Starting phenix.real_space_refine on Thu Mar 21 16:20:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r40_14250/03_2024/7r40_14250.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r40_14250/03_2024/7r40_14250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r40_14250/03_2024/7r40_14250.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r40_14250/03_2024/7r40_14250.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r40_14250/03_2024/7r40_14250.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r40_14250/03_2024/7r40_14250.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 19449 2.51 5 N 5052 2.21 5 O 5982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30615 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8230 Classifications: {'peptide': 1053} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 996} Chain breaks: 7 Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 905 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "B" Number of atoms: 8230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8230 Classifications: {'peptide': 1053} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 996} Chain breaks: 7 Chain: "F" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "D" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 905 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "C" Number of atoms: 8230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8230 Classifications: {'peptide': 1053} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 996} Chain breaks: 7 Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "E" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 905 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} 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: "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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 15.31, per 1000 atoms: 0.50 Number of scatterers: 30615 At special positions: 0 Unit cell: (152.52, 158.72, 230.64, 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 132 16.00 O 5982 8.00 N 5052 7.00 C 19449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=3, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 17 " " NAG A1308 " - " ASN A 331 " " NAG A1309 " - " ASN A 343 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B 17 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B 343 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C 17 " " NAG C1308 " - " ASN C 331 " " NAG C1309 " - " ASN C 343 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A1134 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C1134 " " NAG U 1 " - " ASN C 801 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.58 Conformation dependent library (CDL) restraints added in 5.7 seconds 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7122 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 63 sheets defined 18.2% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.77 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.598A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.898A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 341 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 341' Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.015A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.534A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.845A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.797A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.711A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 897 through 908 removed outlier: 4.770A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.588A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.560A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.869A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 984 removed outlier: 3.667A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1032 removed outlier: 4.528A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.609A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.642A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.598A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.898A pdb=" N GLU B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 341 " --> pdb=" O PHE B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 337 through 341' Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.015A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 742 removed outlier: 3.534A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.846A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.798A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.711A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 Processing helix chain 'B' and resid 897 through 908 removed outlier: 4.770A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.588A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.560A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.869A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 977 through 984 removed outlier: 3.667A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1032 removed outlier: 4.527A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.608A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.642A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.598A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.898A pdb=" N GLU C 340 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 341 " --> pdb=" O PHE C 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 337 through 341' Processing helix chain 'C' and resid 365 through 370 removed outlier: 4.015A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 742 removed outlier: 3.534A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.845A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.798A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.711A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 Processing helix chain 'C' and resid 897 through 908 removed outlier: 4.770A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.588A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.561A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.870A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 984 removed outlier: 3.667A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1032 removed outlier: 4.528A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.609A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.642A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.022A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.487A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.718A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 49 removed outlier: 8.036A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.874A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 157 removed outlier: 4.020A pdb=" N SER A 155 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 141 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL A 143 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR A 145 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.462A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.538A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.734A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 448 through 454 removed outlier: 6.309A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.711A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.398A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.219A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.309A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.666A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'L' and resid 5 through 6 removed outlier: 4.206A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.650A pdb=" N ARG L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 20 through 21 removed outlier: 3.846A pdb=" N LEU H 20 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.899A pdb=" N GLU H 46 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS H 98 " --> pdb=" O PHE H 109 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE H 109 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.899A pdb=" N GLU H 46 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA H 92 " --> pdb=" O VAL H 116 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.021A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.487A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC8, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.718A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 48 through 49 removed outlier: 8.037A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.874A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 151 through 157 removed outlier: 4.019A pdb=" N SER B 155 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 141 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL B 143 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 246 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR B 145 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.463A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.537A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.733A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 448 through 454 removed outlier: 6.311A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.398A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.219A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.309A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE2, first strand: chain 'B' and resid 787 through 789 removed outlier: 5.732A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'F' and resid 5 through 6 removed outlier: 4.205A pdb=" N CYS F 23 " --> pdb=" O PHE F 71 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.649A pdb=" N ARG F 45 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 20 through 21 removed outlier: 3.847A pdb=" N LEU D 20 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.898A pdb=" N GLU D 46 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 37 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS D 98 " --> pdb=" O PHE D 109 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE D 109 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.898A pdb=" N GLU D 46 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 37 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA D 92 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.022A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 48 through 49 removed outlier: 3.718A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 48 through 49 removed outlier: 8.037A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.874A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 151 through 157 removed outlier: 4.019A pdb=" N SER C 155 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C 141 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL C 143 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG C 246 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR C 145 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.463A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 325 through 327 removed outlier: 3.539A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.733A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 448 through 454 removed outlier: 6.309A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.397A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.219A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.309A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG5, first strand: chain 'G' and resid 5 through 6 removed outlier: 4.206A pdb=" N CYS G 23 " --> pdb=" O PHE G 71 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE G 71 " --> pdb=" O CYS G 23 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.650A pdb=" N ARG G 45 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 20 through 21 removed outlier: 3.847A pdb=" N LEU E 20 " --> pdb=" O LEU E 81 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.899A pdb=" N GLU E 46 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS E 98 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE E 109 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.899A pdb=" N GLU E 46 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA E 92 " --> pdb=" O VAL E 116 " (cutoff:3.500A) 895 hydrogen bonds defined for protein. 2505 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: 14.24 Time building geometry restraints manager: 12.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9759 1.35 - 1.47: 8051 1.47 - 1.60: 13339 1.60 - 1.72: 0 1.72 - 1.84: 168 Bond restraints: 31317 Sorted by residual: bond pdb=" N PRO C 899 " pdb=" CD PRO C 899 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.69e+01 bond pdb=" N PRO A 899 " pdb=" CD PRO A 899 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.66e+01 bond pdb=" N PRO B 899 " pdb=" CD PRO B 899 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.22e+00 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.17e+00 ... (remaining 31312 not shown) Histogram of bond angle deviations from ideal: 99.29 - 106.38: 869 106.38 - 113.47: 16820 113.47 - 120.55: 12028 120.55 - 127.64: 12655 127.64 - 134.73: 219 Bond angle restraints: 42591 Sorted by residual: angle pdb=" CA PRO B 899 " pdb=" N PRO B 899 " pdb=" CD PRO B 899 " ideal model delta sigma weight residual 112.00 99.29 12.71 1.40e+00 5.10e-01 8.24e+01 angle pdb=" CA PRO A 899 " pdb=" N PRO A 899 " pdb=" CD PRO A 899 " ideal model delta sigma weight residual 112.00 99.31 12.69 1.40e+00 5.10e-01 8.22e+01 angle pdb=" CA PRO C 899 " pdb=" N PRO C 899 " pdb=" CD PRO C 899 " ideal model delta sigma weight residual 112.00 99.33 12.67 1.40e+00 5.10e-01 8.19e+01 angle pdb=" C LYS A 529 " pdb=" CA LYS A 529 " pdb=" CB LYS A 529 " ideal model delta sigma weight residual 115.89 109.77 6.12 1.32e+00 5.74e-01 2.15e+01 angle pdb=" C LYS C 529 " pdb=" CA LYS C 529 " pdb=" CB LYS C 529 " ideal model delta sigma weight residual 115.89 109.80 6.09 1.32e+00 5.74e-01 2.13e+01 ... (remaining 42586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 17418 17.63 - 35.26: 1421 35.26 - 52.89: 313 52.89 - 70.52: 52 70.52 - 88.15: 53 Dihedral angle restraints: 19257 sinusoidal: 8148 harmonic: 11109 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -24.11 -61.89 1 1.00e+01 1.00e-02 5.08e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -24.14 -61.86 1 1.00e+01 1.00e-02 5.07e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -24.15 -61.85 1 1.00e+01 1.00e-02 5.07e+01 ... (remaining 19254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4299 0.083 - 0.167: 596 0.167 - 0.250: 19 0.250 - 0.333: 0 0.333 - 0.416: 6 Chirality restraints: 4920 Sorted by residual: chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.32e+00 ... (remaining 4917 not shown) Planarity restraints: 5487 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 898 " -0.093 5.00e-02 4.00e+02 1.30e-01 2.71e+01 pdb=" N PRO A 899 " 0.225 5.00e-02 4.00e+02 pdb=" CA PRO A 899 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 899 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 898 " 0.093 5.00e-02 4.00e+02 1.30e-01 2.71e+01 pdb=" N PRO B 899 " -0.224 5.00e-02 4.00e+02 pdb=" CA PRO B 899 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO B 899 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 898 " 0.093 5.00e-02 4.00e+02 1.30e-01 2.70e+01 pdb=" N PRO C 899 " -0.224 5.00e-02 4.00e+02 pdb=" CA PRO C 899 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO C 899 " 0.066 5.00e-02 4.00e+02 ... (remaining 5484 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 9813 2.84 - 3.35: 24845 3.35 - 3.87: 49774 3.87 - 4.38: 54111 4.38 - 4.90: 93784 Nonbonded interactions: 232327 Sorted by model distance: nonbonded pdb=" O THR B1116 " pdb=" OG1 THR B1120 " model vdw 2.324 2.440 nonbonded pdb=" O THR C1116 " pdb=" OG1 THR C1120 " model vdw 2.325 2.440 nonbonded pdb=" O THR A1116 " pdb=" OG1 THR A1120 " model vdw 2.325 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.326 2.440 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.326 2.440 ... (remaining 232322 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.460 Check model and map are aligned: 0.490 Set scattering table: 0.350 Process input model: 82.290 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.290 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:10.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6160 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 0.058 31317 Z= 0.247 Angle : 0.732 12.706 42591 Z= 0.370 Chirality : 0.052 0.416 4920 Planarity : 0.007 0.130 5448 Dihedral : 13.999 88.155 11991 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.12), residues: 3780 helix: -3.72 (0.09), residues: 603 sheet: -0.50 (0.18), residues: 831 loop : -1.75 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 47 HIS 0.003 0.000 HIS B1048 PHE 0.016 0.001 PHE G 49 TYR 0.010 0.001 TYR C 351 ARG 0.005 0.000 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 776 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.6741 (m) cc_final: 0.6457 (t) REVERT: A 58 PHE cc_start: 0.7383 (m-10) cc_final: 0.7019 (m-80) REVERT: A 129 LYS cc_start: 0.6947 (mppt) cc_final: 0.6629 (mppt) REVERT: A 310 LYS cc_start: 0.8167 (ttpt) cc_final: 0.7785 (ttpp) REVERT: A 319 ARG cc_start: 0.7123 (ptp90) cc_final: 0.6697 (ptt180) REVERT: A 374 PHE cc_start: 0.6948 (m-80) cc_final: 0.6659 (m-10) REVERT: A 455 LEU cc_start: 0.8268 (mm) cc_final: 0.7864 (mm) REVERT: A 511 VAL cc_start: 0.8113 (t) cc_final: 0.7894 (p) REVERT: A 572 THR cc_start: 0.8105 (t) cc_final: 0.7668 (p) REVERT: A 606 ASN cc_start: 0.8119 (m-40) cc_final: 0.7883 (m-40) REVERT: A 612 TYR cc_start: 0.8288 (m-80) cc_final: 0.7890 (m-80) REVERT: A 671 CYS cc_start: 0.5055 (m) cc_final: 0.4817 (m) REVERT: A 673 SER cc_start: 0.8365 (t) cc_final: 0.8029 (p) REVERT: A 725 GLU cc_start: 0.7325 (tt0) cc_final: 0.7069 (tt0) REVERT: A 736 VAL cc_start: 0.7929 (t) cc_final: 0.7715 (m) REVERT: A 790 LYS cc_start: 0.7401 (mmpt) cc_final: 0.7087 (mmpt) REVERT: A 933 LYS cc_start: 0.7924 (mttt) cc_final: 0.7710 (mttt) REVERT: A 936 ASP cc_start: 0.7675 (m-30) cc_final: 0.7327 (m-30) REVERT: A 947 LYS cc_start: 0.7924 (mtpt) cc_final: 0.7615 (mtpp) REVERT: A 964 LYS cc_start: 0.7858 (mttt) cc_final: 0.7643 (mttt) REVERT: A 975 SER cc_start: 0.8576 (p) cc_final: 0.8228 (t) REVERT: A 1045 LYS cc_start: 0.7927 (mttt) cc_final: 0.7533 (mttt) REVERT: A 1082 CYS cc_start: 0.5882 (t) cc_final: 0.5446 (t) REVERT: A 1086 LYS cc_start: 0.6615 (mtmm) cc_final: 0.6110 (mtmm) REVERT: A 1092 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6811 (mt-10) REVERT: A 1101 HIS cc_start: 0.7475 (m-70) cc_final: 0.7185 (m170) REVERT: A 1138 TYR cc_start: 0.7675 (t80) cc_final: 0.7439 (t80) REVERT: L 71 PHE cc_start: 0.5786 (t80) cc_final: 0.5218 (t80) REVERT: B 53 ASP cc_start: 0.5842 (t0) cc_final: 0.5597 (t0) REVERT: B 54 LEU cc_start: 0.7550 (mm) cc_final: 0.7343 (mm) REVERT: B 153 MET cc_start: 0.4381 (mpp) cc_final: 0.4166 (mpp) REVERT: B 192 PHE cc_start: 0.7684 (m-80) cc_final: 0.7335 (m-80) REVERT: B 269 TYR cc_start: 0.6950 (m-80) cc_final: 0.6349 (m-80) REVERT: B 319 ARG cc_start: 0.7154 (ptp90) cc_final: 0.6841 (ptt180) REVERT: B 340 GLU cc_start: 0.6812 (mp0) cc_final: 0.6420 (mp0) REVERT: B 374 PHE cc_start: 0.6793 (m-80) cc_final: 0.6208 (m-80) REVERT: B 427 ASP cc_start: 0.7460 (p0) cc_final: 0.7215 (p0) REVERT: B 511 VAL cc_start: 0.8281 (t) cc_final: 0.7949 (p) REVERT: B 541 PHE cc_start: 0.6432 (p90) cc_final: 0.6087 (p90) REVERT: B 586 ASP cc_start: 0.7245 (m-30) cc_final: 0.6991 (m-30) REVERT: B 612 TYR cc_start: 0.8224 (m-80) cc_final: 0.7990 (m-80) REVERT: B 655 HIS cc_start: 0.7519 (t70) cc_final: 0.7299 (t-170) REVERT: B 675 GLN cc_start: 0.7175 (mt0) cc_final: 0.6971 (mt0) REVERT: B 725 GLU cc_start: 0.7045 (tt0) cc_final: 0.6786 (tt0) REVERT: B 731 MET cc_start: 0.8013 (mtm) cc_final: 0.7718 (mtm) REVERT: B 764 ASN cc_start: 0.7218 (m-40) cc_final: 0.7015 (m-40) REVERT: B 772 VAL cc_start: 0.8514 (p) cc_final: 0.8195 (t) REVERT: B 790 LYS cc_start: 0.7328 (mmpt) cc_final: 0.6852 (mmmt) REVERT: B 933 LYS cc_start: 0.7898 (mttt) cc_final: 0.7306 (mmtm) REVERT: B 947 LYS cc_start: 0.7805 (mtpt) cc_final: 0.7508 (mtpp) REVERT: B 950 ASP cc_start: 0.7513 (m-30) cc_final: 0.7108 (m-30) REVERT: B 1050 MET cc_start: 0.8046 (ptm) cc_final: 0.7769 (ptm) REVERT: B 1082 CYS cc_start: 0.5844 (t) cc_final: 0.5394 (t) REVERT: B 1138 TYR cc_start: 0.7570 (t80) cc_final: 0.7204 (t80) REVERT: F 35 TRP cc_start: 0.4773 (m-10) cc_final: 0.4556 (m-10) REVERT: F 71 PHE cc_start: 0.5833 (t80) cc_final: 0.5452 (t80) REVERT: C 29 THR cc_start: 0.7104 (m) cc_final: 0.6759 (t) REVERT: C 45 SER cc_start: 0.7750 (t) cc_final: 0.7383 (p) REVERT: C 47 VAL cc_start: 0.8166 (m) cc_final: 0.7951 (m) REVERT: C 53 ASP cc_start: 0.6313 (t0) cc_final: 0.6031 (t70) REVERT: C 54 LEU cc_start: 0.7405 (mm) cc_final: 0.7091 (mm) REVERT: C 138 ASP cc_start: 0.6414 (t0) cc_final: 0.6155 (t0) REVERT: C 192 PHE cc_start: 0.7483 (m-80) cc_final: 0.7214 (m-80) REVERT: C 237 ARG cc_start: 0.6765 (mtp85) cc_final: 0.6230 (mpp80) REVERT: C 340 GLU cc_start: 0.6712 (mp0) cc_final: 0.6468 (mp0) REVERT: C 374 PHE cc_start: 0.6729 (m-80) cc_final: 0.6322 (m-80) REVERT: C 427 ASP cc_start: 0.7512 (p0) cc_final: 0.7240 (p0) REVERT: C 453 TYR cc_start: 0.6947 (p90) cc_final: 0.5541 (p90) REVERT: C 511 VAL cc_start: 0.8263 (t) cc_final: 0.7968 (p) REVERT: C 532 ASN cc_start: 0.8300 (t0) cc_final: 0.8090 (t0) REVERT: C 541 PHE cc_start: 0.6507 (p90) cc_final: 0.5979 (p90) REVERT: C 553 THR cc_start: 0.8147 (p) cc_final: 0.7929 (p) REVERT: C 572 THR cc_start: 0.8110 (m) cc_final: 0.7857 (p) REVERT: C 612 TYR cc_start: 0.8135 (m-80) cc_final: 0.7789 (m-80) REVERT: C 725 GLU cc_start: 0.7187 (tt0) cc_final: 0.6904 (tt0) REVERT: C 772 VAL cc_start: 0.8442 (p) cc_final: 0.8235 (t) REVERT: C 773 GLU cc_start: 0.7237 (pt0) cc_final: 0.7033 (tt0) REVERT: C 790 LYS cc_start: 0.7371 (mmpt) cc_final: 0.7023 (mmpt) REVERT: C 868 GLU cc_start: 0.7122 (mp0) cc_final: 0.6830 (mp0) REVERT: C 933 LYS cc_start: 0.7927 (mttt) cc_final: 0.7419 (mptt) REVERT: C 936 ASP cc_start: 0.7347 (m-30) cc_final: 0.7138 (m-30) REVERT: C 947 LYS cc_start: 0.7952 (mtpt) cc_final: 0.7664 (mtpp) REVERT: C 950 ASP cc_start: 0.7478 (m-30) cc_final: 0.7165 (m-30) REVERT: C 954 GLN cc_start: 0.7959 (mt0) cc_final: 0.7629 (mt0) REVERT: C 964 LYS cc_start: 0.7848 (mttt) cc_final: 0.7554 (mttt) REVERT: C 975 SER cc_start: 0.8623 (p) cc_final: 0.8324 (t) REVERT: C 1091 ARG cc_start: 0.7576 (mtt-85) cc_final: 0.7369 (mmt90) REVERT: C 1101 HIS cc_start: 0.7635 (m-70) cc_final: 0.7426 (m-70) REVERT: G 71 PHE cc_start: 0.5991 (t80) cc_final: 0.5570 (t80) REVERT: G 92 PHE cc_start: 0.6863 (m-80) cc_final: 0.6616 (m-80) REVERT: E 68 PHE cc_start: 0.7039 (m-10) cc_final: 0.6694 (m-10) outliers start: 0 outliers final: 4 residues processed: 776 average time/residue: 1.2371 time to fit residues: 1144.3694 Evaluate side-chains 659 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 655 time to evaluate : 3.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 321 optimal weight: 0.9980 chunk 288 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 298 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 222 optimal weight: 0.9980 chunk 345 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN A 957 GLN A1010 GLN L 27 GLN ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN B 317 ASN B 448 ASN B 540 ASN B 607 GLN B 804 GLN B 919 ASN B 957 GLN B 960 ASN B1101 HIS C 49 HIS ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 764 ASN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C1010 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31317 Z= 0.230 Angle : 0.643 11.993 42591 Z= 0.321 Chirality : 0.047 0.477 4920 Planarity : 0.005 0.060 5448 Dihedral : 7.299 101.327 5209 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.44 % Allowed : 11.95 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.13), residues: 3780 helix: -0.36 (0.19), residues: 588 sheet: -0.45 (0.18), residues: 855 loop : -1.62 (0.12), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 353 HIS 0.005 0.001 HIS A 49 PHE 0.026 0.002 PHE B 490 TYR 0.028 0.002 TYR A 453 ARG 0.008 0.001 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 691 time to evaluate : 3.407 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 58 PHE cc_start: 0.7376 (m-10) cc_final: 0.7033 (m-10) REVERT: A 153 MET cc_start: 0.3599 (mpp) cc_final: 0.3285 (mpp) REVERT: A 208 THR cc_start: 0.8207 (t) cc_final: 0.7983 (p) REVERT: A 319 ARG cc_start: 0.7437 (ptp90) cc_final: 0.6997 (ptt180) REVERT: A 420 ASP cc_start: 0.5388 (p0) cc_final: 0.4390 (p0) REVERT: A 421 TYR cc_start: 0.6384 (m-80) cc_final: 0.6077 (m-80) REVERT: A 572 THR cc_start: 0.8403 (t) cc_final: 0.8165 (p) REVERT: A 612 TYR cc_start: 0.8232 (m-80) cc_final: 0.7772 (m-80) REVERT: A 651 ILE cc_start: 0.8636 (mm) cc_final: 0.8430 (mp) REVERT: A 673 SER cc_start: 0.8375 (t) cc_final: 0.8022 (p) REVERT: A 719 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.8044 (p) REVERT: A 736 VAL cc_start: 0.8116 (t) cc_final: 0.7807 (m) REVERT: A 776 LYS cc_start: 0.7780 (tmmt) cc_final: 0.7516 (ttpp) REVERT: A 790 LYS cc_start: 0.7446 (mmpt) cc_final: 0.6991 (mmmt) REVERT: A 811 LYS cc_start: 0.6957 (mmpt) cc_final: 0.6579 (mtpp) REVERT: A 933 LYS cc_start: 0.7897 (mttt) cc_final: 0.7508 (mtmm) REVERT: A 936 ASP cc_start: 0.7518 (m-30) cc_final: 0.7247 (m-30) REVERT: A 975 SER cc_start: 0.8628 (p) cc_final: 0.8275 (t) REVERT: A 1045 LYS cc_start: 0.7880 (mttt) cc_final: 0.7504 (mttt) REVERT: A 1086 LYS cc_start: 0.6760 (mtmm) cc_final: 0.6236 (mtmm) REVERT: L 71 PHE cc_start: 0.6047 (t80) cc_final: 0.5214 (t80) REVERT: L 81 GLU cc_start: 0.7364 (mp0) cc_final: 0.7089 (mp0) REVERT: H 34 MET cc_start: 0.5981 (ppp) cc_final: 0.5450 (ppp) REVERT: H 114 THR cc_start: 0.5146 (p) cc_final: 0.4943 (m) REVERT: B 49 HIS cc_start: 0.7575 (t-90) cc_final: 0.7356 (t70) REVERT: B 53 ASP cc_start: 0.6118 (t0) cc_final: 0.5892 (t0) REVERT: B 54 LEU cc_start: 0.7626 (mm) cc_final: 0.7407 (mm) REVERT: B 129 LYS cc_start: 0.7132 (mmtm) cc_final: 0.6917 (mmtm) REVERT: B 153 MET cc_start: 0.4592 (mpp) cc_final: 0.4330 (mpp) REVERT: B 192 PHE cc_start: 0.7950 (m-80) cc_final: 0.7666 (m-80) REVERT: B 286 THR cc_start: 0.7721 (OUTLIER) cc_final: 0.7444 (t) REVERT: B 319 ARG cc_start: 0.7483 (ptp90) cc_final: 0.7076 (ptt180) REVERT: B 340 GLU cc_start: 0.6541 (mp0) cc_final: 0.6301 (mp0) REVERT: B 421 TYR cc_start: 0.6433 (m-80) cc_final: 0.6184 (m-10) REVERT: B 427 ASP cc_start: 0.7557 (p0) cc_final: 0.7305 (p0) REVERT: B 497 PHE cc_start: 0.3772 (m-10) cc_final: 0.2967 (m-10) REVERT: B 541 PHE cc_start: 0.6368 (p90) cc_final: 0.5992 (p90) REVERT: B 586 ASP cc_start: 0.7038 (m-30) cc_final: 0.6583 (m-30) REVERT: B 675 GLN cc_start: 0.7250 (mt0) cc_final: 0.7026 (mt0) REVERT: B 725 GLU cc_start: 0.7351 (tt0) cc_final: 0.7133 (tt0) REVERT: B 764 ASN cc_start: 0.7088 (m-40) cc_final: 0.6826 (m-40) REVERT: B 772 VAL cc_start: 0.8436 (p) cc_final: 0.8217 (t) REVERT: B 776 LYS cc_start: 0.7939 (tmmt) cc_final: 0.7725 (ttpp) REVERT: B 780 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7119 (pt0) REVERT: B 859 THR cc_start: 0.8058 (t) cc_final: 0.7841 (p) REVERT: B 931 ILE cc_start: 0.7716 (mm) cc_final: 0.7460 (tp) REVERT: B 933 LYS cc_start: 0.7985 (mttt) cc_final: 0.7353 (mmtm) REVERT: B 947 LYS cc_start: 0.7816 (mtpt) cc_final: 0.7537 (mtpp) REVERT: B 950 ASP cc_start: 0.7433 (m-30) cc_final: 0.7000 (m-30) REVERT: B 1029 MET cc_start: 0.7971 (ttm) cc_final: 0.7729 (tpp) REVERT: B 1050 MET cc_start: 0.8082 (ptm) cc_final: 0.7854 (ptm) REVERT: B 1055 SER cc_start: 0.8054 (t) cc_final: 0.7667 (m) REVERT: B 1082 CYS cc_start: 0.5839 (t) cc_final: 0.5330 (t) REVERT: B 1138 TYR cc_start: 0.7613 (t80) cc_final: 0.7151 (t80) REVERT: F 71 PHE cc_start: 0.6021 (t80) cc_final: 0.5559 (t80) REVERT: D 39 GLN cc_start: 0.6825 (tp40) cc_final: 0.6458 (pp30) REVERT: C 45 SER cc_start: 0.7934 (t) cc_final: 0.7638 (p) REVERT: C 53 ASP cc_start: 0.6383 (t0) cc_final: 0.6090 (t0) REVERT: C 54 LEU cc_start: 0.7472 (mm) cc_final: 0.7259 (mm) REVERT: C 84 LEU cc_start: 0.6724 (mt) cc_final: 0.6515 (mp) REVERT: C 138 ASP cc_start: 0.6362 (t0) cc_final: 0.6040 (t0) REVERT: C 192 PHE cc_start: 0.7830 (m-80) cc_final: 0.7576 (m-80) REVERT: C 208 THR cc_start: 0.8394 (t) cc_final: 0.8183 (p) REVERT: C 314 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7372 (tp40) REVERT: C 427 ASP cc_start: 0.7599 (p0) cc_final: 0.7364 (p0) REVERT: C 436 TRP cc_start: 0.5969 (p90) cc_final: 0.5664 (p90) REVERT: C 497 PHE cc_start: 0.3756 (m-10) cc_final: 0.3204 (m-10) REVERT: C 541 PHE cc_start: 0.6762 (p90) cc_final: 0.6234 (p90) REVERT: C 551 VAL cc_start: 0.7548 (p) cc_final: 0.7340 (t) REVERT: C 572 THR cc_start: 0.8264 (m) cc_final: 0.7898 (p) REVERT: C 586 ASP cc_start: 0.7369 (m-30) cc_final: 0.6958 (m-30) REVERT: C 725 GLU cc_start: 0.7213 (tt0) cc_final: 0.6888 (tt0) REVERT: C 754 LEU cc_start: 0.8229 (mt) cc_final: 0.7929 (mt) REVERT: C 765 ARG cc_start: 0.6897 (ttp-110) cc_final: 0.6683 (ttp80) REVERT: C 775 ASP cc_start: 0.7465 (m-30) cc_final: 0.7208 (m-30) REVERT: C 790 LYS cc_start: 0.7361 (mmpt) cc_final: 0.6928 (mmmt) REVERT: C 933 LYS cc_start: 0.8043 (mttt) cc_final: 0.7452 (mptt) REVERT: C 947 LYS cc_start: 0.7894 (mtpt) cc_final: 0.7589 (mtpp) REVERT: C 964 LYS cc_start: 0.7868 (mttt) cc_final: 0.7619 (mttt) REVERT: C 995 ARG cc_start: 0.8032 (mmm-85) cc_final: 0.7581 (mtp85) REVERT: C 1038 LYS cc_start: 0.7198 (tppt) cc_final: 0.6908 (mmmm) REVERT: C 1045 LYS cc_start: 0.7583 (mttt) cc_final: 0.7302 (tttt) REVERT: C 1101 HIS cc_start: 0.7831 (m-70) cc_final: 0.7529 (m-70) REVERT: C 1138 TYR cc_start: 0.7698 (t80) cc_final: 0.7454 (t80) REVERT: G 71 PHE cc_start: 0.6086 (t80) cc_final: 0.5551 (t80) REVERT: G 92 PHE cc_start: 0.6994 (m-80) cc_final: 0.6701 (m-80) REVERT: E 31 SER cc_start: 0.7476 (p) cc_final: 0.6990 (p) REVERT: E 32 TYR cc_start: 0.7284 (m-80) cc_final: 0.6719 (m-80) outliers start: 81 outliers final: 43 residues processed: 724 average time/residue: 1.2473 time to fit residues: 1078.7161 Evaluate side-chains 694 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 647 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 120 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 192 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 287 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 346 optimal weight: 3.9990 chunk 374 optimal weight: 9.9990 chunk 308 optimal weight: 0.1980 chunk 343 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 278 optimal weight: 0.8980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN A 955 ASN A 992 GLN A1002 GLN A1101 HIS L 27 GLN B 61 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 960 ASN B 992 GLN B1101 HIS D 74 ASN C 764 ASN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN C1010 GLN ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 31317 Z= 0.407 Angle : 0.718 13.956 42591 Z= 0.365 Chirality : 0.050 0.342 4920 Planarity : 0.006 0.069 5448 Dihedral : 7.171 114.089 5201 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.76 % Allowed : 15.09 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.13), residues: 3780 helix: 0.08 (0.20), residues: 681 sheet: -0.58 (0.17), residues: 873 loop : -1.79 (0.12), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 353 HIS 0.008 0.002 HIS A 49 PHE 0.029 0.003 PHE C 559 TYR 0.030 0.002 TYR B 204 ARG 0.013 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 689 time to evaluate : 3.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7301 (ttm-80) cc_final: 0.7009 (ttm-80) REVERT: A 46 SER cc_start: 0.8093 (m) cc_final: 0.7668 (p) REVERT: A 153 MET cc_start: 0.3869 (mpp) cc_final: 0.3491 (mpp) REVERT: A 202 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7398 (mtmp) REVERT: A 319 ARG cc_start: 0.7753 (ptp90) cc_final: 0.7237 (ptt180) REVERT: A 541 PHE cc_start: 0.6790 (p90) cc_final: 0.6444 (p90) REVERT: A 572 THR cc_start: 0.8388 (t) cc_final: 0.8112 (p) REVERT: A 588 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8264 (p) REVERT: A 651 ILE cc_start: 0.8625 (mm) cc_final: 0.8371 (mp) REVERT: A 725 GLU cc_start: 0.7496 (tt0) cc_final: 0.7197 (tt0) REVERT: A 736 VAL cc_start: 0.8139 (t) cc_final: 0.7841 (m) REVERT: A 763 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6845 (mp) REVERT: A 790 LYS cc_start: 0.7377 (mmpt) cc_final: 0.7096 (mmpt) REVERT: A 811 LYS cc_start: 0.7175 (mmpt) cc_final: 0.6729 (mtpp) REVERT: A 815 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6232 (mtm110) REVERT: A 933 LYS cc_start: 0.7922 (mttt) cc_final: 0.7539 (mtmm) REVERT: A 947 LYS cc_start: 0.7792 (mtpp) cc_final: 0.7581 (mtpt) REVERT: A 975 SER cc_start: 0.8724 (p) cc_final: 0.8380 (t) REVERT: A 1045 LYS cc_start: 0.7892 (mttt) cc_final: 0.7517 (mttt) REVERT: A 1072 GLU cc_start: 0.7856 (pm20) cc_final: 0.7423 (pm20) REVERT: A 1107 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7204 (mtt-85) REVERT: A 1141 LEU cc_start: 0.7896 (tm) cc_final: 0.7650 (tt) REVERT: L 81 GLU cc_start: 0.7400 (mp0) cc_final: 0.7146 (mp0) REVERT: H 39 GLN cc_start: 0.6798 (tp40) cc_final: 0.5856 (tp40) REVERT: B 49 HIS cc_start: 0.7867 (t-90) cc_final: 0.7475 (t70) REVERT: B 130 VAL cc_start: 0.7810 (OUTLIER) cc_final: 0.7491 (m) REVERT: B 140 PHE cc_start: 0.7286 (p90) cc_final: 0.7078 (p90) REVERT: B 153 MET cc_start: 0.4924 (mpp) cc_final: 0.4640 (mpp) REVERT: B 319 ARG cc_start: 0.7816 (ptp90) cc_final: 0.7436 (ptt180) REVERT: B 340 GLU cc_start: 0.6760 (mp0) cc_final: 0.6487 (mp0) REVERT: B 421 TYR cc_start: 0.6501 (m-80) cc_final: 0.6145 (m-10) REVERT: B 427 ASP cc_start: 0.7648 (p0) cc_final: 0.7399 (p0) REVERT: B 448 ASN cc_start: 0.4554 (p0) cc_final: 0.4073 (p0) REVERT: B 586 ASP cc_start: 0.6968 (m-30) cc_final: 0.6417 (m-30) REVERT: B 675 GLN cc_start: 0.7306 (mt0) cc_final: 0.7106 (mt0) REVERT: B 725 GLU cc_start: 0.7413 (tt0) cc_final: 0.7114 (tt0) REVERT: B 772 VAL cc_start: 0.8396 (p) cc_final: 0.8163 (t) REVERT: B 780 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7368 (pt0) REVERT: B 859 THR cc_start: 0.8153 (t) cc_final: 0.7899 (p) REVERT: B 913 GLN cc_start: 0.7743 (mt0) cc_final: 0.7528 (mt0) REVERT: B 933 LYS cc_start: 0.8042 (mttt) cc_final: 0.7384 (mmtm) REVERT: B 947 LYS cc_start: 0.7865 (mtpt) cc_final: 0.7595 (mtpp) REVERT: B 949 GLN cc_start: 0.7416 (mm-40) cc_final: 0.7200 (tp40) REVERT: B 950 ASP cc_start: 0.7264 (m-30) cc_final: 0.6904 (m-30) REVERT: B 1029 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7808 (tpp) REVERT: B 1118 ASP cc_start: 0.7428 (m-30) cc_final: 0.7188 (m-30) REVERT: F 71 PHE cc_start: 0.6373 (t80) cc_final: 0.5962 (t80) REVERT: D 36 TRP cc_start: 0.6030 (m-90) cc_final: 0.5264 (m-10) REVERT: C 45 SER cc_start: 0.7968 (t) cc_final: 0.7768 (p) REVERT: C 53 ASP cc_start: 0.6630 (t0) cc_final: 0.6360 (t0) REVERT: C 129 LYS cc_start: 0.7418 (mppt) cc_final: 0.7002 (mmtm) REVERT: C 138 ASP cc_start: 0.6327 (t0) cc_final: 0.5946 (t0) REVERT: C 314 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7467 (tp40) REVERT: C 374 PHE cc_start: 0.6908 (m-80) cc_final: 0.6639 (m-80) REVERT: C 427 ASP cc_start: 0.7654 (p0) cc_final: 0.7422 (p0) REVERT: C 429 PHE cc_start: 0.6084 (t80) cc_final: 0.5766 (t80) REVERT: C 448 ASN cc_start: 0.5207 (p0) cc_final: 0.4992 (p0) REVERT: C 541 PHE cc_start: 0.6829 (p90) cc_final: 0.6506 (p90) REVERT: C 586 ASP cc_start: 0.7294 (m-30) cc_final: 0.6919 (m-30) REVERT: C 651 ILE cc_start: 0.8580 (mm) cc_final: 0.8260 (mt) REVERT: C 750 SER cc_start: 0.7834 (t) cc_final: 0.7500 (p) REVERT: C 776 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7032 (ttmm) REVERT: C 780 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7180 (pm20) REVERT: C 815 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7370 (mtm-85) REVERT: C 931 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.6950 (mp) REVERT: C 933 LYS cc_start: 0.8032 (mttt) cc_final: 0.7432 (mptt) REVERT: C 947 LYS cc_start: 0.7981 (mtpt) cc_final: 0.7717 (mtpp) REVERT: C 964 LYS cc_start: 0.7990 (mttt) cc_final: 0.7688 (mttt) REVERT: C 1038 LYS cc_start: 0.7561 (tppt) cc_final: 0.7319 (mmpt) REVERT: C 1045 LYS cc_start: 0.7570 (mttt) cc_final: 0.7310 (tttt) REVERT: C 1055 SER cc_start: 0.8384 (t) cc_final: 0.8123 (m) REVERT: C 1101 HIS cc_start: 0.7903 (m-70) cc_final: 0.7507 (m-70) REVERT: G 42 ARG cc_start: 0.6765 (tpm170) cc_final: 0.6545 (tpp-160) REVERT: G 71 PHE cc_start: 0.6363 (t80) cc_final: 0.5762 (t80) REVERT: G 92 PHE cc_start: 0.7566 (m-80) cc_final: 0.7212 (m-80) REVERT: E 31 SER cc_start: 0.7589 (p) cc_final: 0.7156 (p) REVERT: E 32 TYR cc_start: 0.7315 (m-80) cc_final: 0.6814 (m-80) outliers start: 125 outliers final: 65 residues processed: 738 average time/residue: 1.2147 time to fit residues: 1075.0419 Evaluate side-chains 734 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 656 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 94 TRP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 94 TRP Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 342 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 165 optimal weight: 5.9990 chunk 232 optimal weight: 1.9990 chunk 347 optimal weight: 3.9990 chunk 368 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 329 optimal weight: 0.9980 chunk 99 optimal weight: 0.1980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1010 GLN A1101 HIS L 27 GLN H 84 ASN B 61 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B 960 ASN B1101 HIS ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 764 ASN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN C1010 GLN ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31317 Z= 0.238 Angle : 0.640 13.078 42591 Z= 0.317 Chirality : 0.046 0.349 4920 Planarity : 0.005 0.072 5448 Dihedral : 6.745 111.844 5201 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.82 % Allowed : 18.10 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 3780 helix: 0.75 (0.21), residues: 654 sheet: -0.53 (0.17), residues: 879 loop : -1.66 (0.12), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 36 HIS 0.004 0.001 HIS A 49 PHE 0.023 0.002 PHE B 490 TYR 0.023 0.001 TYR A 495 ARG 0.008 0.001 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 688 time to evaluate : 2.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7283 (ttm-80) cc_final: 0.6932 (ttm-80) REVERT: A 46 SER cc_start: 0.8047 (m) cc_final: 0.7670 (p) REVERT: A 153 MET cc_start: 0.4014 (mpp) cc_final: 0.3606 (mpp) REVERT: A 319 ARG cc_start: 0.7639 (ptp90) cc_final: 0.7156 (ptt180) REVERT: A 532 ASN cc_start: 0.8330 (t0) cc_final: 0.8116 (t0) REVERT: A 541 PHE cc_start: 0.6862 (p90) cc_final: 0.6591 (p90) REVERT: A 572 THR cc_start: 0.8425 (t) cc_final: 0.8218 (p) REVERT: A 588 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8266 (p) REVERT: A 651 ILE cc_start: 0.8623 (mm) cc_final: 0.8352 (mp) REVERT: A 736 VAL cc_start: 0.8082 (t) cc_final: 0.7779 (m) REVERT: A 795 LYS cc_start: 0.8478 (mptm) cc_final: 0.8260 (mptp) REVERT: A 811 LYS cc_start: 0.7197 (mmpt) cc_final: 0.6720 (mtpp) REVERT: A 815 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6276 (mtm110) REVERT: A 933 LYS cc_start: 0.7941 (mttt) cc_final: 0.7533 (mtmm) REVERT: A 947 LYS cc_start: 0.7807 (mtpp) cc_final: 0.7565 (mtpt) REVERT: A 1045 LYS cc_start: 0.7874 (mttt) cc_final: 0.7511 (mttt) REVERT: A 1072 GLU cc_start: 0.7847 (pm20) cc_final: 0.7467 (pm20) REVERT: A 1111 GLU cc_start: 0.7289 (tt0) cc_final: 0.7001 (tt0) REVERT: A 1141 LEU cc_start: 0.7915 (tm) cc_final: 0.7697 (tt) REVERT: H 34 MET cc_start: 0.6270 (ppp) cc_final: 0.5798 (ppp) REVERT: B 49 HIS cc_start: 0.7866 (t-90) cc_final: 0.7482 (t70) REVERT: B 129 LYS cc_start: 0.7542 (mmtm) cc_final: 0.7209 (mmtm) REVERT: B 140 PHE cc_start: 0.7351 (p90) cc_final: 0.7103 (p90) REVERT: B 153 MET cc_start: 0.4927 (mpp) cc_final: 0.4663 (mpp) REVERT: B 206 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6826 (ttmm) REVERT: B 319 ARG cc_start: 0.7842 (ptp90) cc_final: 0.7508 (ptt180) REVERT: B 329 PHE cc_start: 0.5732 (OUTLIER) cc_final: 0.5528 (m-80) REVERT: B 340 GLU cc_start: 0.6819 (mp0) cc_final: 0.6454 (mp0) REVERT: B 374 PHE cc_start: 0.6981 (m-80) cc_final: 0.6776 (m-80) REVERT: B 421 TYR cc_start: 0.6537 (m-80) cc_final: 0.6183 (m-10) REVERT: B 541 PHE cc_start: 0.6779 (p90) cc_final: 0.6402 (p90) REVERT: B 586 ASP cc_start: 0.6939 (m-30) cc_final: 0.6349 (m-30) REVERT: B 663 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.7192 (p0) REVERT: B 675 GLN cc_start: 0.7269 (mt0) cc_final: 0.7067 (mt0) REVERT: B 725 GLU cc_start: 0.7386 (tt0) cc_final: 0.7062 (tt0) REVERT: B 772 VAL cc_start: 0.8385 (p) cc_final: 0.8138 (t) REVERT: B 780 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7376 (pt0) REVERT: B 859 THR cc_start: 0.8122 (t) cc_final: 0.7874 (p) REVERT: B 933 LYS cc_start: 0.8041 (mttt) cc_final: 0.7389 (mmtm) REVERT: B 947 LYS cc_start: 0.7868 (mtpt) cc_final: 0.7593 (mtpp) REVERT: B 950 ASP cc_start: 0.7187 (m-30) cc_final: 0.6785 (m-30) REVERT: B 1029 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7739 (tpp) REVERT: B 1118 ASP cc_start: 0.7423 (m-30) cc_final: 0.7191 (m-30) REVERT: F 71 PHE cc_start: 0.6535 (t80) cc_final: 0.5996 (t80) REVERT: D 34 MET cc_start: 0.6366 (ppp) cc_final: 0.5955 (ppp) REVERT: D 36 TRP cc_start: 0.5796 (m-90) cc_final: 0.4756 (m-10) REVERT: D 83 MET cc_start: 0.4046 (tmt) cc_final: 0.3628 (tmt) REVERT: C 53 ASP cc_start: 0.6425 (t0) cc_final: 0.6156 (t0) REVERT: C 83 VAL cc_start: 0.7294 (OUTLIER) cc_final: 0.6725 (p) REVERT: C 129 LYS cc_start: 0.7412 (mppt) cc_final: 0.7104 (mmtm) REVERT: C 138 ASP cc_start: 0.6318 (t0) cc_final: 0.5928 (t0) REVERT: C 190 ARG cc_start: 0.7144 (ptp90) cc_final: 0.6929 (ptp90) REVERT: C 237 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6388 (ttm-80) REVERT: C 314 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7465 (tp40) REVERT: C 541 PHE cc_start: 0.6855 (p90) cc_final: 0.6535 (p90) REVERT: C 586 ASP cc_start: 0.7269 (m-30) cc_final: 0.6873 (m-30) REVERT: C 651 ILE cc_start: 0.8596 (mm) cc_final: 0.8294 (mt) REVERT: C 663 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7135 (p0) REVERT: C 705 VAL cc_start: 0.6637 (OUTLIER) cc_final: 0.6410 (p) REVERT: C 750 SER cc_start: 0.7802 (t) cc_final: 0.7481 (p) REVERT: C 776 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7270 (tmmm) REVERT: C 790 LYS cc_start: 0.7591 (mtmm) cc_final: 0.7268 (mmpt) REVERT: C 883 THR cc_start: 0.8206 (m) cc_final: 0.7842 (p) REVERT: C 933 LYS cc_start: 0.8055 (mttt) cc_final: 0.7478 (mptt) REVERT: C 947 LYS cc_start: 0.7963 (mtpt) cc_final: 0.7687 (mtpp) REVERT: C 964 LYS cc_start: 0.8015 (mttt) cc_final: 0.7685 (mttt) REVERT: C 1019 ARG cc_start: 0.7270 (ttp-170) cc_final: 0.6991 (ttp80) REVERT: C 1038 LYS cc_start: 0.7555 (tppt) cc_final: 0.7124 (mmmm) REVERT: C 1045 LYS cc_start: 0.7599 (mttt) cc_final: 0.7317 (mttt) REVERT: C 1055 SER cc_start: 0.8392 (t) cc_final: 0.8092 (m) REVERT: C 1101 HIS cc_start: 0.7937 (m-70) cc_final: 0.7512 (m-70) REVERT: C 1123 SER cc_start: 0.8331 (t) cc_final: 0.8075 (m) REVERT: G 71 PHE cc_start: 0.6348 (t80) cc_final: 0.5786 (t80) REVERT: E 31 SER cc_start: 0.7521 (p) cc_final: 0.7252 (p) REVERT: E 32 TYR cc_start: 0.7317 (m-80) cc_final: 0.6800 (m-80) outliers start: 127 outliers final: 66 residues processed: 743 average time/residue: 1.2512 time to fit residues: 1115.1433 Evaluate side-chains 738 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 659 time to evaluate : 3.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 120 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 306 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 274 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 314 optimal weight: 2.9990 chunk 254 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 188 optimal weight: 0.4980 chunk 330 optimal weight: 0.4980 chunk 92 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1101 HIS L 27 GLN B 61 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1101 HIS ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 764 ASN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31317 Z= 0.243 Angle : 0.634 12.866 42591 Z= 0.314 Chirality : 0.047 0.349 4920 Planarity : 0.004 0.049 5448 Dihedral : 6.482 111.251 5201 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.16 % Allowed : 19.39 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.13), residues: 3780 helix: 0.97 (0.21), residues: 657 sheet: -0.57 (0.17), residues: 879 loop : -1.67 (0.12), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 110 HIS 0.004 0.001 HIS A1083 PHE 0.028 0.002 PHE B 329 TYR 0.030 0.001 TYR E 103 ARG 0.009 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 673 time to evaluate : 3.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7257 (ttm-80) cc_final: 0.7050 (ttm-80) REVERT: A 46 SER cc_start: 0.8041 (m) cc_final: 0.7693 (p) REVERT: A 153 MET cc_start: 0.4056 (mpp) cc_final: 0.3661 (mpp) REVERT: A 177 MET cc_start: -0.0159 (mtt) cc_final: -0.0826 (mtt) REVERT: A 206 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6911 (ttmm) REVERT: A 319 ARG cc_start: 0.7648 (ptp90) cc_final: 0.7181 (ptt180) REVERT: A 453 TYR cc_start: 0.6798 (p90) cc_final: 0.6485 (p90) REVERT: A 541 PHE cc_start: 0.6916 (p90) cc_final: 0.6616 (p90) REVERT: A 551 VAL cc_start: 0.7598 (OUTLIER) cc_final: 0.7352 (t) REVERT: A 572 THR cc_start: 0.8403 (t) cc_final: 0.8192 (p) REVERT: A 588 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8336 (p) REVERT: A 651 ILE cc_start: 0.8631 (mm) cc_final: 0.8346 (mp) REVERT: A 703 ASN cc_start: 0.7815 (t0) cc_final: 0.7462 (t0) REVERT: A 736 VAL cc_start: 0.8074 (t) cc_final: 0.7804 (m) REVERT: A 790 LYS cc_start: 0.7542 (mtpm) cc_final: 0.7103 (mmpt) REVERT: A 795 LYS cc_start: 0.8476 (mptm) cc_final: 0.8079 (mptt) REVERT: A 811 LYS cc_start: 0.7192 (mmpt) cc_final: 0.6695 (mtpp) REVERT: A 815 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.6289 (mtm110) REVERT: A 933 LYS cc_start: 0.7941 (mttt) cc_final: 0.7545 (mtmm) REVERT: A 1045 LYS cc_start: 0.7870 (mttt) cc_final: 0.7508 (mttt) REVERT: A 1072 GLU cc_start: 0.7855 (pm20) cc_final: 0.7422 (pm20) REVERT: A 1111 GLU cc_start: 0.7268 (tt0) cc_final: 0.6974 (tt0) REVERT: A 1141 LEU cc_start: 0.7928 (tm) cc_final: 0.7716 (tt) REVERT: H 34 MET cc_start: 0.6365 (ppp) cc_final: 0.5533 (ppp) REVERT: B 49 HIS cc_start: 0.7861 (t-90) cc_final: 0.7409 (t70) REVERT: B 140 PHE cc_start: 0.7403 (p90) cc_final: 0.7107 (p90) REVERT: B 153 MET cc_start: 0.5006 (mpp) cc_final: 0.4726 (mpp) REVERT: B 206 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6838 (ttmm) REVERT: B 319 ARG cc_start: 0.7852 (ptp90) cc_final: 0.7489 (ptt180) REVERT: B 340 GLU cc_start: 0.6914 (mp0) cc_final: 0.6587 (mp0) REVERT: B 374 PHE cc_start: 0.7340 (m-80) cc_final: 0.7067 (m-80) REVERT: B 508 TYR cc_start: 0.7744 (m-10) cc_final: 0.7021 (m-80) REVERT: B 541 PHE cc_start: 0.6781 (p90) cc_final: 0.6416 (p90) REVERT: B 586 ASP cc_start: 0.6937 (m-30) cc_final: 0.6344 (m-30) REVERT: B 675 GLN cc_start: 0.7278 (mt0) cc_final: 0.7075 (mt0) REVERT: B 725 GLU cc_start: 0.7400 (tt0) cc_final: 0.7158 (tt0) REVERT: B 772 VAL cc_start: 0.8385 (p) cc_final: 0.8133 (t) REVERT: B 780 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7429 (pt0) REVERT: B 859 THR cc_start: 0.8118 (t) cc_final: 0.7859 (p) REVERT: B 933 LYS cc_start: 0.8052 (mttt) cc_final: 0.7408 (mmtm) REVERT: B 947 LYS cc_start: 0.7853 (mtpt) cc_final: 0.7571 (mtpp) REVERT: B 950 ASP cc_start: 0.7199 (m-30) cc_final: 0.6775 (m-30) REVERT: B 1118 ASP cc_start: 0.7451 (m-30) cc_final: 0.7195 (m-30) REVERT: B 1123 SER cc_start: 0.8343 (t) cc_final: 0.8127 (p) REVERT: F 71 PHE cc_start: 0.6689 (t80) cc_final: 0.6172 (t80) REVERT: D 34 MET cc_start: 0.6470 (ppp) cc_final: 0.6071 (ppp) REVERT: D 36 TRP cc_start: 0.5861 (m-90) cc_final: 0.4705 (m-10) REVERT: D 83 MET cc_start: 0.4020 (tmt) cc_final: 0.3759 (tmt) REVERT: C 81 ASN cc_start: 0.7538 (p0) cc_final: 0.7208 (p0) REVERT: C 83 VAL cc_start: 0.7318 (OUTLIER) cc_final: 0.6812 (p) REVERT: C 129 LYS cc_start: 0.7443 (mppt) cc_final: 0.7192 (mmtm) REVERT: C 138 ASP cc_start: 0.6324 (t0) cc_final: 0.5905 (t0) REVERT: C 190 ARG cc_start: 0.7162 (ptp90) cc_final: 0.6955 (ptp90) REVERT: C 237 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6366 (ttm-80) REVERT: C 314 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7449 (tp40) REVERT: C 541 PHE cc_start: 0.6879 (p90) cc_final: 0.6584 (p90) REVERT: C 578 ASP cc_start: 0.6794 (OUTLIER) cc_final: 0.5823 (p0) REVERT: C 586 ASP cc_start: 0.7242 (m-30) cc_final: 0.6847 (m-30) REVERT: C 663 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7143 (p0) REVERT: C 705 VAL cc_start: 0.6816 (OUTLIER) cc_final: 0.6580 (p) REVERT: C 750 SER cc_start: 0.7792 (t) cc_final: 0.7485 (p) REVERT: C 780 GLU cc_start: 0.7491 (pm20) cc_final: 0.6969 (pt0) REVERT: C 790 LYS cc_start: 0.7601 (mtmm) cc_final: 0.7265 (mmpt) REVERT: C 815 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7073 (mtm-85) REVERT: C 883 THR cc_start: 0.8082 (m) cc_final: 0.7846 (p) REVERT: C 933 LYS cc_start: 0.8020 (mttt) cc_final: 0.7421 (mptt) REVERT: C 947 LYS cc_start: 0.7990 (mtpt) cc_final: 0.7696 (mtpp) REVERT: C 964 LYS cc_start: 0.7970 (mttt) cc_final: 0.7677 (mttt) REVERT: C 994 ASP cc_start: 0.7144 (t70) cc_final: 0.6916 (m-30) REVERT: C 1019 ARG cc_start: 0.7204 (ttp-170) cc_final: 0.6928 (ttp80) REVERT: C 1038 LYS cc_start: 0.7577 (tppt) cc_final: 0.7130 (mmmm) REVERT: C 1045 LYS cc_start: 0.7620 (mttt) cc_final: 0.7340 (mttt) REVERT: C 1055 SER cc_start: 0.8384 (t) cc_final: 0.8070 (m) REVERT: C 1101 HIS cc_start: 0.7938 (m-70) cc_final: 0.7470 (m-70) REVERT: C 1123 SER cc_start: 0.8335 (t) cc_final: 0.8054 (m) REVERT: G 71 PHE cc_start: 0.6378 (t80) cc_final: 0.5865 (t80) REVERT: E 31 SER cc_start: 0.7734 (p) cc_final: 0.7462 (p) REVERT: E 32 TYR cc_start: 0.7328 (m-80) cc_final: 0.6828 (m-80) outliers start: 138 outliers final: 80 residues processed: 740 average time/residue: 1.1994 time to fit residues: 1066.8331 Evaluate side-chains 754 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 661 time to evaluate : 3.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 123 optimal weight: 0.0170 chunk 331 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 368 optimal weight: 0.4980 chunk 306 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 overall best weight: 0.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1010 GLN A1101 HIS L 27 GLN B 422 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 607 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN B1101 HIS F 37 GLN C 764 ASN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31317 Z= 0.197 Angle : 0.624 13.991 42591 Z= 0.306 Chirality : 0.046 0.350 4920 Planarity : 0.004 0.050 5448 Dihedral : 6.323 110.564 5201 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.58 % Allowed : 20.45 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 3780 helix: 1.38 (0.22), residues: 636 sheet: -0.60 (0.17), residues: 885 loop : -1.66 (0.12), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 47 HIS 0.003 0.001 HIS A 49 PHE 0.027 0.001 PHE B 490 TYR 0.025 0.001 TYR H 103 ARG 0.009 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 670 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7210 (ttm-80) cc_final: 0.6871 (ttm-80) REVERT: A 46 SER cc_start: 0.8034 (m) cc_final: 0.7676 (p) REVERT: A 52 GLN cc_start: 0.7200 (tm-30) cc_final: 0.6974 (tp-100) REVERT: A 129 LYS cc_start: 0.7528 (mmmt) cc_final: 0.7269 (mmmt) REVERT: A 140 PHE cc_start: 0.7080 (p90) cc_final: 0.6429 (p90) REVERT: A 153 MET cc_start: 0.4090 (mpp) cc_final: 0.3686 (mpp) REVERT: A 177 MET cc_start: -0.0142 (mtt) cc_final: -0.0810 (mtt) REVERT: A 278 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7253 (tmtp) REVERT: A 319 ARG cc_start: 0.7628 (ptp90) cc_final: 0.7244 (ptt180) REVERT: A 453 TYR cc_start: 0.6689 (p90) cc_final: 0.6313 (p90) REVERT: A 454 ARG cc_start: 0.7746 (mmt90) cc_final: 0.6798 (mmt90) REVERT: A 541 PHE cc_start: 0.6948 (p90) cc_final: 0.6291 (p90) REVERT: A 588 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8297 (p) REVERT: A 651 ILE cc_start: 0.8635 (mm) cc_final: 0.8344 (mp) REVERT: A 703 ASN cc_start: 0.7731 (t0) cc_final: 0.7445 (t0) REVERT: A 736 VAL cc_start: 0.8090 (t) cc_final: 0.7834 (m) REVERT: A 790 LYS cc_start: 0.7567 (mtpm) cc_final: 0.7094 (mmpt) REVERT: A 795 LYS cc_start: 0.8479 (mptm) cc_final: 0.8084 (mptt) REVERT: A 811 LYS cc_start: 0.7277 (mmpt) cc_final: 0.6780 (mtpp) REVERT: A 815 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.6313 (mtm110) REVERT: A 933 LYS cc_start: 0.7959 (mttt) cc_final: 0.7552 (mtmm) REVERT: A 1045 LYS cc_start: 0.7851 (mttt) cc_final: 0.7486 (mttt) REVERT: A 1072 GLU cc_start: 0.7848 (pm20) cc_final: 0.7418 (pm20) REVERT: A 1111 GLU cc_start: 0.7253 (tt0) cc_final: 0.6962 (tt0) REVERT: A 1141 LEU cc_start: 0.7937 (tm) cc_final: 0.7711 (tt) REVERT: H 34 MET cc_start: 0.6162 (ppp) cc_final: 0.5662 (ppp) REVERT: B 49 HIS cc_start: 0.7850 (t-90) cc_final: 0.7393 (t70) REVERT: B 140 PHE cc_start: 0.7444 (p90) cc_final: 0.7128 (p90) REVERT: B 153 MET cc_start: 0.5149 (mpp) cc_final: 0.4809 (mpp) REVERT: B 206 LYS cc_start: 0.7063 (OUTLIER) cc_final: 0.6837 (ttmm) REVERT: B 319 ARG cc_start: 0.7865 (ptp90) cc_final: 0.7503 (ptt180) REVERT: B 340 GLU cc_start: 0.6927 (mp0) cc_final: 0.6526 (mp0) REVERT: B 374 PHE cc_start: 0.7205 (m-80) cc_final: 0.6957 (m-80) REVERT: B 454 ARG cc_start: 0.8347 (mmt180) cc_final: 0.7778 (mmt90) REVERT: B 508 TYR cc_start: 0.7704 (m-10) cc_final: 0.7491 (m-80) REVERT: B 541 PHE cc_start: 0.6831 (p90) cc_final: 0.6411 (p90) REVERT: B 586 ASP cc_start: 0.6931 (m-30) cc_final: 0.6333 (m-30) REVERT: B 725 GLU cc_start: 0.7393 (tt0) cc_final: 0.7144 (tt0) REVERT: B 772 VAL cc_start: 0.8393 (p) cc_final: 0.8146 (t) REVERT: B 859 THR cc_start: 0.8096 (t) cc_final: 0.7853 (p) REVERT: B 933 LYS cc_start: 0.8042 (mttt) cc_final: 0.7401 (mmtm) REVERT: B 935 GLN cc_start: 0.8063 (mt0) cc_final: 0.7740 (mt0) REVERT: B 947 LYS cc_start: 0.7844 (mtpt) cc_final: 0.7551 (mtpp) REVERT: B 950 ASP cc_start: 0.7172 (m-30) cc_final: 0.6751 (m-30) REVERT: B 1029 MET cc_start: 0.7941 (ttm) cc_final: 0.7671 (tpp) REVERT: B 1118 ASP cc_start: 0.7448 (m-30) cc_final: 0.7198 (m-30) REVERT: B 1123 SER cc_start: 0.8323 (t) cc_final: 0.8118 (p) REVERT: F 71 PHE cc_start: 0.6610 (t80) cc_final: 0.6092 (t80) REVERT: D 36 TRP cc_start: 0.5735 (m-90) cc_final: 0.4563 (m-10) REVERT: D 46 GLU cc_start: 0.7042 (pm20) cc_final: 0.6782 (mp0) REVERT: D 102 TYR cc_start: 0.7770 (OUTLIER) cc_final: 0.7564 (t80) REVERT: C 83 VAL cc_start: 0.7276 (OUTLIER) cc_final: 0.6798 (p) REVERT: C 129 LYS cc_start: 0.7449 (mppt) cc_final: 0.7227 (mmtm) REVERT: C 138 ASP cc_start: 0.6355 (t0) cc_final: 0.5932 (t0) REVERT: C 237 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.6339 (ttm-80) REVERT: C 314 GLN cc_start: 0.7690 (tt0) cc_final: 0.7438 (tp40) REVERT: C 541 PHE cc_start: 0.6911 (p90) cc_final: 0.6617 (p90) REVERT: C 578 ASP cc_start: 0.6766 (OUTLIER) cc_final: 0.5786 (p0) REVERT: C 586 ASP cc_start: 0.7246 (m-30) cc_final: 0.6856 (m-30) REVERT: C 651 ILE cc_start: 0.8595 (mm) cc_final: 0.8298 (mt) REVERT: C 663 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7153 (p0) REVERT: C 705 VAL cc_start: 0.6823 (OUTLIER) cc_final: 0.6585 (p) REVERT: C 750 SER cc_start: 0.7759 (t) cc_final: 0.7433 (p) REVERT: C 780 GLU cc_start: 0.7481 (pm20) cc_final: 0.7028 (OUTLIER) REVERT: C 883 THR cc_start: 0.8070 (m) cc_final: 0.7810 (p) REVERT: C 933 LYS cc_start: 0.8049 (mttt) cc_final: 0.7461 (mptt) REVERT: C 947 LYS cc_start: 0.7983 (mtpt) cc_final: 0.7661 (mtpp) REVERT: C 964 LYS cc_start: 0.7938 (mttt) cc_final: 0.7664 (mttt) REVERT: C 994 ASP cc_start: 0.7111 (t70) cc_final: 0.6902 (m-30) REVERT: C 1006 THR cc_start: 0.7893 (OUTLIER) cc_final: 0.7648 (p) REVERT: C 1019 ARG cc_start: 0.7193 (ttp-170) cc_final: 0.6964 (ttp80) REVERT: C 1038 LYS cc_start: 0.7573 (tppt) cc_final: 0.7303 (mmpt) REVERT: C 1045 LYS cc_start: 0.7623 (mttt) cc_final: 0.7341 (mttt) REVERT: C 1055 SER cc_start: 0.8368 (t) cc_final: 0.8037 (m) REVERT: C 1101 HIS cc_start: 0.7934 (m-70) cc_final: 0.7484 (m-70) REVERT: C 1123 SER cc_start: 0.8319 (t) cc_final: 0.8042 (m) REVERT: C 1141 LEU cc_start: 0.7938 (tp) cc_final: 0.7729 (tm) REVERT: G 71 PHE cc_start: 0.6332 (t80) cc_final: 0.5818 (t80) REVERT: E 31 SER cc_start: 0.7666 (p) cc_final: 0.7423 (p) REVERT: E 32 TYR cc_start: 0.7259 (m-80) cc_final: 0.6772 (m-80) outliers start: 119 outliers final: 81 residues processed: 731 average time/residue: 1.1929 time to fit residues: 1051.0561 Evaluate side-chains 749 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 658 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 355 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 210 optimal weight: 0.6980 chunk 269 optimal weight: 0.8980 chunk 208 optimal weight: 0.6980 chunk 310 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 chunk 367 optimal weight: 1.9990 chunk 229 optimal weight: 0.8980 chunk 223 optimal weight: 0.6980 chunk 169 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1010 GLN A1101 HIS L 27 GLN B 61 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1101 HIS C 764 ASN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31317 Z= 0.198 Angle : 0.634 13.521 42591 Z= 0.309 Chirality : 0.047 0.610 4920 Planarity : 0.004 0.049 5448 Dihedral : 6.232 109.957 5201 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.76 % Allowed : 20.96 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.13), residues: 3780 helix: 1.41 (0.22), residues: 642 sheet: -0.61 (0.17), residues: 876 loop : -1.67 (0.12), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 47 HIS 0.003 0.001 HIS A1083 PHE 0.027 0.001 PHE C 490 TYR 0.026 0.001 TYR H 59 ARG 0.011 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 661 time to evaluate : 3.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.8028 (m) cc_final: 0.7688 (p) REVERT: A 52 GLN cc_start: 0.7339 (tm-30) cc_final: 0.7088 (tp-100) REVERT: A 140 PHE cc_start: 0.7087 (p90) cc_final: 0.6420 (p90) REVERT: A 153 MET cc_start: 0.4208 (mpp) cc_final: 0.3780 (mpp) REVERT: A 177 MET cc_start: -0.0096 (mtt) cc_final: -0.0764 (mtt) REVERT: A 206 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6898 (ttmm) REVERT: A 319 ARG cc_start: 0.7623 (ptp90) cc_final: 0.7291 (ptt180) REVERT: A 453 TYR cc_start: 0.6714 (p90) cc_final: 0.6315 (p90) REVERT: A 454 ARG cc_start: 0.7749 (mmt90) cc_final: 0.7205 (mmt90) REVERT: A 541 PHE cc_start: 0.6954 (p90) cc_final: 0.6302 (p90) REVERT: A 651 ILE cc_start: 0.8629 (mm) cc_final: 0.8355 (mp) REVERT: A 703 ASN cc_start: 0.7734 (t0) cc_final: 0.7446 (t0) REVERT: A 736 VAL cc_start: 0.8099 (t) cc_final: 0.7850 (m) REVERT: A 790 LYS cc_start: 0.7584 (mtpm) cc_final: 0.7074 (mmpt) REVERT: A 795 LYS cc_start: 0.8486 (mptm) cc_final: 0.8088 (mptt) REVERT: A 811 LYS cc_start: 0.7269 (mmpt) cc_final: 0.6770 (mtpp) REVERT: A 864 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8142 (tt) REVERT: A 933 LYS cc_start: 0.7949 (mttt) cc_final: 0.7551 (mtmm) REVERT: A 947 LYS cc_start: 0.7620 (mtpp) cc_final: 0.7312 (mtmt) REVERT: A 1045 LYS cc_start: 0.7845 (mttt) cc_final: 0.7497 (mttt) REVERT: A 1072 GLU cc_start: 0.7848 (pm20) cc_final: 0.7422 (pm20) REVERT: A 1111 GLU cc_start: 0.7252 (tt0) cc_final: 0.6970 (tt0) REVERT: A 1141 LEU cc_start: 0.7949 (tm) cc_final: 0.7726 (tt) REVERT: H 34 MET cc_start: 0.6025 (ppp) cc_final: 0.5798 (ppp) REVERT: H 102 TYR cc_start: 0.7671 (OUTLIER) cc_final: 0.7394 (t80) REVERT: B 49 HIS cc_start: 0.7853 (t-90) cc_final: 0.7442 (t70) REVERT: B 140 PHE cc_start: 0.7409 (p90) cc_final: 0.7080 (p90) REVERT: B 153 MET cc_start: 0.5147 (mpp) cc_final: 0.4799 (mpp) REVERT: B 206 LYS cc_start: 0.7061 (OUTLIER) cc_final: 0.6816 (ttmm) REVERT: B 319 ARG cc_start: 0.7877 (ptp90) cc_final: 0.7527 (ptt180) REVERT: B 340 GLU cc_start: 0.6946 (mp0) cc_final: 0.6637 (mp0) REVERT: B 374 PHE cc_start: 0.7255 (m-80) cc_final: 0.6980 (m-80) REVERT: B 454 ARG cc_start: 0.8350 (mmt180) cc_final: 0.7816 (mmt90) REVERT: B 508 TYR cc_start: 0.7713 (m-10) cc_final: 0.7495 (m-80) REVERT: B 541 PHE cc_start: 0.6841 (p90) cc_final: 0.6406 (p90) REVERT: B 586 ASP cc_start: 0.6936 (m-30) cc_final: 0.6329 (m-30) REVERT: B 725 GLU cc_start: 0.7393 (tt0) cc_final: 0.7140 (tt0) REVERT: B 772 VAL cc_start: 0.8393 (p) cc_final: 0.8145 (t) REVERT: B 859 THR cc_start: 0.8087 (t) cc_final: 0.7835 (p) REVERT: B 933 LYS cc_start: 0.8041 (mttt) cc_final: 0.7402 (mmtm) REVERT: B 935 GLN cc_start: 0.8071 (mt0) cc_final: 0.7853 (mt0) REVERT: B 947 LYS cc_start: 0.7837 (mtpt) cc_final: 0.7550 (mtpp) REVERT: B 950 ASP cc_start: 0.7175 (m-30) cc_final: 0.6715 (m-30) REVERT: B 1029 MET cc_start: 0.7963 (ttm) cc_final: 0.7508 (tpp) REVERT: B 1050 MET cc_start: 0.8043 (ptm) cc_final: 0.7838 (ptt) REVERT: B 1118 ASP cc_start: 0.7454 (m-30) cc_final: 0.7201 (m-30) REVERT: B 1123 SER cc_start: 0.8282 (t) cc_final: 0.8055 (p) REVERT: F 71 PHE cc_start: 0.6540 (t80) cc_final: 0.6058 (t80) REVERT: C 83 VAL cc_start: 0.7340 (OUTLIER) cc_final: 0.6766 (p) REVERT: C 129 LYS cc_start: 0.7482 (mppt) cc_final: 0.7277 (mmtm) REVERT: C 138 ASP cc_start: 0.6299 (t0) cc_final: 0.5878 (t0) REVERT: C 206 LYS cc_start: 0.7172 (OUTLIER) cc_final: 0.6795 (ttmm) REVERT: C 237 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6323 (ttm-80) REVERT: C 314 GLN cc_start: 0.7687 (tt0) cc_final: 0.7413 (tp40) REVERT: C 541 PHE cc_start: 0.6909 (p90) cc_final: 0.6642 (p90) REVERT: C 578 ASP cc_start: 0.6755 (OUTLIER) cc_final: 0.5777 (p0) REVERT: C 651 ILE cc_start: 0.8588 (mm) cc_final: 0.8279 (mt) REVERT: C 663 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7078 (p0) REVERT: C 705 VAL cc_start: 0.6858 (OUTLIER) cc_final: 0.6625 (p) REVERT: C 750 SER cc_start: 0.7739 (t) cc_final: 0.7393 (p) REVERT: C 780 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7106 (OUTLIER) REVERT: C 790 LYS cc_start: 0.7579 (mtmm) cc_final: 0.7189 (mmpt) REVERT: C 815 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7116 (mtm-85) REVERT: C 883 THR cc_start: 0.8071 (m) cc_final: 0.7757 (p) REVERT: C 933 LYS cc_start: 0.8047 (mttt) cc_final: 0.7461 (mptt) REVERT: C 947 LYS cc_start: 0.7955 (mtpt) cc_final: 0.7672 (mtpp) REVERT: C 964 LYS cc_start: 0.7907 (mttt) cc_final: 0.7630 (mttt) REVERT: C 994 ASP cc_start: 0.7092 (t70) cc_final: 0.6887 (m-30) REVERT: C 1006 THR cc_start: 0.7886 (OUTLIER) cc_final: 0.7644 (p) REVERT: C 1038 LYS cc_start: 0.7587 (tppt) cc_final: 0.7301 (mmpt) REVERT: C 1045 LYS cc_start: 0.7576 (mttt) cc_final: 0.7316 (mttt) REVERT: C 1055 SER cc_start: 0.8341 (t) cc_final: 0.8001 (m) REVERT: C 1101 HIS cc_start: 0.7938 (m-70) cc_final: 0.7500 (m-70) REVERT: C 1123 SER cc_start: 0.8320 (t) cc_final: 0.8046 (m) REVERT: C 1141 LEU cc_start: 0.7927 (tp) cc_final: 0.7726 (tm) REVERT: G 71 PHE cc_start: 0.6350 (t80) cc_final: 0.5951 (t80) REVERT: E 31 SER cc_start: 0.7664 (p) cc_final: 0.7431 (p) REVERT: E 32 TYR cc_start: 0.7270 (m-80) cc_final: 0.6768 (m-80) outliers start: 125 outliers final: 85 residues processed: 726 average time/residue: 1.2122 time to fit residues: 1060.6088 Evaluate side-chains 745 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 648 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 120 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 227 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 219 optimal weight: 5.9990 chunk 110 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 288 optimal weight: 0.3980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1010 GLN A1101 HIS L 27 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 901 GLN B1101 HIS C 764 ASN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31317 Z= 0.211 Angle : 0.642 13.202 42591 Z= 0.314 Chirality : 0.046 0.344 4920 Planarity : 0.004 0.052 5448 Dihedral : 6.153 109.602 5201 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.82 % Allowed : 21.14 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.13), residues: 3780 helix: 1.46 (0.22), residues: 642 sheet: -0.62 (0.17), residues: 876 loop : -1.66 (0.12), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 110 HIS 0.003 0.001 HIS A1083 PHE 0.028 0.001 PHE B 490 TYR 0.021 0.001 TYR A 369 ARG 0.011 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 655 time to evaluate : 3.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.8044 (m) cc_final: 0.7663 (p) REVERT: A 52 GLN cc_start: 0.7227 (tm-30) cc_final: 0.7000 (tp-100) REVERT: A 140 PHE cc_start: 0.7140 (p90) cc_final: 0.6463 (p90) REVERT: A 153 MET cc_start: 0.4247 (mpp) cc_final: 0.3812 (mpp) REVERT: A 177 MET cc_start: -0.0044 (mtt) cc_final: -0.0712 (mtt) REVERT: A 206 LYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6922 (ttmm) REVERT: A 319 ARG cc_start: 0.7671 (ptp90) cc_final: 0.7289 (ptt180) REVERT: A 453 TYR cc_start: 0.6767 (p90) cc_final: 0.6315 (p90) REVERT: A 454 ARG cc_start: 0.7725 (mmt90) cc_final: 0.7144 (mmt90) REVERT: A 541 PHE cc_start: 0.6970 (p90) cc_final: 0.6313 (p90) REVERT: A 651 ILE cc_start: 0.8633 (mm) cc_final: 0.8358 (mp) REVERT: A 703 ASN cc_start: 0.7750 (t0) cc_final: 0.7455 (t0) REVERT: A 736 VAL cc_start: 0.8113 (t) cc_final: 0.7868 (m) REVERT: A 790 LYS cc_start: 0.7604 (mtpm) cc_final: 0.7400 (mtpm) REVERT: A 795 LYS cc_start: 0.8484 (mptm) cc_final: 0.8102 (mptt) REVERT: A 811 LYS cc_start: 0.7269 (mmpt) cc_final: 0.6804 (mtpp) REVERT: A 815 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6323 (mtm110) REVERT: A 864 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8144 (tt) REVERT: A 933 LYS cc_start: 0.7948 (mttt) cc_final: 0.7550 (mtmm) REVERT: A 947 LYS cc_start: 0.7602 (mtpp) cc_final: 0.7362 (mtmt) REVERT: A 1045 LYS cc_start: 0.7806 (mttt) cc_final: 0.7455 (mttt) REVERT: A 1072 GLU cc_start: 0.7853 (pm20) cc_final: 0.7428 (pm20) REVERT: A 1111 GLU cc_start: 0.7273 (tt0) cc_final: 0.7003 (tt0) REVERT: A 1141 LEU cc_start: 0.7953 (tm) cc_final: 0.7727 (tt) REVERT: B 49 HIS cc_start: 0.7866 (t-90) cc_final: 0.7435 (t70) REVERT: B 140 PHE cc_start: 0.7456 (p90) cc_final: 0.7104 (p90) REVERT: B 153 MET cc_start: 0.5193 (mpp) cc_final: 0.4838 (mpp) REVERT: B 206 LYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6751 (ttmt) REVERT: B 319 ARG cc_start: 0.7891 (ptp90) cc_final: 0.7548 (ptt180) REVERT: B 340 GLU cc_start: 0.6976 (mp0) cc_final: 0.6582 (mp0) REVERT: B 374 PHE cc_start: 0.7430 (m-80) cc_final: 0.7187 (m-80) REVERT: B 454 ARG cc_start: 0.8315 (mmt180) cc_final: 0.7761 (mpt-90) REVERT: B 508 TYR cc_start: 0.7723 (m-10) cc_final: 0.7237 (m-80) REVERT: B 541 PHE cc_start: 0.6804 (p90) cc_final: 0.6383 (p90) REVERT: B 586 ASP cc_start: 0.6943 (m-30) cc_final: 0.6333 (m-30) REVERT: B 725 GLU cc_start: 0.7397 (tt0) cc_final: 0.7142 (tt0) REVERT: B 772 VAL cc_start: 0.8398 (p) cc_final: 0.8148 (t) REVERT: B 859 THR cc_start: 0.8096 (t) cc_final: 0.7824 (p) REVERT: B 933 LYS cc_start: 0.8044 (mttt) cc_final: 0.7398 (mmtm) REVERT: B 935 GLN cc_start: 0.8084 (mt0) cc_final: 0.7867 (mt0) REVERT: B 947 LYS cc_start: 0.7834 (mtpt) cc_final: 0.7545 (mtpp) REVERT: B 950 ASP cc_start: 0.7157 (m-30) cc_final: 0.6731 (m-30) REVERT: B 991 VAL cc_start: 0.8115 (t) cc_final: 0.7911 (p) REVERT: B 1029 MET cc_start: 0.7964 (ttm) cc_final: 0.7726 (tpp) REVERT: B 1118 ASP cc_start: 0.7459 (m-30) cc_final: 0.7207 (m-30) REVERT: B 1123 SER cc_start: 0.8291 (t) cc_final: 0.8057 (p) REVERT: F 71 PHE cc_start: 0.6489 (t80) cc_final: 0.5897 (t80) REVERT: C 83 VAL cc_start: 0.7388 (OUTLIER) cc_final: 0.6794 (p) REVERT: C 138 ASP cc_start: 0.6324 (t0) cc_final: 0.5849 (t0) REVERT: C 206 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6816 (ttmm) REVERT: C 237 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.6327 (ttm-80) REVERT: C 314 GLN cc_start: 0.7748 (tt0) cc_final: 0.7478 (tp40) REVERT: C 454 ARG cc_start: 0.8051 (mmt90) cc_final: 0.7652 (mpt-90) REVERT: C 541 PHE cc_start: 0.6946 (p90) cc_final: 0.6650 (p90) REVERT: C 578 ASP cc_start: 0.6769 (OUTLIER) cc_final: 0.5803 (p0) REVERT: C 651 ILE cc_start: 0.8597 (mm) cc_final: 0.8296 (mt) REVERT: C 663 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7085 (p0) REVERT: C 705 VAL cc_start: 0.6883 (OUTLIER) cc_final: 0.6651 (p) REVERT: C 750 SER cc_start: 0.7697 (t) cc_final: 0.7389 (p) REVERT: C 780 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7099 (OUTLIER) REVERT: C 790 LYS cc_start: 0.7569 (mtmm) cc_final: 0.7190 (mmpt) REVERT: C 815 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7134 (mtm-85) REVERT: C 859 THR cc_start: 0.8112 (t) cc_final: 0.7733 (p) REVERT: C 883 THR cc_start: 0.8102 (m) cc_final: 0.7734 (p) REVERT: C 933 LYS cc_start: 0.8045 (mttt) cc_final: 0.7466 (mptt) REVERT: C 947 LYS cc_start: 0.7960 (mtpt) cc_final: 0.7675 (mtpp) REVERT: C 964 LYS cc_start: 0.7911 (mttt) cc_final: 0.7635 (mttt) REVERT: C 994 ASP cc_start: 0.7081 (t70) cc_final: 0.6880 (m-30) REVERT: C 1006 THR cc_start: 0.7895 (OUTLIER) cc_final: 0.7630 (p) REVERT: C 1038 LYS cc_start: 0.7619 (tppt) cc_final: 0.7304 (mmpt) REVERT: C 1045 LYS cc_start: 0.7569 (mttt) cc_final: 0.7312 (mttt) REVERT: C 1055 SER cc_start: 0.8349 (t) cc_final: 0.8016 (m) REVERT: C 1101 HIS cc_start: 0.7941 (m-70) cc_final: 0.7499 (m-70) REVERT: C 1123 SER cc_start: 0.8314 (t) cc_final: 0.8038 (m) REVERT: C 1141 LEU cc_start: 0.7927 (tp) cc_final: 0.7725 (tm) REVERT: G 71 PHE cc_start: 0.6366 (t80) cc_final: 0.5980 (t80) REVERT: E 31 SER cc_start: 0.7679 (p) cc_final: 0.7463 (p) REVERT: E 32 TYR cc_start: 0.7271 (m-80) cc_final: 0.6772 (m-80) REVERT: E 34 MET cc_start: 0.6204 (ppp) cc_final: 0.5632 (ppp) outliers start: 127 outliers final: 90 residues processed: 723 average time/residue: 1.1933 time to fit residues: 1034.0541 Evaluate side-chains 758 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 656 time to evaluate : 3.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 334 optimal weight: 0.1980 chunk 351 optimal weight: 2.9990 chunk 320 optimal weight: 2.9990 chunk 342 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 149 optimal weight: 0.0370 chunk 268 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 309 optimal weight: 4.9990 chunk 323 optimal weight: 3.9990 chunk 341 optimal weight: 1.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN A1101 HIS L 27 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B1101 HIS C 764 ASN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31317 Z= 0.220 Angle : 0.663 13.242 42591 Z= 0.322 Chirality : 0.047 0.384 4920 Planarity : 0.004 0.052 5448 Dihedral : 6.219 109.313 5201 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.79 % Allowed : 21.59 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.13), residues: 3780 helix: 1.52 (0.21), residues: 654 sheet: -0.61 (0.17), residues: 876 loop : -1.72 (0.12), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 47 HIS 0.007 0.001 HIS B 207 PHE 0.029 0.001 PHE B 168 TYR 0.067 0.002 TYR E 60 ARG 0.011 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 660 time to evaluate : 3.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.8067 (m) cc_final: 0.7659 (p) REVERT: A 52 GLN cc_start: 0.7344 (tm-30) cc_final: 0.7089 (tp-100) REVERT: A 92 PHE cc_start: 0.7499 (t80) cc_final: 0.7058 (t80) REVERT: A 140 PHE cc_start: 0.7153 (p90) cc_final: 0.6478 (p90) REVERT: A 153 MET cc_start: 0.4275 (mpp) cc_final: 0.3842 (mpp) REVERT: A 177 MET cc_start: 0.0002 (mtt) cc_final: -0.0666 (mtt) REVERT: A 206 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6931 (ttmm) REVERT: A 282 ASN cc_start: 0.6698 (OUTLIER) cc_final: 0.6462 (m110) REVERT: A 319 ARG cc_start: 0.7653 (ptp90) cc_final: 0.7183 (ptt180) REVERT: A 453 TYR cc_start: 0.6785 (p90) cc_final: 0.6312 (p90) REVERT: A 454 ARG cc_start: 0.7715 (mmt90) cc_final: 0.7121 (mmt90) REVERT: A 541 PHE cc_start: 0.6991 (p90) cc_final: 0.6343 (p90) REVERT: A 651 ILE cc_start: 0.8632 (mm) cc_final: 0.8360 (mp) REVERT: A 703 ASN cc_start: 0.7890 (t0) cc_final: 0.7535 (t0) REVERT: A 736 VAL cc_start: 0.8126 (t) cc_final: 0.7881 (m) REVERT: A 790 LYS cc_start: 0.7580 (mtpm) cc_final: 0.7376 (mtpm) REVERT: A 795 LYS cc_start: 0.8496 (mptm) cc_final: 0.8120 (mptt) REVERT: A 811 LYS cc_start: 0.7280 (mmpt) cc_final: 0.6813 (mtpp) REVERT: A 815 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.6326 (mtm110) REVERT: A 864 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8164 (tt) REVERT: A 933 LYS cc_start: 0.7948 (mttt) cc_final: 0.7548 (mtmm) REVERT: A 947 LYS cc_start: 0.7595 (mtpp) cc_final: 0.7339 (mtmt) REVERT: A 1045 LYS cc_start: 0.7801 (mttt) cc_final: 0.7452 (mttt) REVERT: A 1072 GLU cc_start: 0.7853 (pm20) cc_final: 0.7427 (pm20) REVERT: A 1111 GLU cc_start: 0.7275 (tt0) cc_final: 0.7004 (tt0) REVERT: A 1141 LEU cc_start: 0.7955 (tm) cc_final: 0.7734 (tt) REVERT: B 49 HIS cc_start: 0.7867 (t-90) cc_final: 0.7425 (t70) REVERT: B 140 PHE cc_start: 0.7484 (p90) cc_final: 0.7111 (p90) REVERT: B 153 MET cc_start: 0.5230 (mpp) cc_final: 0.4868 (mpp) REVERT: B 206 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6904 (ttmm) REVERT: B 319 ARG cc_start: 0.7899 (ptp90) cc_final: 0.7558 (ptt180) REVERT: B 340 GLU cc_start: 0.7033 (mp0) cc_final: 0.6642 (mp0) REVERT: B 374 PHE cc_start: 0.7204 (m-80) cc_final: 0.7000 (m-80) REVERT: B 508 TYR cc_start: 0.7750 (m-10) cc_final: 0.7311 (m-80) REVERT: B 541 PHE cc_start: 0.6814 (p90) cc_final: 0.6391 (p90) REVERT: B 586 ASP cc_start: 0.6947 (m-30) cc_final: 0.6336 (m-30) REVERT: B 725 GLU cc_start: 0.7401 (tt0) cc_final: 0.7138 (tt0) REVERT: B 772 VAL cc_start: 0.8404 (p) cc_final: 0.8162 (t) REVERT: B 859 THR cc_start: 0.8094 (t) cc_final: 0.7822 (p) REVERT: B 933 LYS cc_start: 0.8039 (mttt) cc_final: 0.7401 (mmtm) REVERT: B 935 GLN cc_start: 0.8060 (mt0) cc_final: 0.7711 (mt0) REVERT: B 947 LYS cc_start: 0.7838 (mtpt) cc_final: 0.7545 (mtpp) REVERT: B 949 GLN cc_start: 0.7386 (tp40) cc_final: 0.7123 (mm-40) REVERT: B 950 ASP cc_start: 0.7234 (m-30) cc_final: 0.6687 (m-30) REVERT: B 1029 MET cc_start: 0.7966 (ttm) cc_final: 0.7716 (tpp) REVERT: B 1118 ASP cc_start: 0.7461 (m-30) cc_final: 0.7210 (m-30) REVERT: B 1123 SER cc_start: 0.8284 (t) cc_final: 0.8060 (p) REVERT: F 71 PHE cc_start: 0.6564 (t80) cc_final: 0.6000 (t80) REVERT: C 82 PRO cc_start: 0.8427 (Cg_endo) cc_final: 0.8212 (Cg_exo) REVERT: C 83 VAL cc_start: 0.7421 (OUTLIER) cc_final: 0.6826 (p) REVERT: C 206 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6821 (ttmm) REVERT: C 237 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.6391 (ttm-80) REVERT: C 314 GLN cc_start: 0.7745 (tt0) cc_final: 0.7475 (tp40) REVERT: C 454 ARG cc_start: 0.8046 (mmt90) cc_final: 0.7715 (mpt-90) REVERT: C 541 PHE cc_start: 0.6975 (p90) cc_final: 0.6689 (p90) REVERT: C 578 ASP cc_start: 0.6735 (OUTLIER) cc_final: 0.5793 (p0) REVERT: C 651 ILE cc_start: 0.8604 (mm) cc_final: 0.8312 (mt) REVERT: C 705 VAL cc_start: 0.6908 (OUTLIER) cc_final: 0.6665 (p) REVERT: C 750 SER cc_start: 0.7695 (t) cc_final: 0.7390 (p) REVERT: C 780 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7107 (OUTLIER) REVERT: C 790 LYS cc_start: 0.7561 (mtmm) cc_final: 0.7192 (mmpt) REVERT: C 815 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7127 (mtm-85) REVERT: C 859 THR cc_start: 0.8112 (t) cc_final: 0.7708 (p) REVERT: C 883 THR cc_start: 0.8111 (m) cc_final: 0.7739 (p) REVERT: C 933 LYS cc_start: 0.8046 (mttt) cc_final: 0.7460 (mptt) REVERT: C 947 LYS cc_start: 0.7961 (mtpt) cc_final: 0.7674 (mtpp) REVERT: C 964 LYS cc_start: 0.7903 (mttt) cc_final: 0.7632 (mttt) REVERT: C 1006 THR cc_start: 0.7892 (OUTLIER) cc_final: 0.7627 (p) REVERT: C 1038 LYS cc_start: 0.7620 (tppt) cc_final: 0.7128 (mmmm) REVERT: C 1045 LYS cc_start: 0.7553 (mttt) cc_final: 0.7299 (mttt) REVERT: C 1055 SER cc_start: 0.8359 (t) cc_final: 0.8042 (m) REVERT: C 1101 HIS cc_start: 0.7953 (m-70) cc_final: 0.7506 (m-70) REVERT: C 1123 SER cc_start: 0.8316 (t) cc_final: 0.8040 (m) REVERT: C 1141 LEU cc_start: 0.7950 (tp) cc_final: 0.7749 (tm) REVERT: G 71 PHE cc_start: 0.6364 (t80) cc_final: 0.5996 (t80) REVERT: E 31 SER cc_start: 0.7721 (p) cc_final: 0.7511 (p) REVERT: E 32 TYR cc_start: 0.7266 (m-80) cc_final: 0.6811 (m-80) REVERT: E 34 MET cc_start: 0.6269 (ppp) cc_final: 0.5831 (ppp) outliers start: 126 outliers final: 93 residues processed: 723 average time/residue: 1.2039 time to fit residues: 1047.1089 Evaluate side-chains 750 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 645 time to evaluate : 3.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 224 optimal weight: 3.9990 chunk 361 optimal weight: 0.0870 chunk 220 optimal weight: 3.9990 chunk 171 optimal weight: 0.0030 chunk 251 optimal weight: 2.9990 chunk 379 optimal weight: 1.9990 chunk 349 optimal weight: 2.9990 chunk 302 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.6174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1010 GLN A1101 HIS L 27 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 607 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 31317 Z= 0.372 Angle : 0.741 12.873 42591 Z= 0.371 Chirality : 0.050 0.357 4920 Planarity : 0.005 0.077 5448 Dihedral : 6.540 108.636 5201 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.70 % Allowed : 22.13 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.13), residues: 3780 helix: 0.82 (0.20), residues: 684 sheet: -0.81 (0.17), residues: 888 loop : -1.86 (0.12), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 886 HIS 0.009 0.001 HIS B 207 PHE 0.028 0.002 PHE B 92 TYR 0.039 0.002 TYR E 60 ARG 0.011 0.001 ARG B 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 666 time to evaluate : 3.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.8002 (m) cc_final: 0.7626 (p) REVERT: A 128 ILE cc_start: 0.6122 (mm) cc_final: 0.5802 (mp) REVERT: A 140 PHE cc_start: 0.7393 (p90) cc_final: 0.6599 (p90) REVERT: A 153 MET cc_start: 0.4313 (mpp) cc_final: 0.3911 (mpp) REVERT: A 177 MET cc_start: 0.0237 (mtt) cc_final: -0.0409 (mtt) REVERT: A 206 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.7036 (ttmm) REVERT: A 282 ASN cc_start: 0.6851 (OUTLIER) cc_final: 0.6526 (m110) REVERT: A 319 ARG cc_start: 0.7725 (ptp90) cc_final: 0.7339 (ptt180) REVERT: A 453 TYR cc_start: 0.6913 (p90) cc_final: 0.6458 (p90) REVERT: A 454 ARG cc_start: 0.7910 (mmt90) cc_final: 0.7450 (mmm-85) REVERT: A 541 PHE cc_start: 0.7071 (p90) cc_final: 0.6423 (p90) REVERT: A 651 ILE cc_start: 0.8650 (mm) cc_final: 0.8385 (mp) REVERT: A 654 GLU cc_start: 0.7297 (pt0) cc_final: 0.7015 (pt0) REVERT: A 736 VAL cc_start: 0.8139 (t) cc_final: 0.7862 (m) REVERT: A 790 LYS cc_start: 0.7580 (mtpm) cc_final: 0.7039 (mmpt) REVERT: A 795 LYS cc_start: 0.8556 (mptm) cc_final: 0.8309 (mptp) REVERT: A 811 LYS cc_start: 0.7366 (mmpt) cc_final: 0.6931 (mtpp) REVERT: A 815 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6228 (mtm110) REVERT: A 864 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8202 (tt) REVERT: A 933 LYS cc_start: 0.7931 (mttt) cc_final: 0.7540 (mtmm) REVERT: A 947 LYS cc_start: 0.7625 (mtpp) cc_final: 0.7361 (mtmt) REVERT: A 1045 LYS cc_start: 0.7909 (mttt) cc_final: 0.7551 (mttt) REVERT: A 1072 GLU cc_start: 0.7850 (pm20) cc_final: 0.7424 (pm20) REVERT: A 1111 GLU cc_start: 0.7318 (tt0) cc_final: 0.7046 (tt0) REVERT: B 49 HIS cc_start: 0.7889 (t-90) cc_final: 0.7429 (t70) REVERT: B 53 ASP cc_start: 0.6512 (t0) cc_final: 0.6124 (t0) REVERT: B 140 PHE cc_start: 0.7671 (p90) cc_final: 0.7126 (p90) REVERT: B 153 MET cc_start: 0.5331 (mpp) cc_final: 0.4985 (mpp) REVERT: B 168 PHE cc_start: 0.5882 (t80) cc_final: 0.5314 (t80) REVERT: B 319 ARG cc_start: 0.7867 (ptp90) cc_final: 0.7527 (ptt180) REVERT: B 340 GLU cc_start: 0.7255 (mp0) cc_final: 0.6846 (mp0) REVERT: B 454 ARG cc_start: 0.8253 (mmt180) cc_final: 0.7857 (mmt90) REVERT: B 484 GLU cc_start: 0.5393 (OUTLIER) cc_final: 0.4734 (tp30) REVERT: B 541 PHE cc_start: 0.6950 (p90) cc_final: 0.6511 (p90) REVERT: B 586 ASP cc_start: 0.6937 (m-30) cc_final: 0.6362 (m-30) REVERT: B 615 VAL cc_start: 0.8282 (p) cc_final: 0.7950 (t) REVERT: B 725 GLU cc_start: 0.7466 (tt0) cc_final: 0.7175 (tt0) REVERT: B 772 VAL cc_start: 0.8399 (p) cc_final: 0.8172 (t) REVERT: B 859 THR cc_start: 0.8154 (t) cc_final: 0.7898 (p) REVERT: B 933 LYS cc_start: 0.8056 (mttt) cc_final: 0.7413 (mmtm) REVERT: B 947 LYS cc_start: 0.7852 (mtpt) cc_final: 0.7541 (mtpp) REVERT: B 950 ASP cc_start: 0.7239 (m-30) cc_final: 0.6721 (m-30) REVERT: B 1029 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7647 (tpp) REVERT: B 1050 MET cc_start: 0.8161 (ptt) cc_final: 0.7909 (ptm) REVERT: B 1118 ASP cc_start: 0.7515 (m-30) cc_final: 0.7248 (m-30) REVERT: B 1123 SER cc_start: 0.8356 (t) cc_final: 0.8126 (p) REVERT: F 45 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.5772 (ppt90) REVERT: F 71 PHE cc_start: 0.6765 (t80) cc_final: 0.6179 (t80) REVERT: C 83 VAL cc_start: 0.7516 (OUTLIER) cc_final: 0.6919 (p) REVERT: C 129 LYS cc_start: 0.7551 (mmtm) cc_final: 0.7114 (mmtm) REVERT: C 206 LYS cc_start: 0.7355 (OUTLIER) cc_final: 0.7046 (ttmm) REVERT: C 237 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6494 (ttm-80) REVERT: C 314 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7491 (tp40) REVERT: C 319 ARG cc_start: 0.7891 (ptp90) cc_final: 0.7615 (ptt180) REVERT: C 454 ARG cc_start: 0.8047 (mmt90) cc_final: 0.7743 (mpt-90) REVERT: C 578 ASP cc_start: 0.6701 (OUTLIER) cc_final: 0.5738 (p0) REVERT: C 651 ILE cc_start: 0.8616 (mm) cc_final: 0.8406 (mt) REVERT: C 705 VAL cc_start: 0.7161 (OUTLIER) cc_final: 0.6932 (p) REVERT: C 750 SER cc_start: 0.7842 (t) cc_final: 0.7546 (p) REVERT: C 776 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7470 (tmmm) REVERT: C 780 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7100 (pt0) REVERT: C 790 LYS cc_start: 0.7570 (mtmm) cc_final: 0.7247 (mmpt) REVERT: C 815 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7294 (mtm-85) REVERT: C 883 THR cc_start: 0.8217 (m) cc_final: 0.7828 (p) REVERT: C 931 ILE cc_start: 0.7345 (OUTLIER) cc_final: 0.6893 (mp) REVERT: C 933 LYS cc_start: 0.8009 (mttt) cc_final: 0.7408 (mptt) REVERT: C 947 LYS cc_start: 0.7998 (mtpt) cc_final: 0.7702 (mtpp) REVERT: C 964 LYS cc_start: 0.7921 (mttt) cc_final: 0.7672 (mttt) REVERT: C 1006 THR cc_start: 0.7938 (OUTLIER) cc_final: 0.7589 (p) REVERT: C 1038 LYS cc_start: 0.7704 (tppt) cc_final: 0.7209 (mmmm) REVERT: C 1045 LYS cc_start: 0.7539 (mttt) cc_final: 0.7321 (mttt) REVERT: C 1055 SER cc_start: 0.8346 (t) cc_final: 0.8008 (m) REVERT: C 1101 HIS cc_start: 0.7995 (m-70) cc_final: 0.7582 (m-70) REVERT: C 1123 SER cc_start: 0.8301 (t) cc_final: 0.8022 (m) REVERT: C 1141 LEU cc_start: 0.7973 (tp) cc_final: 0.7759 (tm) REVERT: G 45 ARG cc_start: 0.6889 (tmm160) cc_final: 0.6678 (tmm160) REVERT: G 71 PHE cc_start: 0.6624 (t80) cc_final: 0.6118 (t80) REVERT: E 31 SER cc_start: 0.7961 (p) cc_final: 0.7622 (p) REVERT: E 32 TYR cc_start: 0.7200 (m-80) cc_final: 0.6763 (m-80) outliers start: 123 outliers final: 81 residues processed: 729 average time/residue: 1.2277 time to fit residues: 1092.1494 Evaluate side-chains 758 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 659 time to evaluate : 3.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 94 TRP Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 94 TRP Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 240 optimal weight: 2.9990 chunk 321 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 278 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 302 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 310 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1005 GLN A1010 GLN A1101 HIS L 27 GLN B 207 HIS ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 764 ASN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.196964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.175365 restraints weight = 57628.586| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 3.69 r_work: 0.4018 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 31317 Z= 0.301 Angle : 0.709 12.682 42591 Z= 0.349 Chirality : 0.049 0.414 4920 Planarity : 0.005 0.062 5448 Dihedral : 6.449 107.955 5201 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.34 % Allowed : 22.94 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.13), residues: 3780 helix: 0.91 (0.21), residues: 684 sheet: -0.76 (0.17), residues: 882 loop : -1.85 (0.12), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 886 HIS 0.010 0.001 HIS B 207 PHE 0.027 0.002 PHE C 490 TYR 0.032 0.002 TYR E 60 ARG 0.010 0.001 ARG B 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14668.22 seconds wall clock time: 259 minutes 31.42 seconds (15571.42 seconds total)