVERT: C 529 ASN cc_start: 0.4961 (OUTLIER) cc_final: 0.4615 (m-40) REVERT: C 540 PHE cc_start: 0.5362 (m-10) cc_final: 0.4937 (m-80) REVERT: C 544 LYS cc_start: 0.6310 (OUTLIER) cc_final: 0.5626 (mmmt) REVERT: C 717 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.6932 (mt) REVERT: C 792 LYS cc_start: 0.5489 (mmtm) cc_final: 0.5157 (tppt) REVERT: C 1001 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7126 (tp) REVERT: C 1048 SER cc_start: 0.8500 (m) cc_final: 0.8175 (t) REVERT: C 1117 THR cc_start: 0.6581 (p) cc_final: 0.6296 (t) REVERT: G 37 TRP cc_start: 0.1185 (m100) cc_final: -0.0065 (m100) REVERT: F 33 TYR cc_start: 0.5846 (m-10) cc_final: 0.5261 (m-80) REVERT: F 38 PHE cc_start: 0.1234 (m-80) cc_final: 0.0465 (m-80) outliers start: 94 outliers final: 50 residues processed: 331 average time/residue: 0.1804 time to fit residues: 99.5233 Evaluate side-chains 256 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 194 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 362 TYR 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 711 ILE Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 350 TRP Chi-restraints excluded: chain B residue 500 VAL 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 584 ILE Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 739 ILE 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 C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 379 VAL 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 503 GLN Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 544 LYS 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 605 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 739 ILE Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain G residue 71 PHE 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 163 optimal weight: 8.9990 chunk 151 optimal weight: 9.9990 chunk 321 optimal weight: 9.9990 chunk 323 optimal weight: 0.9980 chunk 274 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 31 optimal weight: 0.3980 chunk 346 optimal weight: 4.9990 chunk 260 optimal weight: 3.9990 chunk 10 optimal weight: 0.0980 chunk 345 optimal weight: 0.0570 overall best weight: 1.1100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 577 GLN ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1132 ASN B 119 ASN ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 ASN ** 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 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 GLN C 950 ASN ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 GLN ** G 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.087183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.068588 restraints weight = 342114.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.068415 restraints weight = 213238.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.068771 restraints weight = 179512.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.068918 restraints weight = 149305.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.069137 restraints weight = 134964.853| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6055 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 29958 Z= 0.133 Angle : 0.670 10.616 40863 Z= 0.331 Chirality : 0.046 0.325 4656 Planarity : 0.005 0.050 5226 Dihedral : 8.499 106.023 4670 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.84 % Favored : 92.91 % Rotamer: Outliers : 3.76 % Allowed : 21.55 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.13), residues: 3645 helix: 1.30 (0.21), residues: 672 sheet: -0.45 (0.21), residues: 636 loop : -1.79 (0.12), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 185 TYR 0.022 0.002 TYR C 165 PHE 0.031 0.002 PHE B 852 TRP 0.025 0.002 TRP A 630 HIS 0.005 0.001 HIS B 622 Details of bonding type rmsd covalent geometry : bond 0.00302 (29877) covalent geometry : angle 0.64934 (40668) SS BOND : bond 0.00294 ( 48) SS BOND : angle 1.10763 ( 96) hydrogen bonds : bond 0.03587 ( 909) hydrogen bonds : angle 5.77070 ( 2609) link_BETA1-4 : bond 0.01521 ( 12) link_BETA1-4 : angle 4.40705 ( 36) link_NAG-ASN : bond 0.00385 ( 21) link_NAG-ASN : angle 2.48069 ( 63) *********************** 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 337 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 220 time to evaluate : 1.149 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 196 PHE cc_start: 0.7763 (t80) cc_final: 0.7212 (t80) REVERT: A 295 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6671 (tp30) REVERT: A 694 MET cc_start: 0.6042 (ptm) cc_final: 0.5519 (ttp) REVERT: A 742 ASP cc_start: 0.5495 (OUTLIER) cc_final: 0.5186 (t0) REVERT: A 878 THR cc_start: 0.8260 (m) cc_final: 0.8020 (p) REVERT: B 115 LEU cc_start: 0.5365 (OUTLIER) cc_final: 0.4938 (mt) REVERT: B 195 TYR cc_start: 0.6547 (OUTLIER) cc_final: 0.6224 (m-80) REVERT: B 208 ARG cc_start: 0.3545 (OUTLIER) cc_final: 0.2534 (mmp80) REVERT: B 314 ASN cc_start: 0.5969 (m110) cc_final: 0.5371 (p0) REVERT: B 464 ASP cc_start: 0.2718 (OUTLIER) cc_final: 0.0319 (t70) REVERT: B 506 ARG cc_start: 0.3271 (OUTLIER) cc_final: 0.2553 (ptp90) REVERT: B 531 VAL cc_start: 0.5446 (p) cc_final: 0.5133 (p) REVERT: B 532 LYS cc_start: 0.5430 (OUTLIER) cc_final: 0.5092 (tttp) REVERT: B 534 LYS cc_start: 0.5512 (mmtm) cc_final: 0.5106 (ptpt) REVERT: B 540 PHE cc_start: 0.3428 (OUTLIER) cc_final: 0.2550 (m-10) REVERT: B 963 LEU cc_start: 0.6541 (mt) cc_final: 0.6183 (pp) REVERT: B 974 LEU cc_start: 0.6160 (mm) cc_final: 0.5948 (mt) REVERT: C 43 PHE cc_start: 0.5811 (OUTLIER) cc_final: 0.5534 (t80) REVERT: C 123 ASN cc_start: 0.2776 (m110) cc_final: 0.2393 (t0) REVERT: C 127 LYS cc_start: 0.3416 (tptt) cc_final: 0.2327 (mtpt) REVERT: C 143 ASN cc_start: 0.3303 (m-40) cc_final: 0.3076 (p0) REVERT: C 148 MET cc_start: -0.0611 (tpt) cc_final: -0.1689 (ppp) REVERT: C 323 ILE cc_start: 0.6409 (tt) cc_final: 0.6161 (tt) REVERT: C 469 ILE cc_start: 0.0938 (OUTLIER) cc_final: 0.0565 (mp) REVERT: C 503 GLN cc_start: 0.4803 (OUTLIER) cc_final: 0.4352 (pm20) REVERT: C 540 PHE cc_start: 0.5285 (m-10) cc_final: 0.4987 (m-10) REVERT: C 544 LYS cc_start: 0.6396 (OUTLIER) cc_final: 0.5597 (mmmt) REVERT: C 694 MET cc_start: 0.6445 (tpt) cc_final: 0.6117 (tpt) REVERT: C 1001 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7313 (tp) REVERT: C 1002 GLN cc_start: 0.7441 (mm-40) cc_final: 0.7064 (mm-40) REVERT: C 1048 SER cc_start: 0.8424 (m) cc_final: 0.8130 (t) REVERT: C 1117 THR cc_start: 0.6611 (p) cc_final: 0.6357 (t) REVERT: E 73 MET cc_start: 0.1602 (ttt) cc_final: 0.1357 (ttp) REVERT: F 38 PHE cc_start: 0.1228 (m-80) cc_final: 0.0268 (m-80) outliers start: 117 outliers final: 72 residues processed: 325 average time/residue: 0.1734 time to fit residues: 93.7812 Evaluate side-chains 265 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 179 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 382 THR 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 500 VAL Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 816 GLU 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 990 ILE Chi-restraints excluded: chain A residue 1062 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 195 TYR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 305 VAL 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 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 702 VAL Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 800 SER Chi-restraints excluded: chain B residue 824 THR 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 43 PHE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 379 VAL 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 503 GLN Chi-restraints excluded: chain C residue 544 LYS Chi-restraints excluded: chain C residue 548 VAL 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 717 ILE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 739 ILE 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 874 LEU Chi-restraints excluded: chain C residue 992 ARG Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain G residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 193 optimal weight: 4.9990 chunk 311 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 338 optimal weight: 0.9990 chunk 319 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 217 optimal weight: 0.9980 chunk 357 optimal weight: 0.0770 chunk 273 optimal weight: 10.0000 chunk 86 optimal weight: 0.0470 overall best weight: 0.5236 ------------------------------------------------------------------------------- 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** ** 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 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 989 GLN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 GLN ** G 57 HIS ** 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 = 0.4171 r_free = 0.4171 target = 0.087136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.067259 restraints weight = 282409.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.068293 restraints weight = 174293.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.068438 restraints weight = 117551.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.068815 restraints weight = 106149.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.069237 restraints weight = 89048.600| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29958 Z= 0.120 Angle : 0.658 11.913 40863 Z= 0.324 Chirality : 0.046 0.298 4656 Planarity : 0.005 0.051 5226 Dihedral : 8.179 104.387 4670 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.96 % Favored : 93.79 % Rotamer: Outliers : 2.98 % Allowed : 22.18 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.13), residues: 3645 helix: 1.40 (0.21), residues: 690 sheet: -0.42 (0.21), residues: 612 loop : -1.76 (0.12), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C1104 TYR 0.029 0.001 TYR A 89 PHE 0.037 0.002 PHE A1100 TRP 0.020 0.001 TRP A 630 HIS 0.004 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00272 (29877) covalent geometry : angle 0.63578 (40668) SS BOND : bond 0.00483 ( 48) SS BOND : angle 1.58205 ( 96) hydrogen bonds : bond 0.03403 ( 909) hydrogen bonds : angle 5.58825 ( 2609) link_BETA1-4 : bond 0.01488 ( 12) link_BETA1-4 : angle 4.41870 ( 36) link_NAG-ASN : bond 0.00348 ( 21) link_NAG-ASN : angle 2.28751 ( 63) *********************** 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 304 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 212 time to evaluate : 1.141 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: 0.7730 (t80) cc_final: 0.7197 (t80) REVERT: A 694 MET cc_start: 0.5987 (ptm) cc_final: 0.5443 (ttp) REVERT: A 742 ASP cc_start: 0.5633 (OUTLIER) cc_final: 0.5372 (t0) REVERT: A 832 LYS cc_start: 0.3218 (mptt) cc_final: 0.2984 (mmtm) REVERT: A 878 THR cc_start: 0.8273 (m) cc_final: 0.8021 (p) REVERT: A 978 PHE cc_start: 0.4650 (OUTLIER) cc_final: 0.3957 (t80) REVERT: B 115 LEU cc_start: 0.5348 (mm) cc_final: 0.4858 (mt) REVERT: B 195 TYR cc_start: 0.6480 (OUTLIER) cc_final: 0.6131 (m-80) REVERT: B 208 ARG cc_start: 0.3520 (OUTLIER) cc_final: 0.2832 (mmp80) REVERT: B 314 ASN cc_start: 0.6019 (m110) cc_final: 0.5261 (p0) REVERT: B 324 VAL cc_start: 0.4106 (OUTLIER) cc_final: 0.3808 (t) REVERT: B 464 ASP cc_start: 0.2882 (OUTLIER) cc_final: 0.0345 (t70) REVERT: B 506 ARG cc_start: 0.3428 (OUTLIER) cc_final: 0.2788 (ptp90) REVERT: B 531 VAL cc_start: 0.5404 (p) cc_final: 0.5080 (p) REVERT: B 532 LYS cc_start: 0.5379 (OUTLIER) cc_final: 0.5028 (tttp) REVERT: B 534 LYS cc_start: 0.5391 (mmtm) cc_final: 0.4965 (ptpt) REVERT: B 540 PHE cc_start: 0.3336 (OUTLIER) cc_final: 0.2552 (m-10) REVERT: B 963 LEU cc_start: 0.6700 (mt) cc_final: 0.6344 (pp) REVERT: C 123 ASN cc_start: 0.2685 (m110) cc_final: 0.2313 (t0) REVERT: C 127 LYS cc_start: 0.3215 (tptt) cc_final: 0.2156 (mtpt) REVERT: C 148 MET cc_start: -0.0652 (tpt) cc_final: -0.1739 (ppp) REVERT: C 469 ILE cc_start: 0.0765 (OUTLIER) cc_final: 0.0428 (mp) REVERT: C 503 GLN cc_start: 0.4829 (OUTLIER) cc_final: 0.4343 (pm20) REVERT: C 540 PHE cc_start: 0.5434 (m-10) cc_final: 0.5136 (m-10) REVERT: C 544 LYS cc_start: 0.6171 (OUTLIER) cc_final: 0.5487 (mmmt) REVERT: C 694 MET cc_start: 0.6486 (tpt) cc_final: 0.6183 (tpt) REVERT: C 717 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.6937 (mt) REVERT: C 792 LYS cc_start: 0.5516 (mmtm) cc_final: 0.5185 (tppt) REVERT: C 1001 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7470 (tp) REVERT: C 1048 SER cc_start: 0.8456 (m) cc_final: 0.8116 (t) REVERT: C 1104 ARG cc_start: 0.5651 (OUTLIER) cc_final: 0.5165 (ptt-90) REVERT: C 1117 THR cc_start: 0.6632 (p) cc_final: 0.6392 (t) REVERT: C 1133 THR cc_start: 0.6659 (OUTLIER) cc_final: 0.6409 (p) REVERT: F 38 PHE cc_start: 0.1215 (m-80) cc_final: 0.0343 (m-80) outliers start: 92 outliers final: 59 residues processed: 297 average time/residue: 0.1810 time to fit residues: 89.5055 Evaluate side-chains 248 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 173 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 362 TYR 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 500 VAL Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 742 ASP 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 B residue 47 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 195 TYR 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 305 VAL Chi-restraints excluded: chain B residue 324 VAL 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 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 633 TYR 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 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 C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 379 VAL 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 503 GLN Chi-restraints excluded: chain C residue 544 LYS Chi-restraints excluded: chain C residue 548 VAL 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 717 ILE Chi-restraints excluded: chain C residue 739 ILE Chi-restraints excluded: chain C residue 755 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1104 ARG Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 110 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 230 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 354 optimal weight: 0.9990 chunk 234 optimal weight: 0.8980 chunk 311 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 267 optimal weight: 0.0970 chunk 5 optimal weight: 0.0070 chunk 331 optimal weight: 0.9980 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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** ** 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 904 ASN ** 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 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 687 GLN C 932 GLN ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 GLN ** G 57 HIS ** 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 = 0.4172 r_free = 0.4172 target = 0.087136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.067018 restraints weight = 294204.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.068806 restraints weight = 150968.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.069148 restraints weight = 88784.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.069236 restraints weight = 89414.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.069357 restraints weight = 77724.227| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6077 moved from start: 0.5823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29958 Z= 0.117 Angle : 0.664 21.918 40863 Z= 0.325 Chirality : 0.046 0.320 4656 Planarity : 0.005 0.050 5226 Dihedral : 7.876 103.145 4670 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.40 % Favored : 93.35 % Rotamer: Outliers : 2.88 % Allowed : 22.43 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.14), residues: 3645 helix: 1.41 (0.21), residues: 690 sheet: -0.42 (0.20), residues: 672 loop : -1.76 (0.12), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 762 TYR 0.029 0.001 TYR A 89 PHE 0.036 0.002 PHE F 71 TRP 0.020 0.001 TRP A 630 HIS 0.003 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00262 (29877) covalent geometry : angle 0.64005 (40668) SS BOND : bond 0.00478 ( 48) SS BOND : angle 1.96248 ( 96) hydrogen bonds : bond 0.03318 ( 909) hydrogen bonds : angle 5.45667 ( 2609) link_BETA1-4 : bond 0.01526 ( 12) link_BETA1-4 : angle 4.40614 ( 36) link_NAG-ASN : bond 0.00335 ( 21) link_NAG-ASN : angle 2.21238 ( 63) *********************** 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 289 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 200 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.7671 (t80) cc_final: 0.7141 (t80) REVERT: A 228 ILE cc_start: 0.6053 (pt) cc_final: 0.5569 (mt) REVERT: A 694 MET cc_start: 0.6002 (ptm) cc_final: 0.5584 (ttp) REVERT: A 832 LYS cc_start: 0.3210 (mptt) cc_final: 0.2960 (mmtm) REVERT: A 978 PHE cc_start: 0.4707 (OUTLIER) cc_final: 0.4054 (t80) REVERT: B 115 LEU cc_start: 0.5370 (OUTLIER) cc_final: 0.4866 (mt) REVERT: B 195 TYR cc_start: 0.6550 (OUTLIER) cc_final: 0.6182 (m-80) REVERT: B 208 ARG cc_start: 0.3181 (OUTLIER) cc_final: 0.2544 (mmp80) REVERT: B 314 ASN cc_start: 0.6049 (m110) cc_final: 0.5293 (p0) REVERT: B 324 VAL cc_start: 0.4129 (OUTLIER) cc_final: 0.3826 (t) REVERT: B 433 TRP cc_start: 0.1215 (p90) cc_final: 0.0085 (p90) REVERT: B 464 ASP cc_start: 0.2641 (OUTLIER) cc_final: 0.0264 (t70) REVERT: B 506 ARG cc_start: 0.3632 (OUTLIER) cc_final: 0.2763 (ptp90) REVERT: B 531 VAL cc_start: 0.5435 (p) cc_final: 0.5104 (p) REVERT: B 532 LYS cc_start: 0.5361 (OUTLIER) cc_final: 0.5009 (tttp) REVERT: B 534 LYS cc_start: 0.5409 (mmtm) cc_final: 0.4974 (ptpt) REVERT: B 540 PHE cc_start: 0.3320 (OUTLIER) cc_final: 0.2601 (m-10) REVERT: B 963 LEU cc_start: 0.6682 (mt) cc_final: 0.6340 (pp) REVERT: C 123 ASN cc_start: 0.2957 (m110) cc_final: 0.2516 (t0) REVERT: C 127 LYS cc_start: 0.3223 (tptt) cc_final: 0.2133 (mtpt) REVERT: C 148 MET cc_start: -0.0669 (tpt) cc_final: -0.1779 (ppp) REVERT: C 494 PHE cc_start: 0.3692 (OUTLIER) cc_final: 0.2993 (m-10) REVERT: C 540 PHE cc_start: 0.5375 (m-10) cc_final: 0.5048 (m-10) REVERT: C 544 LYS cc_start: 0.6007 (OUTLIER) cc_final: 0.5367 (mmmt) REVERT: C 694 MET cc_start: 0.6604 (tpt) cc_final: 0.6306 (tpt) REVERT: C 717 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.6946 (mt) REVERT: C 792 LYS cc_start: 0.5517 (mmtm) cc_final: 0.5183 (tppt) REVERT: C 1001 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7398 (tp) REVERT: C 1048 SER cc_start: 0.8279 (m) cc_final: 0.7902 (t) REVERT: C 1104 ARG cc_start: 0.5722 (OUTLIER) cc_final: 0.5425 (ptp-110) REVERT: C 1117 THR cc_start: 0.6726 (p) cc_final: 0.6490 (t) REVERT: C 1133 THR cc_start: 0.6708 (m) cc_final: 0.6449 (p) REVERT: F 38 PHE cc_start: 0.1104 (m-80) cc_final: 0.0343 (m-80) outliers start: 89 outliers final: 60 residues processed: 279 average time/residue: 0.1767 time to fit residues: 82.9515 Evaluate side-chains 250 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 176 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 392 VAL 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 500 VAL Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 627 THR 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 978 PHE Chi-restraints excluded: chain A residue 1062 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 195 TYR 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 305 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 338 VAL 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 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 702 VAL 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 800 SER Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 446 TYR Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 503 GLN Chi-restraints excluded: chain C residue 544 LYS Chi-restraints excluded: chain C residue 548 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 717 ILE 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 755 SER Chi-restraints excluded: chain C residue 932 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1104 ARG Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain G residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 24 optimal weight: 20.0000 chunk 236 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 254 optimal weight: 2.9990 chunk 334 optimal weight: 3.9990 chunk 314 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 chunk 75 optimal weight: 0.5980 chunk 120 optimal weight: 0.8980 chunk 295 optimal weight: 2.9990 chunk 352 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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** ** A1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN B 202 HIS ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 ASN ** 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 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 GLN ** G 57 HIS ** 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 = 0.4158 r_free = 0.4158 target = 0.086513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.066489 restraints weight = 278941.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.067883 restraints weight = 167218.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.067889 restraints weight = 112111.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.068183 restraints weight = 110957.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.068338 restraints weight = 90498.795| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 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 = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 moved from start: 0.6155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 29958 Z= 0.135 Angle : 0.683 16.069 40863 Z= 0.337 Chirality : 0.046 0.271 4656 Planarity : 0.005 0.050 5226 Dihedral : 7.821 106.255 4670 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.46 % Favored : 93.29 % Rotamer: Outliers : 2.91 % Allowed : 22.46 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.13), residues: 3645 helix: 1.26 (0.21), residues: 690 sheet: -0.52 (0.21), residues: 627 loop : -1.78 (0.12), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 234 TYR 0.025 0.002 TYR A 89 PHE 0.032 0.002 PHE B 756 TRP 0.022 0.002 TRP A 630 HIS 0.005 0.001 HIS B 622 Details of bonding type rmsd covalent geometry : bond 0.00309 (29877) covalent geometry : angle 0.66054 (40668) SS BOND : bond 0.00344 ( 48) SS BOND : angle 1.81271 ( 96) hydrogen bonds : bond 0.03497 ( 909) hydrogen bonds : angle 5.53318 ( 2609) link_BETA1-4 : bond 0.01466 ( 12) link_BETA1-4 : angle 4.35663 ( 36) link_NAG-ASN : bond 0.00317 ( 21) link_NAG-ASN : angle 2.33240 ( 63) *********************** 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 279 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 189 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.7682 (t80) cc_final: 0.7166 (t80) REVERT: A 228 ILE cc_start: 0.5962 (pt) cc_final: 0.5531 (mt) REVERT: A 978 PHE cc_start: 0.4523 (OUTLIER) cc_final: 0.3896 (t80) REVERT: B 115 LEU cc_start: 0.5366 (OUTLIER) cc_final: 0.4839 (mt) REVERT: B 208 ARG cc_start: 0.3588 (OUTLIER) cc_final: 0.2902 (mmp80) REVERT: B 314 ASN cc_start: 0.6009 (m110) cc_final: 0.5390 (p0) REVERT: B 324 VAL cc_start: 0.3960 (OUTLIER) cc_final: 0.3639 (t) REVERT: B 433 TRP cc_start: 0.1352 (p90) cc_final: 0.0236 (p90) REVERT: B 464 ASP cc_start: 0.3329 (OUTLIER) cc_final: 0.0395 (t70) REVERT: B 506 ARG cc_start: 0.3577 (OUTLIER) cc_final: 0.2674 (ptp90) REVERT: B 531 VAL cc_start: 0.5474 (p) cc_final: 0.5121 (p) REVERT: B 532 LYS cc_start: 0.5306 (OUTLIER) cc_final: 0.4985 (tttp) REVERT: B 534 LYS cc_start: 0.5284 (mmtm) cc_final: 0.4923 (ptpt) REVERT: B 540 PHE cc_start: 0.3167 (OUTLIER) cc_final: 0.2374 (m-10) REVERT: B 866 MET cc_start: 0.5035 (ptp) cc_final: 0.4601 (ptp) REVERT: B 963 LEU cc_start: 0.6499 (mt) cc_final: 0.6227 (pp) REVERT: C 123 ASN cc_start: 0.2993 (m110) cc_final: 0.2550 (t0) REVERT: C 127 LYS cc_start: 0.3297 (tptt) cc_final: 0.2440 (mttp) REVERT: C 148 MET cc_start: -0.0549 (tpt) cc_final: -0.1748 (ppp) REVERT: C 544 LYS cc_start: 0.6027 (OUTLIER) cc_final: 0.5514 (mmmt) REVERT: C 694 MET cc_start: 0.6564 (tpt) cc_final: 0.6140 (tpt) REVERT: C 717 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.6833 (mt) REVERT: C 1001 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7210 (tp) REVERT: C 1002 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7465 (mm-40) REVERT: C 1048 SER cc_start: 0.8338 (m) cc_final: 0.7951 (t) REVERT: E 21 LEU cc_start: 0.2720 (mt) cc_final: 0.2288 (tp) REVERT: G 39 ARG cc_start: 0.3319 (ptt90) cc_final: 0.2938 (ptp90) outliers start: 90 outliers final: 67 residues processed: 266 average time/residue: 0.1831 time to fit residues: 81.8304 Evaluate side-chains 250 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 172 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 392 VAL 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 500 VAL Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 816 GLU 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 978 PHE Chi-restraints excluded: chain A residue 1062 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 200 SER Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 338 VAL 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 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 739 ILE Chi-restraints excluded: chain B residue 800 SER Chi-restraints excluded: chain B residue 824 THR 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 52 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 379 VAL 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 544 LYS Chi-restraints excluded: chain C residue 548 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 717 ILE 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 755 SER Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1104 ARG Chi-restraints excluded: chain E residue 86 MET 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 G residue 110 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 320 optimal weight: 2.9990 chunk 313 optimal weight: 6.9990 chunk 328 optimal weight: 10.0000 chunk 185 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 274 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 54 optimal weight: 7.9990 chunk 296 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 211 optimal weight: 4.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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 892 GLN ** 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 ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN ** B 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 ASN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN C 202 HIS ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1098 HIS C1116 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.085212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.065086 restraints weight = 332762.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.066653 restraints weight = 172673.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.066723 restraints weight = 109932.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.066924 restraints weight = 106481.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.067055 restraints weight = 95788.200| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.6939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.180 29958 Z= 0.223 Angle : 0.834 11.046 40863 Z= 0.420 Chirality : 0.052 0.351 4656 Planarity : 0.006 0.060 5226 Dihedral : 8.878 122.412 4670 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.66 % Favored : 91.07 % Rotamer: Outliers : 3.26 % Allowed : 22.40 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.13), residues: 3645 helix: 0.46 (0.20), residues: 693 sheet: -0.90 (0.20), residues: 636 loop : -2.00 (0.12), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 902 TYR 0.028 0.003 TYR F 98 PHE 0.033 0.003 PHE G 71 TRP 0.032 0.003 TRP C 147 HIS 0.012 0.002 HIS B 622 Details of bonding type rmsd covalent geometry : bond 0.00505 (29877) covalent geometry : angle 0.81046 (40668) SS BOND : bond 0.00846 ( 48) SS BOND : angle 1.83993 ( 96) hydrogen bonds : bond 0.04308 ( 909) hydrogen bonds : angle 6.13318 ( 2609) link_BETA1-4 : bond 0.01805 ( 12) link_BETA1-4 : angle 4.53062 ( 36) link_NAG-ASN : bond 0.00514 ( 21) link_NAG-ASN : angle 3.15888 ( 63) ********************** 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 313 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 212 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.7768 (t80) cc_final: 0.7196 (t80) REVERT: A 555 LYS cc_start: 0.6054 (mppt) cc_final: 0.4973 (mtpp) REVERT: A 935 LEU cc_start: 0.7412 (mm) cc_final: 0.6984 (mt) REVERT: A 978 PHE cc_start: 0.4594 (OUTLIER) cc_final: 0.3964 (t80) REVERT: B 102 TRP cc_start: 0.6138 (m-90) cc_final: 0.5148 (m-90) REVERT: B 115 LEU cc_start: 0.5456 (OUTLIER) cc_final: 0.4841 (mt) REVERT: B 195 TYR cc_start: 0.6494 (OUTLIER) cc_final: 0.6220 (m-80) REVERT: B 208 ARG cc_start: 0.3591 (OUTLIER) cc_final: 0.3324 (mmp-170) REVERT: B 433 TRP cc_start: 0.1219 (p90) cc_final: 0.0679 (p90) REVERT: B 464 ASP cc_start: 0.2986 (OUTLIER) cc_final: 0.0303 (t70) REVERT: B 506 ARG cc_start: 0.3448 (OUTLIER) cc_final: 0.2246 (ptp90) REVERT: B 514 LEU cc_start: 0.2297 (OUTLIER) cc_final: 0.1857 (tp) REVERT: B 531 VAL cc_start: 0.5419 (p) cc_final: 0.5019 (p) REVERT: B 532 LYS cc_start: 0.5590 (OUTLIER) cc_final: 0.5109 (tttp) REVERT: B 540 PHE cc_start: 0.3067 (OUTLIER) cc_final: 0.2436 (m-10) REVERT: C 123 ASN cc_start: 0.3643 (m110) cc_final: 0.3090 (t0) REVERT: C 127 LYS cc_start: 0.3150 (tptt) cc_final: 0.2216 (mttp) REVERT: C 148 MET cc_start: -0.0346 (tpt) cc_final: -0.1778 (ppp) REVERT: C 544 LYS cc_start: 0.6357 (OUTLIER) cc_final: 0.5869 (mmmt) REVERT: C 745 GLU cc_start: 0.5712 (pm20) cc_final: 0.5339 (tt0) REVERT: C 792 LYS cc_start: 0.5937 (mmtm) cc_final: 0.5686 (mmtm) REVERT: C 852 PHE cc_start: 0.6540 (m-80) cc_final: 0.6101 (m-80) REVERT: C 1001 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7149 (tp) REVERT: C 1002 GLN cc_start: 0.7495 (mm-40) cc_final: 0.7225 (mm-40) REVERT: E 73 MET cc_start: 0.1782 (ttp) cc_final: 0.1448 (ttt) REVERT: E 106 TYR cc_start: 0.3978 (m-80) cc_final: 0.3740 (m-80) REVERT: G 47 GLU cc_start: 0.3670 (pp20) cc_final: 0.2315 (pm20) REVERT: G 86 MET cc_start: 0.1463 (mmm) cc_final: 0.1095 (mmm) outliers start: 101 outliers final: 70 residues processed: 303 average time/residue: 0.1799 time to fit residues: 91.1984 Evaluate side-chains 259 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 178 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 392 VAL 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 500 VAL Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 816 GLU 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 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 195 TYR 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 305 VAL Chi-restraints excluded: chain B residue 338 VAL 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 514 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 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 791 ILE Chi-restraints excluded: chain B residue 800 SER Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 1037 VAL 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 81 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 436 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 544 LYS Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 585 THR 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 717 ILE Chi-restraints excluded: chain C residue 729 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 755 SER Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain G residue 71 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 9 optimal weight: 8.9990 chunk 240 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 230 optimal weight: 0.8980 chunk 335 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 357 optimal weight: 6.9990 chunk 305 optimal weight: 0.9990 chunk 235 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 263 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 HIS ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 ASN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.085910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.066282 restraints weight = 293028.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.067240 restraints weight = 177925.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.067099 restraints weight = 128957.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.067611 restraints weight = 120592.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.067825 restraints weight = 101954.472| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.6954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 29958 Z= 0.136 Angle : 0.709 9.867 40863 Z= 0.351 Chirality : 0.048 0.380 4656 Planarity : 0.005 0.055 5226 Dihedral : 8.127 118.009 4670 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.43 % Favored : 93.29 % Rotamer: Outliers : 2.60 % Allowed : 23.65 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.13), residues: 3645 helix: 0.80 (0.21), residues: 693 sheet: -0.73 (0.19), residues: 702 loop : -1.87 (0.12), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 70 TYR 0.027 0.002 TYR A 89 PHE 0.031 0.002 PHE B 756 TRP 0.028 0.002 TRP A 630 HIS 0.006 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00308 (29877) covalent geometry : angle 0.68624 (40668) SS BOND : bond 0.00365 ( 48) SS BOND : angle 1.38801 ( 96) hydrogen bonds : bond 0.03613 ( 909) hydrogen bonds : angle 5.66645 ( 2609) link_BETA1-4 : bond 0.01432 ( 12) link_BETA1-4 : angle 4.56535 ( 36) link_NAG-ASN : bond 0.00342 ( 21) link_NAG-ASN : angle 2.60241 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6052.10 seconds wall clock time: 105 minutes 20.50 seconds (6320.50 seconds total)