Starting phenix.real_space_refine on Fri Jan 16 07:35:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h7l_34522/01_2026/8h7l_34522.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h7l_34522/01_2026/8h7l_34522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h7l_34522/01_2026/8h7l_34522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h7l_34522/01_2026/8h7l_34522.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h7l_34522/01_2026/8h7l_34522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h7l_34522/01_2026/8h7l_34522.map" } resolution = 2.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.060 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 150 5.16 5 C 21891 2.51 5 N 5676 2.21 5 O 6663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34380 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 7981 Classifications: {'peptide': 1018} Link IDs: {'PTRANS': 56, 'TRANS': 961} Chain breaks: 7 Chain: "B" Number of atoms: 7981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 7981 Classifications: {'peptide': 1018} Link IDs: {'PTRANS': 56, 'TRANS': 961} Chain breaks: 7 Chain: "C" Number of atoms: 7981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 7981 Classifications: {'peptide': 1018} Link IDs: {'PTRANS': 56, 'TRANS': 961} Chain breaks: 7 Chain: "D" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1685 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "E" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1685 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "F" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1685 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "G" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1626 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain: "H" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1626 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain: "I" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1626 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 7.96, per 1000 atoms: 0.23 Number of scatterers: 34380 At special positions: 0 Unit cell: (142.952, 137.608, 255.844, 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 150 16.00 O 6663 8.00 N 5676 7.00 C 21891 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 166 " 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=2.04 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 B 133 " - pdb=" SG CYS B 166 " 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 C 133 " - pdb=" SG CYS C 166 " 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 D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 206 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 206 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 150 " - pdb=" SG CYS F 206 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 194 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1201 " - " ASN A1134 " " NAG A1202 " - " ASN A 709 " " NAG A1203 " - " ASN A1074 " " NAG A1204 " - " ASN A 657 " " NAG B1201 " - " ASN B1134 " " NAG B1202 " - " ASN B 709 " " NAG B1203 " - " ASN B1074 " " NAG B1204 " - " ASN B 657 " " NAG C1201 " - " ASN C1134 " " NAG C1202 " - " ASN C 709 " " NAG C1203 " - " ASN C1074 " " NAG C1204 " - " ASN C 657 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A 331 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B 331 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C 331 " Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.4 seconds 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8148 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 81 sheets defined 19.5% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.181A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.590A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.536A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.529A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.507A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 747 through 754 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 760 through 783 removed outlier: 3.612A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.632A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.276A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 933 removed outlier: 3.674A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 941 removed outlier: 3.857A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.540A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.849A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.386A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.011A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.651A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 372 " --> pdb=" O TYR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.659A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.797A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.567A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.378A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.175A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.739A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 988 Processing helix chain 'B' and resid 989 through 1033 removed outlier: 3.716A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.605A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.872A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.636A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.915A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 783 removed outlier: 3.607A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.522A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.604A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.057A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.594A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.874A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 4.055A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.629A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C1004 " --> pdb=" O ARG C1000 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.607A pdb=" N SER D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.908A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 168 No H-bonds generated for 'chain 'D' and resid 166 through 168' Processing helix chain 'D' and resid 196 through 200 removed outlier: 3.987A pdb=" N GLY D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 196 through 200' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.743A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.766A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 168 No H-bonds generated for 'chain 'E' and resid 166 through 168' Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.571A pdb=" N SER F 31 " --> pdb=" O THR F 28 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.967A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 139 No H-bonds generated for 'chain 'F' and resid 137 through 139' Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.061A pdb=" N ALA G 83 " --> pdb=" O SER G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 128 Processing helix chain 'G' and resid 183 through 189 Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.172A pdb=" N ALA H 83 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 128 removed outlier: 3.536A pdb=" N LEU H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 189 removed outlier: 3.597A pdb=" N LYS H 188 " --> pdb=" O ALA H 184 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS H 189 " --> pdb=" O ASP H 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.691A pdb=" N ALA I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 128 Processing helix chain 'I' and resid 183 through 189 removed outlier: 3.526A pdb=" N LYS I 188 " --> pdb=" O ALA I 184 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS I 189 " --> pdb=" O ASP I 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 32 removed outlier: 8.121A pdb=" N ASN A 63 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYR A 269 " --> pdb=" O ASN A 63 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 45 removed outlier: 6.573A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 57 removed outlier: 8.017A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA5, first strand: chain 'A' and resid 86 through 87 removed outlier: 4.231A pdb=" N GLY A 105 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA A 243 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE A 103 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ARG A 104 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 168 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.431A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.593A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE A 565 " --> pdb=" O PHE C 45 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.657A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.884A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.653A pdb=" N LYS A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASN A 658 " --> pdb=" O LYS A 696 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.748A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.576A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.889A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 25 through 32 removed outlier: 3.766A pdb=" N THR B 27 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ASN B 63 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR B 269 " --> pdb=" O ASN B 63 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 44 through 45 removed outlier: 6.680A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 49 through 57 removed outlier: 4.076A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 86 through 87 removed outlier: 6.224A pdb=" N LEU B 143 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 86 through 87 removed outlier: 3.850A pdb=" N GLY B 105 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA B 243 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE B 103 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ARG B 104 " --> pdb=" O ASN B 123 " (cutoff:3.500A) removed outlier: 11.315A pdb=" N VAL B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N GLU B 169 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 11.549A pdb=" N ILE B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N THR B 167 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASN B 165 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA B 163 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLN B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.952A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.663A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.763A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.200A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N LYS B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.707A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.707A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.622A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 787 through 790 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.176A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 32 removed outlier: 8.280A pdb=" N ASN C 63 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TYR C 269 " --> pdb=" O ASN C 63 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 49 through 57 removed outlier: 7.980A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 86 through 87 removed outlier: 6.345A pdb=" N LEU C 143 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 86 through 87 removed outlier: 4.181A pdb=" N GLY C 105 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA C 243 " --> pdb=" O ILE C 103 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE C 103 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ARG C 104 " --> pdb=" O ASN C 123 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N VAL C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.924A pdb=" N GLU C 169 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 11.530A pdb=" N ILE C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N THR C 167 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASN C 165 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA C 163 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.514A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.732A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 374 through 380 removed outlier: 8.137A pdb=" N PHE C 374 " --> pdb=" O ASN C 437 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASN C 437 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.244A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N LYS C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.713A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.713A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.561A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.253A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.553A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.788A pdb=" N MET D 34 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.046A pdb=" N VAL D 112 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 131 through 134 removed outlier: 3.907A pdb=" N GLY D 149 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER D 190 " --> pdb=" O CYS D 150 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 161 through 164 removed outlier: 3.573A pdb=" N THR D 161 " --> pdb=" O ASN D 209 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS D 219 " --> pdb=" O CYS D 206 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL D 208 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL D 217 " --> pdb=" O VAL D 208 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.726A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.789A pdb=" N MET E 34 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.819A pdb=" N ARG E 98 " --> pdb=" O ASP E 111 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 129 through 134 removed outlier: 3.839A pdb=" N GLY E 149 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER E 190 " --> pdb=" O CYS E 150 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 129 through 134 removed outlier: 3.839A pdb=" N GLY E 149 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER E 190 " --> pdb=" O CYS E 150 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 161 through 164 removed outlier: 3.529A pdb=" N THR E 161 " --> pdb=" O ASN E 209 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL E 217 " --> pdb=" O VAL E 208 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.692A pdb=" N GLN F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.812A pdb=" N MET F 34 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.807A pdb=" N ARG F 98 " --> pdb=" O ASP F 111 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 133 through 134 removed outlier: 3.764A pdb=" N GLY F 149 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 133 through 134 removed outlier: 3.764A pdb=" N GLY F 149 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 153 through 155 Processing sheet with id=AH3, first strand: chain 'F' and resid 160 through 164 removed outlier: 3.660A pdb=" N VAL F 208 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL F 217 " --> pdb=" O VAL F 208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS F 210 " --> pdb=" O THR F 215 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 4 through 7 removed outlier: 6.277A pdb=" N THR G 69 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 11.074A pdb=" N GLN G 27 " --> pdb=" O TYR G 67 " (cutoff:3.500A) removed outlier: 10.278A pdb=" N TYR G 67 " --> pdb=" O GLN G 27 " (cutoff:3.500A) removed outlier: 12.122A pdb=" N ILE G 29 " --> pdb=" O SER G 65 " (cutoff:3.500A) removed outlier: 11.862A pdb=" N SER G 65 " --> pdb=" O ILE G 29 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 10 through 13 removed outlier: 7.178A pdb=" N MET G 33 " --> pdb=" O GLN G 49 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLN G 49 " --> pdb=" O MET G 33 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP G 35 " --> pdb=" O ILE G 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.864A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 114 through 118 Processing sheet with id=AH8, first strand: chain 'G' and resid 153 through 155 removed outlier: 4.625A pdb=" N TRP G 148 " --> pdb=" O GLN G 155 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AI1, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.590A pdb=" N THR H 102 " --> pdb=" O TYR H 86 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N MET H 33 " --> pdb=" O GLN H 49 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLN H 49 " --> pdb=" O MET H 33 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP H 35 " --> pdb=" O ILE H 47 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.590A pdb=" N THR H 102 " --> pdb=" O TYR H 86 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR H 97 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'H' and resid 114 through 118 Processing sheet with id=AI4, first strand: chain 'H' and resid 153 through 155 removed outlier: 4.491A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AI6, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.662A pdb=" N GLU I 105 " --> pdb=" O MET I 11 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.496A pdb=" N TRP I 35 " --> pdb=" O ILE I 47 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLN I 49 " --> pdb=" O MET I 33 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N MET I 33 " --> pdb=" O GLN I 49 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'I' and resid 114 through 118 Processing sheet with id=AI9, first strand: chain 'I' and resid 153 through 155 removed outlier: 4.405A pdb=" N TRP I 148 " --> pdb=" O GLN I 155 " (cutoff:3.500A) 1414 hydrogen bonds defined for protein. 3834 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: 9.55 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10950 1.34 - 1.47: 8767 1.47 - 1.59: 15272 1.59 - 1.71: 0 1.71 - 1.83: 195 Bond restraints: 35184 Sorted by residual: bond pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.38e-02 5.25e+03 4.23e+00 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" C1 NAG C1203 " pdb=" O5 NAG C1203 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.76e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.69e+00 ... (remaining 35179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 47193 2.18 - 4.36: 630 4.36 - 6.53: 39 6.53 - 8.71: 10 8.71 - 10.89: 5 Bond angle restraints: 47877 Sorted by residual: angle pdb=" N SER A 316 " pdb=" CA SER A 316 " pdb=" C SER A 316 " ideal model delta sigma weight residual 108.45 117.94 -9.49 1.26e+00 6.30e-01 5.67e+01 angle pdb=" N TRP B 353 " pdb=" CA TRP B 353 " pdb=" C TRP B 353 " ideal model delta sigma weight residual 110.33 117.63 -7.30 1.29e+00 6.01e-01 3.20e+01 angle pdb=" N VAL B 350 " pdb=" CA VAL B 350 " pdb=" C VAL B 350 " ideal model delta sigma weight residual 109.34 118.93 -9.59 2.08e+00 2.31e-01 2.13e+01 angle pdb=" N LYS F 153 " pdb=" CA LYS F 153 " pdb=" C LYS F 153 " ideal model delta sigma weight residual 108.69 115.33 -6.64 1.77e+00 3.19e-01 1.41e+01 angle pdb=" N ASP B 389 " pdb=" CA ASP B 389 " pdb=" C ASP B 389 " ideal model delta sigma weight residual 113.17 108.55 4.62 1.26e+00 6.30e-01 1.34e+01 ... (remaining 47872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 19808 17.96 - 35.91: 1388 35.91 - 53.87: 199 53.87 - 71.83: 53 71.83 - 89.78: 17 Dihedral angle restraints: 21465 sinusoidal: 8787 harmonic: 12678 Sorted by residual: dihedral pdb=" CB CYS G 134 " pdb=" SG CYS G 134 " pdb=" SG CYS G 194 " pdb=" CB CYS G 194 " ideal model delta sinusoidal sigma weight residual 93.00 143.45 -50.45 1 1.00e+01 1.00e-02 3.49e+01 dihedral pdb=" CB CYS H 134 " pdb=" SG CYS H 134 " pdb=" SG CYS H 194 " pdb=" CB CYS H 194 " ideal model delta sinusoidal sigma weight residual 93.00 132.85 -39.85 1 1.00e+01 1.00e-02 2.23e+01 dihedral pdb=" CB CYS F 150 " pdb=" SG CYS F 150 " pdb=" SG CYS F 206 " pdb=" CB CYS F 206 " ideal model delta sinusoidal sigma weight residual -86.00 -118.94 32.94 1 1.00e+01 1.00e-02 1.54e+01 ... (remaining 21462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 5475 0.129 - 0.257: 38 0.257 - 0.386: 0 0.386 - 0.514: 0 0.514 - 0.643: 1 Chirality restraints: 5514 Sorted by residual: chirality pdb=" C1 NAG B1204 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B1204 " pdb=" O5 NAG B1204 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA ASP F 154 " pdb=" N ASP F 154 " pdb=" C ASP F 154 " pdb=" CB ASP F 154 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" CA ASN C 417 " pdb=" N ASN C 417 " pdb=" C ASN C 417 " pdb=" CB ASN C 417 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 5511 not shown) Planarity restraints: 6159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 372 " 0.063 5.00e-02 4.00e+02 9.57e-02 1.47e+01 pdb=" N PRO B 373 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO B 373 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 373 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 811 " 0.045 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO B 812 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 812 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 812 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " -0.037 5.00e-02 4.00e+02 5.59e-02 5.01e+00 pdb=" N PRO A 987 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " -0.032 5.00e-02 4.00e+02 ... (remaining 6156 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1119 2.71 - 3.26: 32094 3.26 - 3.81: 51290 3.81 - 4.35: 65172 4.35 - 4.90: 114161 Nonbonded interactions: 263836 Sorted by model distance: nonbonded pdb=" OG SER D 25 " pdb=" OE1 GLU D 26 " model vdw 2.167 3.040 nonbonded pdb=" OG SER E 25 " pdb=" OE1 GLU E 26 " model vdw 2.177 3.040 nonbonded pdb=" O LYS D 153 " pdb=" OG SER D 187 " model vdw 2.178 3.040 nonbonded pdb=" OG SER F 25 " pdb=" OE1 GLU F 26 " model vdw 2.209 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.232 3.040 ... (remaining 263831 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.980 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 34.040 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 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 0.079 35268 Z= 0.169 Angle : 0.631 16.907 48081 Z= 0.338 Chirality : 0.045 0.643 5514 Planarity : 0.004 0.096 6135 Dihedral : 12.425 89.781 13173 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.35 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.13), residues: 4296 helix: 1.36 (0.21), residues: 696 sheet: 0.97 (0.14), residues: 1401 loop : -1.15 (0.13), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 498 TYR 0.017 0.001 TYR E 155 PHE 0.031 0.001 PHE A 906 TRP 0.022 0.001 TRP C 886 HIS 0.004 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00357 (35184) covalent geometry : angle 0.61644 (47877) SS BOND : bond 0.00353 ( 48) SS BOND : angle 0.95063 ( 96) hydrogen bonds : bond 0.17327 ( 1343) hydrogen bonds : angle 7.23119 ( 3834) link_BETA1-4 : bond 0.00469 ( 12) link_BETA1-4 : angle 0.96932 ( 36) link_NAG-ASN : bond 0.00445 ( 24) link_NAG-ASN : angle 3.40223 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 448 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 GLU cc_start: 0.7711 (tt0) cc_final: 0.7446 (pp20) REVERT: A 1125 ASN cc_start: 0.7501 (m-40) cc_final: 0.6797 (p0) REVERT: C 690 GLN cc_start: 0.6737 (mm-40) cc_final: 0.6462 (mt0) REVERT: E 188 LEU cc_start: 0.1362 (pp) cc_final: 0.1141 (tt) REVERT: H 126 LYS cc_start: 0.2919 (ptpp) cc_final: 0.2288 (tppt) REVERT: H 188 LYS cc_start: 0.3342 (mtpp) cc_final: 0.2421 (tmtp) outliers start: 0 outliers final: 0 residues processed: 448 average time/residue: 0.6233 time to fit residues: 338.8005 Evaluate side-chains 214 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 690 GLN A 762 GLN A1005 GLN B 675 GLN B1002 GLN B1119 ASN C 71 HIS C 218 GLN C 450 ASN C 532 ASN C 544 ASN C 787 GLN C 804 GLN C 950 ASN E 207 ASN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 GLN G 93 ASN ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.224932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.160666 restraints weight = 47080.845| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 5.18 r_work: 0.3336 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 35268 Z= 0.201 Angle : 0.736 16.814 48081 Z= 0.375 Chirality : 0.051 0.663 5514 Planarity : 0.005 0.072 6135 Dihedral : 6.278 59.638 5424 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.65 % Favored : 96.32 % Rotamer: Outliers : 2.06 % Allowed : 8.12 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.12), residues: 4296 helix: 1.45 (0.20), residues: 683 sheet: 0.97 (0.14), residues: 1352 loop : -1.30 (0.12), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 72 TYR 0.021 0.002 TYR B 796 PHE 0.040 0.002 PHE A 906 TRP 0.020 0.002 TRP B 436 HIS 0.007 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00467 (35184) covalent geometry : angle 0.71197 (47877) SS BOND : bond 0.00449 ( 48) SS BOND : angle 1.76011 ( 96) hydrogen bonds : bond 0.07100 ( 1343) hydrogen bonds : angle 5.88720 ( 3834) link_BETA1-4 : bond 0.00648 ( 12) link_BETA1-4 : angle 1.65765 ( 36) link_NAG-ASN : bond 0.01270 ( 24) link_NAG-ASN : angle 4.33966 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 237 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.6469 (m-80) cc_final: 0.5581 (m-80) REVERT: A 661 GLU cc_start: 0.8415 (tt0) cc_final: 0.8066 (pp20) REVERT: A 957 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7466 (mt0) REVERT: A 964 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7419 (mppt) REVERT: A 1125 ASN cc_start: 0.8422 (m-40) cc_final: 0.7818 (p0) REVERT: B 738 CYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7536 (t) REVERT: B 1034 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8354 (pp) REVERT: C 115 LYS cc_start: 0.7224 (mtpt) cc_final: 0.6909 (mtmm) REVERT: C 586 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8303 (m-30) REVERT: C 690 GLN cc_start: 0.7187 (mm-40) cc_final: 0.6734 (mt0) REVERT: C 786 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8026 (ptpt) REVERT: D 94 TYR cc_start: 0.2275 (m-80) cc_final: 0.1937 (m-80) REVERT: D 148 LEU cc_start: -0.0456 (OUTLIER) cc_final: -0.0688 (pp) REVERT: E 58 LYS cc_start: 0.3447 (mmmt) cc_final: 0.3208 (mmmm) REVERT: E 219 LYS cc_start: -0.0339 (OUTLIER) cc_final: -0.0566 (tmmm) REVERT: F 83 MET cc_start: 0.3125 (OUTLIER) cc_final: 0.2889 (mtm) outliers start: 78 outliers final: 25 residues processed: 289 average time/residue: 0.6216 time to fit residues: 219.6117 Evaluate side-chains 222 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 186 TYR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 191 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 335 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 371 optimal weight: 7.9990 chunk 402 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 HIS A1005 GLN B 89 ASN B 675 GLN C 422 ASN C 950 ASN F 57 ASN ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.223841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.161037 restraints weight = 46860.860| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 5.21 r_work: 0.3315 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35268 Z= 0.188 Angle : 0.710 24.073 48081 Z= 0.358 Chirality : 0.051 0.988 5514 Planarity : 0.005 0.063 6135 Dihedral : 6.350 64.457 5424 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 3.19 % Allowed : 10.25 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.12), residues: 4296 helix: 1.38 (0.20), residues: 700 sheet: 0.89 (0.13), residues: 1361 loop : -1.38 (0.12), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 983 TYR 0.019 0.002 TYR B 170 PHE 0.025 0.002 PHE I 87 TRP 0.017 0.002 TRP B 436 HIS 0.008 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00439 (35184) covalent geometry : angle 0.67501 (47877) SS BOND : bond 0.00445 ( 48) SS BOND : angle 1.74083 ( 96) hydrogen bonds : bond 0.06940 ( 1343) hydrogen bonds : angle 5.75224 ( 3834) link_BETA1-4 : bond 0.00552 ( 12) link_BETA1-4 : angle 2.10477 ( 36) link_NAG-ASN : bond 0.00518 ( 24) link_NAG-ASN : angle 5.25592 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 207 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.6562 (m-80) cc_final: 0.5422 (m-80) REVERT: A 661 GLU cc_start: 0.8422 (tt0) cc_final: 0.8008 (pp20) REVERT: A 957 GLN cc_start: 0.7780 (tm-30) cc_final: 0.7385 (mt0) REVERT: A 1125 ASN cc_start: 0.8427 (m-40) cc_final: 0.7842 (p0) REVERT: B 54 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7854 (tt0) REVERT: B 274 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8407 (m) REVERT: B 994 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7097 (t0) REVERT: B 1034 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8317 (pp) REVERT: C 102 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.7185 (mm) REVERT: C 115 LYS cc_start: 0.7267 (mtpt) cc_final: 0.6987 (mtmm) REVERT: C 120 LEU cc_start: 0.8267 (tt) cc_final: 0.7904 (tm) REVERT: C 586 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8271 (m-30) REVERT: C 690 GLN cc_start: 0.7320 (mm-40) cc_final: 0.6732 (mt0) REVERT: C 780 GLU cc_start: 0.8284 (tt0) cc_final: 0.8080 (tt0) REVERT: C 786 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7978 (ptpt) REVERT: D 94 TYR cc_start: 0.2486 (m-80) cc_final: 0.2264 (m-80) REVERT: D 139 LYS cc_start: 0.0501 (mttt) cc_final: 0.0203 (mmmt) REVERT: D 148 LEU cc_start: -0.0503 (OUTLIER) cc_final: -0.0771 (pp) REVERT: D 153 LYS cc_start: 0.4729 (ptmt) cc_final: 0.4342 (pptt) REVERT: D 186 TYR cc_start: 0.4701 (OUTLIER) cc_final: 0.3849 (m-80) REVERT: D 188 LEU cc_start: 0.0965 (OUTLIER) cc_final: 0.0710 (tt) REVERT: E 58 LYS cc_start: 0.3233 (mmmt) cc_final: 0.2942 (mmmm) REVERT: E 169 LEU cc_start: -0.0539 (OUTLIER) cc_final: -0.0827 (tt) REVERT: E 219 LYS cc_start: -0.0622 (OUTLIER) cc_final: -0.0825 (tmmt) REVERT: F 169 LEU cc_start: 0.0786 (pt) cc_final: 0.0283 (mp) REVERT: H 11 MET cc_start: 0.2164 (ttp) cc_final: 0.1810 (ttm) REVERT: H 47 ILE cc_start: 0.5599 (OUTLIER) cc_final: 0.5294 (mp) REVERT: I 27 GLN cc_start: 0.3775 (mt0) cc_final: 0.3467 (mp10) outliers start: 121 outliers final: 52 residues processed: 291 average time/residue: 0.6024 time to fit residues: 215.4903 Evaluate side-chains 252 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 187 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 54 GLN Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 186 TYR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 191 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 133 optimal weight: 20.0000 chunk 343 optimal weight: 20.0000 chunk 255 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 413 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 chunk 381 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 306 optimal weight: 5.9990 chunk 270 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 690 GLN B 675 GLN C 950 ASN G 37 GLN H 49 GLN ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 155 GLN I 160 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.223659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.159477 restraints weight = 46473.275| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 5.25 r_work: 0.3318 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 35268 Z= 0.171 Angle : 0.675 20.665 48081 Z= 0.342 Chirality : 0.050 0.935 5514 Planarity : 0.005 0.052 6135 Dihedral : 6.391 93.797 5424 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.47 % Favored : 96.51 % Rotamer: Outliers : 3.14 % Allowed : 11.88 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.12), residues: 4296 helix: 1.39 (0.20), residues: 700 sheet: 0.79 (0.13), residues: 1370 loop : -1.42 (0.12), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 995 TYR 0.017 0.002 TYR C1067 PHE 0.020 0.002 PHE C 34 TRP 0.016 0.001 TRP B 436 HIS 0.005 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00400 (35184) covalent geometry : angle 0.64278 (47877) SS BOND : bond 0.00478 ( 48) SS BOND : angle 1.87781 ( 96) hydrogen bonds : bond 0.06571 ( 1343) hydrogen bonds : angle 5.61138 ( 3834) link_BETA1-4 : bond 0.00455 ( 12) link_BETA1-4 : angle 1.85000 ( 36) link_NAG-ASN : bond 0.00544 ( 24) link_NAG-ASN : angle 4.80412 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 198 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.6216 (OUTLIER) cc_final: 0.5959 (mt) REVERT: A 188 ASN cc_start: 0.6271 (OUTLIER) cc_final: 0.5958 (t0) REVERT: A 224 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7917 (mt-10) REVERT: A 393 THR cc_start: 0.6630 (t) cc_final: 0.6246 (p) REVERT: A 661 GLU cc_start: 0.8435 (tt0) cc_final: 0.8013 (pp20) REVERT: A 675 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.6223 (mp10) REVERT: A 957 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7396 (mt0) REVERT: A 1125 ASN cc_start: 0.8448 (m-40) cc_final: 0.7846 (p0) REVERT: B 43 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7624 (mttt) REVERT: B 54 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: B 127 ASN cc_start: 0.6294 (m110) cc_final: 0.5973 (m-40) REVERT: B 274 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8425 (m) REVERT: B 568 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.7004 (m-30) REVERT: B 994 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.7042 (t0) REVERT: B 1034 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8307 (pp) REVERT: C 102 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7220 (mm) REVERT: C 586 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8276 (m-30) REVERT: C 690 GLN cc_start: 0.7328 (mm-40) cc_final: 0.6688 (mt0) REVERT: C 702 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8252 (tp30) REVERT: C 983 ARG cc_start: 0.7327 (mtm110) cc_final: 0.7123 (mtp-110) REVERT: D 139 LYS cc_start: 0.0515 (mttt) cc_final: 0.0209 (mmmt) REVERT: D 148 LEU cc_start: -0.0469 (OUTLIER) cc_final: -0.0782 (pp) REVERT: D 153 LYS cc_start: 0.4765 (ptmt) cc_final: 0.4455 (ttmt) REVERT: D 186 TYR cc_start: 0.4659 (OUTLIER) cc_final: 0.3897 (m-80) REVERT: D 188 LEU cc_start: 0.0989 (OUTLIER) cc_final: 0.0729 (tt) REVERT: E 58 LYS cc_start: 0.3519 (mmmt) cc_final: 0.3295 (mmmm) REVERT: E 219 LYS cc_start: -0.0767 (OUTLIER) cc_final: -0.1060 (tmmm) REVERT: F 83 MET cc_start: 0.3540 (mtm) cc_final: 0.3337 (mtm) REVERT: F 110 MET cc_start: 0.3603 (OUTLIER) cc_final: 0.2680 (tpp) REVERT: F 169 LEU cc_start: 0.0822 (pt) cc_final: 0.0578 (tt) REVERT: G 4 MET cc_start: 0.3708 (OUTLIER) cc_final: 0.2591 (ttm) REVERT: H 11 MET cc_start: 0.2302 (ttp) cc_final: 0.1946 (ttm) REVERT: H 47 ILE cc_start: 0.5563 (pt) cc_final: 0.5245 (mp) REVERT: I 27 GLN cc_start: 0.3728 (mt0) cc_final: 0.3415 (mp10) outliers start: 119 outliers final: 55 residues processed: 287 average time/residue: 0.5262 time to fit residues: 189.1921 Evaluate side-chains 253 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 179 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 54 GLN Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 186 TYR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 191 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 412 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 chunk 305 optimal weight: 2.9990 chunk 415 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 404 optimal weight: 30.0000 chunk 58 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 296 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 690 GLN A1005 GLN B 675 GLN C 207 HIS C 950 ASN H 20 ASN ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.225257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.162640 restraints weight = 46165.036| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 5.57 r_work: 0.3291 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 35268 Z= 0.208 Angle : 0.732 21.609 48081 Z= 0.372 Chirality : 0.052 0.908 5514 Planarity : 0.005 0.058 6135 Dihedral : 6.775 112.185 5424 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.93 % Favored : 96.04 % Rotamer: Outliers : 3.72 % Allowed : 12.65 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.12), residues: 4296 helix: 1.25 (0.20), residues: 694 sheet: 0.66 (0.13), residues: 1369 loop : -1.49 (0.12), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 158 TYR 0.026 0.002 TYR F 155 PHE 0.031 0.002 PHE C 34 TRP 0.017 0.002 TRP B 436 HIS 0.007 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00496 (35184) covalent geometry : angle 0.69782 (47877) SS BOND : bond 0.00719 ( 48) SS BOND : angle 2.12240 ( 96) hydrogen bonds : bond 0.07360 ( 1343) hydrogen bonds : angle 5.73304 ( 3834) link_BETA1-4 : bond 0.00568 ( 12) link_BETA1-4 : angle 2.08176 ( 36) link_NAG-ASN : bond 0.00543 ( 24) link_NAG-ASN : angle 5.04316 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 206 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.6119 (OUTLIER) cc_final: 0.5869 (mt) REVERT: A 188 ASN cc_start: 0.6226 (OUTLIER) cc_final: 0.5921 (t0) REVERT: A 224 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: A 498 ARG cc_start: 0.4964 (OUTLIER) cc_final: 0.4634 (tpp80) REVERT: A 661 GLU cc_start: 0.8429 (tt0) cc_final: 0.7981 (pp20) REVERT: A 675 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.6331 (mp10) REVERT: A 957 GLN cc_start: 0.7778 (tm-30) cc_final: 0.7387 (mt0) REVERT: B 25 THR cc_start: 0.6564 (OUTLIER) cc_final: 0.6204 (t) REVERT: B 43 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7648 (mttt) REVERT: B 54 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: B 127 ASN cc_start: 0.6304 (m110) cc_final: 0.5971 (m-40) REVERT: B 155 SER cc_start: 0.7047 (m) cc_final: 0.6810 (t) REVERT: B 274 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8446 (m) REVERT: B 994 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7089 (t0) REVERT: B 1034 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8373 (pp) REVERT: C 102 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7275 (mm) REVERT: C 115 LYS cc_start: 0.7228 (mtpt) cc_final: 0.6941 (mtmm) REVERT: C 586 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8306 (m-30) REVERT: C 675 GLN cc_start: 0.6620 (mm110) cc_final: 0.6393 (pp30) REVERT: C 690 GLN cc_start: 0.7470 (mm-40) cc_final: 0.6693 (mt0) REVERT: C 702 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8214 (tp30) REVERT: C 754 LEU cc_start: 0.8065 (tm) cc_final: 0.7716 (mt) REVERT: C 786 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8003 (ptpt) REVERT: D 139 LYS cc_start: 0.0430 (mttt) cc_final: 0.0136 (mmmt) REVERT: D 148 LEU cc_start: -0.0616 (OUTLIER) cc_final: -0.0892 (pp) REVERT: D 153 LYS cc_start: 0.4663 (ptmt) cc_final: 0.4296 (ttmt) REVERT: D 186 TYR cc_start: 0.4557 (OUTLIER) cc_final: 0.3762 (m-80) REVERT: D 188 LEU cc_start: 0.0832 (OUTLIER) cc_final: 0.0588 (tt) REVERT: E 58 LYS cc_start: 0.3445 (OUTLIER) cc_final: 0.3224 (mmmm) REVERT: E 219 LYS cc_start: -0.0922 (OUTLIER) cc_final: -0.1211 (tmmm) REVERT: F 59 TYR cc_start: 0.3472 (m-80) cc_final: 0.3222 (t80) REVERT: G 4 MET cc_start: 0.3543 (OUTLIER) cc_final: 0.2390 (ttm) REVERT: G 183 LYS cc_start: 0.2652 (ptmt) cc_final: 0.2346 (mmmm) REVERT: H 11 MET cc_start: 0.2358 (ttp) cc_final: 0.2022 (ttm) REVERT: H 47 ILE cc_start: 0.5588 (pt) cc_final: 0.5093 (mp) REVERT: H 106 ILE cc_start: 0.0491 (mm) cc_final: 0.0142 (tp) REVERT: I 27 GLN cc_start: 0.3803 (mt0) cc_final: 0.3594 (mp10) REVERT: I 89 LEU cc_start: 0.3154 (OUTLIER) cc_final: 0.2425 (tt) outliers start: 141 outliers final: 76 residues processed: 317 average time/residue: 0.5298 time to fit residues: 210.2826 Evaluate side-chains 287 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 189 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 54 GLN Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 186 TYR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain I residue 196 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 3.9990 chunk 229 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 340 optimal weight: 20.0000 chunk 251 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 chunk 243 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 59 optimal weight: 0.0470 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN B 675 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 ASN I 147 GLN ** I 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.228318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.162421 restraints weight = 46562.463| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 4.60 r_work: 0.3402 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 35268 Z= 0.111 Angle : 0.590 17.451 48081 Z= 0.296 Chirality : 0.046 0.781 5514 Planarity : 0.004 0.051 6135 Dihedral : 6.220 117.585 5424 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.84 % Favored : 97.14 % Rotamer: Outliers : 2.21 % Allowed : 14.68 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.13), residues: 4296 helix: 1.63 (0.20), residues: 699 sheet: 0.88 (0.13), residues: 1374 loop : -1.30 (0.13), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 983 TYR 0.027 0.001 TYR F 53 PHE 0.028 0.001 PHE A 135 TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00241 (35184) covalent geometry : angle 0.56208 (47877) SS BOND : bond 0.00409 ( 48) SS BOND : angle 1.50608 ( 96) hydrogen bonds : bond 0.04676 ( 1343) hydrogen bonds : angle 5.29088 ( 3834) link_BETA1-4 : bond 0.00431 ( 12) link_BETA1-4 : angle 1.69920 ( 36) link_NAG-ASN : bond 0.00670 ( 24) link_NAG-ASN : angle 4.23140 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 210 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8327 (pm20) cc_final: 0.8091 (mt-10) REVERT: A 393 THR cc_start: 0.6841 (t) cc_final: 0.6509 (p) REVERT: A 661 GLU cc_start: 0.8250 (tt0) cc_final: 0.7879 (pp20) REVERT: A 675 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6134 (mp10) REVERT: A 957 GLN cc_start: 0.7696 (tm-30) cc_final: 0.7323 (mt0) REVERT: A 963 VAL cc_start: 0.7817 (t) cc_final: 0.7470 (p) REVERT: B 54 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7839 (tt0) REVERT: B 127 ASN cc_start: 0.6351 (m110) cc_final: 0.6021 (m-40) REVERT: B 155 SER cc_start: 0.7059 (m) cc_final: 0.6826 (t) REVERT: B 274 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8457 (m) REVERT: B 513 LEU cc_start: 0.6406 (mt) cc_final: 0.6066 (mp) REVERT: C 102 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.7236 (mm) REVERT: C 115 LYS cc_start: 0.7218 (mtpt) cc_final: 0.6898 (mtmt) REVERT: C 120 LEU cc_start: 0.8274 (tt) cc_final: 0.7877 (tm) REVERT: C 586 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8146 (m-30) REVERT: C 690 GLN cc_start: 0.7365 (mm-40) cc_final: 0.6592 (mt0) REVERT: C 702 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8099 (tp30) REVERT: C 754 LEU cc_start: 0.8066 (tm) cc_final: 0.7732 (mt) REVERT: C 786 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7916 (ptpt) REVERT: D 139 LYS cc_start: 0.0546 (mttt) cc_final: 0.0250 (mmmt) REVERT: D 153 LYS cc_start: 0.4715 (ptmt) cc_final: 0.4438 (ttmt) REVERT: D 186 TYR cc_start: 0.4651 (OUTLIER) cc_final: 0.4048 (m-80) REVERT: D 188 LEU cc_start: 0.1027 (OUTLIER) cc_final: 0.0760 (tt) REVERT: E 58 LYS cc_start: 0.3707 (mmmt) cc_final: 0.3438 (mmmm) REVERT: E 219 LYS cc_start: -0.0751 (OUTLIER) cc_final: -0.1012 (tmmm) REVERT: F 59 TYR cc_start: 0.3516 (m-80) cc_final: 0.3285 (t80) REVERT: F 110 MET cc_start: 0.3476 (mtt) cc_final: 0.2629 (tpp) REVERT: F 150 CYS cc_start: 0.0098 (OUTLIER) cc_final: -0.1000 (t) REVERT: G 183 LYS cc_start: 0.2615 (ptmt) cc_final: 0.2399 (mmmm) REVERT: H 11 MET cc_start: 0.2290 (ttp) cc_final: 0.2021 (ttm) REVERT: H 47 ILE cc_start: 0.5500 (pt) cc_final: 0.5213 (mp) REVERT: H 176 SER cc_start: 0.1028 (p) cc_final: 0.0750 (m) REVERT: I 27 GLN cc_start: 0.3782 (mt0) cc_final: 0.3467 (mp10) REVERT: I 89 LEU cc_start: 0.3094 (OUTLIER) cc_final: 0.2484 (tt) outliers start: 84 outliers final: 32 residues processed: 277 average time/residue: 0.5824 time to fit residues: 199.1195 Evaluate side-chains 232 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 54 GLN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 186 TYR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 150 CYS Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 172 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 12 optimal weight: 10.0000 chunk 424 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 400 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 416 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 405 optimal weight: 40.0000 chunk 53 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN A1005 GLN B 556 ASN B 675 GLN C 950 ASN ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.224465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.161628 restraints weight = 45808.645| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 5.24 r_work: 0.3266 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 35268 Z= 0.259 Angle : 0.790 22.622 48081 Z= 0.403 Chirality : 0.055 0.887 5514 Planarity : 0.005 0.066 6135 Dihedral : 6.929 114.189 5424 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.52 % Favored : 95.46 % Rotamer: Outliers : 3.11 % Allowed : 14.62 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.12), residues: 4296 helix: 1.10 (0.20), residues: 695 sheet: 0.66 (0.14), residues: 1317 loop : -1.49 (0.12), residues: 2284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 983 TYR 0.030 0.002 TYR E 155 PHE 0.029 0.003 PHE C 34 TRP 0.018 0.002 TRP B 436 HIS 0.008 0.002 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00628 (35184) covalent geometry : angle 0.75288 (47877) SS BOND : bond 0.00680 ( 48) SS BOND : angle 2.53586 ( 96) hydrogen bonds : bond 0.08253 ( 1343) hydrogen bonds : angle 5.81802 ( 3834) link_BETA1-4 : bond 0.00656 ( 12) link_BETA1-4 : angle 2.27495 ( 36) link_NAG-ASN : bond 0.00625 ( 24) link_NAG-ASN : angle 5.35856 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 199 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.6138 (OUTLIER) cc_final: 0.5891 (mt) REVERT: A 239 GLN cc_start: 0.7856 (tt0) cc_final: 0.7061 (tm-30) REVERT: A 661 GLU cc_start: 0.8437 (tt0) cc_final: 0.7986 (pp20) REVERT: A 675 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.6326 (mp10) REVERT: A 957 GLN cc_start: 0.7777 (tm-30) cc_final: 0.7372 (mt0) REVERT: B 54 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7968 (tt0) REVERT: B 127 ASN cc_start: 0.6319 (m110) cc_final: 0.5991 (m-40) REVERT: B 131 LYS cc_start: 0.7575 (mtpt) cc_final: 0.7248 (mtmm) REVERT: B 752 LEU cc_start: 0.7544 (mt) cc_final: 0.7280 (mt) REVERT: B 776 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8806 (ttmt) REVERT: B 983 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6959 (mmm-85) REVERT: B 994 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7079 (t0) REVERT: B 1034 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8435 (pp) REVERT: C 102 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7292 (mm) REVERT: C 115 LYS cc_start: 0.7151 (mtpt) cc_final: 0.6876 (mtmt) REVERT: C 586 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8311 (m-30) REVERT: C 675 GLN cc_start: 0.6693 (mm110) cc_final: 0.6473 (pp30) REVERT: C 690 GLN cc_start: 0.7574 (mm-40) cc_final: 0.6782 (mt0) REVERT: C 702 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8238 (tp30) REVERT: C 754 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7750 (mt) REVERT: C 786 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7986 (ptpt) REVERT: D 139 LYS cc_start: 0.0490 (mttt) cc_final: 0.0165 (mmmt) REVERT: D 153 LYS cc_start: 0.4702 (ptmt) cc_final: 0.4317 (ttmt) REVERT: D 186 TYR cc_start: 0.4628 (OUTLIER) cc_final: 0.3981 (m-80) REVERT: D 188 LEU cc_start: 0.0989 (OUTLIER) cc_final: 0.0749 (tt) REVERT: E 58 LYS cc_start: 0.3445 (OUTLIER) cc_final: 0.3165 (mmmm) REVERT: F 59 TYR cc_start: 0.3381 (m-80) cc_final: 0.3128 (t80) REVERT: F 110 MET cc_start: 0.3443 (mtt) cc_final: 0.2466 (tpp) REVERT: F 150 CYS cc_start: 0.0235 (OUTLIER) cc_final: -0.0993 (t) REVERT: G 183 LYS cc_start: 0.2625 (ptmt) cc_final: 0.2399 (mmmm) REVERT: H 11 MET cc_start: 0.2342 (ttp) cc_final: 0.2047 (ttm) REVERT: H 47 ILE cc_start: 0.5549 (pt) cc_final: 0.5197 (mp) REVERT: H 106 ILE cc_start: 0.0531 (mm) cc_final: 0.0181 (tp) REVERT: I 27 GLN cc_start: 0.3811 (mt0) cc_final: 0.3554 (mp10) REVERT: I 89 LEU cc_start: 0.3135 (OUTLIER) cc_final: 0.2440 (tt) outliers start: 118 outliers final: 70 residues processed: 292 average time/residue: 0.5655 time to fit residues: 205.3565 Evaluate side-chains 273 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 186 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 54 GLN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 186 TYR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 150 CYS Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 178 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 212 optimal weight: 1.9990 chunk 273 optimal weight: 2.9990 chunk 353 optimal weight: 30.0000 chunk 65 optimal weight: 1.9990 chunk 143 optimal weight: 0.1980 chunk 98 optimal weight: 2.9990 chunk 395 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 430 optimal weight: 30.0000 chunk 417 optimal weight: 40.0000 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 556 ASN B 675 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 ASN ** I 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.226036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.163258 restraints weight = 46045.442| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 4.71 r_work: 0.3302 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 35268 Z= 0.153 Angle : 0.667 19.521 48081 Z= 0.337 Chirality : 0.049 0.879 5514 Planarity : 0.005 0.056 6135 Dihedral : 6.571 115.812 5424 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.14 % Favored : 96.83 % Rotamer: Outliers : 2.58 % Allowed : 15.60 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.13), residues: 4296 helix: 1.32 (0.20), residues: 703 sheet: 0.67 (0.13), residues: 1371 loop : -1.43 (0.12), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 983 TYR 0.027 0.001 TYR E 155 PHE 0.033 0.002 PHE A 135 TRP 0.011 0.001 TRP C 436 HIS 0.004 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00354 (35184) covalent geometry : angle 0.63175 (47877) SS BOND : bond 0.00576 ( 48) SS BOND : angle 2.17779 ( 96) hydrogen bonds : bond 0.06214 ( 1343) hydrogen bonds : angle 5.54027 ( 3834) link_BETA1-4 : bond 0.00533 ( 12) link_BETA1-4 : angle 1.87611 ( 36) link_NAG-ASN : bond 0.00568 ( 24) link_NAG-ASN : angle 4.82700 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 192 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 GLU cc_start: 0.7365 (tp30) cc_final: 0.7163 (tp30) REVERT: A 661 GLU cc_start: 0.8386 (tt0) cc_final: 0.7925 (pp20) REVERT: A 675 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.6192 (mp10) REVERT: A 957 GLN cc_start: 0.7716 (tm-30) cc_final: 0.7296 (mt0) REVERT: A 963 VAL cc_start: 0.8248 (t) cc_final: 0.7896 (p) REVERT: B 54 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: B 127 ASN cc_start: 0.6361 (m110) cc_final: 0.6010 (m-40) REVERT: B 274 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8441 (m) REVERT: B 776 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8648 (ttmt) REVERT: B 1034 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8430 (pp) REVERT: C 102 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.7264 (mm) REVERT: C 115 LYS cc_start: 0.7135 (mtpt) cc_final: 0.6864 (mtmt) REVERT: C 120 LEU cc_start: 0.8408 (tt) cc_final: 0.7996 (tm) REVERT: C 586 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8254 (m-30) REVERT: C 675 GLN cc_start: 0.6593 (mm110) cc_final: 0.6349 (pp30) REVERT: C 690 GLN cc_start: 0.7471 (mm-40) cc_final: 0.6686 (mt0) REVERT: C 702 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8163 (tp30) REVERT: C 754 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7771 (mt) REVERT: C 786 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7964 (ptpt) REVERT: D 139 LYS cc_start: 0.0471 (mttt) cc_final: 0.0163 (mmmt) REVERT: D 153 LYS cc_start: 0.4580 (ptmt) cc_final: 0.4262 (ttmt) REVERT: D 188 LEU cc_start: 0.1011 (OUTLIER) cc_final: 0.0776 (tt) REVERT: E 58 LYS cc_start: 0.3531 (OUTLIER) cc_final: 0.3254 (mmmm) REVERT: F 110 MET cc_start: 0.3572 (mtt) cc_final: 0.2609 (tpp) REVERT: F 150 CYS cc_start: 0.0274 (OUTLIER) cc_final: -0.0973 (t) REVERT: G 183 LYS cc_start: 0.2630 (ptmt) cc_final: 0.2419 (mmmt) REVERT: H 11 MET cc_start: 0.2268 (ttp) cc_final: 0.2021 (ttm) REVERT: H 47 ILE cc_start: 0.5599 (pt) cc_final: 0.5259 (mp) REVERT: I 27 GLN cc_start: 0.3815 (mt0) cc_final: 0.3591 (mp10) REVERT: I 89 LEU cc_start: 0.3106 (OUTLIER) cc_final: 0.2436 (tt) outliers start: 98 outliers final: 59 residues processed: 268 average time/residue: 0.5736 time to fit residues: 191.0095 Evaluate side-chains 261 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 188 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 54 GLN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 150 CYS Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 178 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 190 optimal weight: 0.8980 chunk 251 optimal weight: 0.9980 chunk 327 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 291 optimal weight: 0.9990 chunk 330 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 337 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 556 ASN B 675 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 ASN ** I 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.227103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.162868 restraints weight = 46010.032| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 4.88 r_work: 0.3323 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 35268 Z= 0.149 Angle : 0.656 18.576 48081 Z= 0.330 Chirality : 0.049 0.846 5514 Planarity : 0.004 0.051 6135 Dihedral : 6.443 115.840 5424 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.68 % Favored : 96.30 % Rotamer: Outliers : 2.56 % Allowed : 15.63 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.13), residues: 4296 helix: 1.46 (0.20), residues: 699 sheet: 0.69 (0.13), residues: 1373 loop : -1.41 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 983 TYR 0.026 0.002 TYR E 155 PHE 0.030 0.002 PHE A 135 TRP 0.015 0.001 TRP F 47 HIS 0.004 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00343 (35184) covalent geometry : angle 0.62442 (47877) SS BOND : bond 0.00553 ( 48) SS BOND : angle 1.87898 ( 96) hydrogen bonds : bond 0.06049 ( 1343) hydrogen bonds : angle 5.47512 ( 3834) link_BETA1-4 : bond 0.00488 ( 12) link_BETA1-4 : angle 1.85292 ( 36) link_NAG-ASN : bond 0.00564 ( 24) link_NAG-ASN : angle 4.62109 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 201 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 VAL cc_start: 0.6529 (OUTLIER) cc_final: 0.6200 (m) REVERT: A 583 GLU cc_start: 0.7315 (tp30) cc_final: 0.7103 (tp30) REVERT: A 661 GLU cc_start: 0.8296 (tt0) cc_final: 0.7862 (pp20) REVERT: A 675 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6190 (mp10) REVERT: A 957 GLN cc_start: 0.7691 (tm-30) cc_final: 0.7317 (mt0) REVERT: A 963 VAL cc_start: 0.8175 (t) cc_final: 0.7791 (p) REVERT: A 980 ILE cc_start: 0.6866 (OUTLIER) cc_final: 0.6649 (mt) REVERT: B 54 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: B 127 ASN cc_start: 0.6326 (m110) cc_final: 0.5974 (m-40) REVERT: B 274 THR cc_start: 0.8806 (OUTLIER) cc_final: 0.8434 (m) REVERT: B 752 LEU cc_start: 0.7491 (mt) cc_final: 0.7281 (mt) REVERT: B 1034 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8491 (pp) REVERT: C 102 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7294 (mm) REVERT: C 115 LYS cc_start: 0.7087 (mtpt) cc_final: 0.6808 (mtmt) REVERT: C 120 LEU cc_start: 0.8367 (tt) cc_final: 0.7966 (tm) REVERT: C 586 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8217 (m-30) REVERT: C 675 GLN cc_start: 0.6585 (mm110) cc_final: 0.6281 (pp30) REVERT: C 690 GLN cc_start: 0.7454 (mm-40) cc_final: 0.6674 (mt0) REVERT: C 702 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8139 (tp30) REVERT: C 754 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7789 (mt) REVERT: C 786 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7948 (ptpt) REVERT: D 139 LYS cc_start: 0.0452 (mttt) cc_final: 0.0141 (mmmt) REVERT: D 153 LYS cc_start: 0.4612 (ptmt) cc_final: 0.4248 (ttmt) REVERT: D 188 LEU cc_start: 0.1062 (OUTLIER) cc_final: 0.0834 (tt) REVERT: E 58 LYS cc_start: 0.3491 (OUTLIER) cc_final: 0.3187 (mmmm) REVERT: F 110 MET cc_start: 0.3582 (mtt) cc_final: 0.2580 (tpp) REVERT: F 150 CYS cc_start: 0.0240 (OUTLIER) cc_final: -0.0886 (t) REVERT: G 183 LYS cc_start: 0.2501 (ptmt) cc_final: 0.2270 (mmmt) REVERT: H 11 MET cc_start: 0.2403 (ttp) cc_final: 0.2108 (ttm) REVERT: H 47 ILE cc_start: 0.5634 (pt) cc_final: 0.5296 (mp) REVERT: I 27 GLN cc_start: 0.3887 (mt0) cc_final: 0.3671 (mp10) REVERT: I 89 LEU cc_start: 0.3054 (OUTLIER) cc_final: 0.2413 (tt) outliers start: 97 outliers final: 62 residues processed: 275 average time/residue: 0.5697 time to fit residues: 195.1375 Evaluate side-chains 267 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 190 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 54 GLN Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 150 CYS Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 178 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 405 optimal weight: 4.9990 chunk 276 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 167 optimal weight: 0.7980 chunk 236 optimal weight: 1.9990 chunk 398 optimal weight: 6.9990 chunk 415 optimal weight: 30.0000 chunk 427 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN B 556 ASN B 675 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 ASN ** I 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.226987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.163436 restraints weight = 46050.928| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 4.99 r_work: 0.3311 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 35268 Z= 0.153 Angle : 0.665 21.786 48081 Z= 0.334 Chirality : 0.050 0.967 5514 Planarity : 0.004 0.051 6135 Dihedral : 6.447 115.593 5424 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.49 % Favored : 96.49 % Rotamer: Outliers : 2.37 % Allowed : 15.94 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.13), residues: 4296 helix: 1.45 (0.20), residues: 699 sheet: 0.69 (0.13), residues: 1377 loop : -1.39 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 983 TYR 0.027 0.001 TYR E 155 PHE 0.032 0.002 PHE A 135 TRP 0.014 0.001 TRP F 47 HIS 0.004 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00355 (35184) covalent geometry : angle 0.63046 (47877) SS BOND : bond 0.00541 ( 48) SS BOND : angle 1.83187 ( 96) hydrogen bonds : bond 0.06120 ( 1343) hydrogen bonds : angle 5.46449 ( 3834) link_BETA1-4 : bond 0.00518 ( 12) link_BETA1-4 : angle 1.92603 ( 36) link_NAG-ASN : bond 0.00540 ( 24) link_NAG-ASN : angle 4.95289 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 209 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.6120 (OUTLIER) cc_final: 0.5800 (mt) REVERT: A 128 VAL cc_start: 0.6538 (OUTLIER) cc_final: 0.6219 (m) REVERT: A 583 GLU cc_start: 0.7358 (tp30) cc_final: 0.7132 (tp30) REVERT: A 661 GLU cc_start: 0.8366 (tt0) cc_final: 0.7900 (pp20) REVERT: A 675 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.6281 (mp10) REVERT: A 963 VAL cc_start: 0.8197 (t) cc_final: 0.7811 (p) REVERT: A 980 ILE cc_start: 0.6916 (OUTLIER) cc_final: 0.6683 (mt) REVERT: B 54 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: B 127 ASN cc_start: 0.6335 (m110) cc_final: 0.5984 (m-40) REVERT: B 274 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8437 (m) REVERT: C 102 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7305 (mm) REVERT: C 115 LYS cc_start: 0.7104 (mtpt) cc_final: 0.6850 (mtmt) REVERT: C 120 LEU cc_start: 0.8408 (tt) cc_final: 0.8003 (tm) REVERT: C 586 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8251 (m-30) REVERT: C 675 GLN cc_start: 0.6591 (mm110) cc_final: 0.6288 (pp30) REVERT: C 690 GLN cc_start: 0.7440 (mm-40) cc_final: 0.6659 (mt0) REVERT: C 702 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8170 (tp30) REVERT: C 754 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7811 (mt) REVERT: C 786 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8001 (ptpt) REVERT: D 139 LYS cc_start: 0.0454 (mttt) cc_final: 0.0147 (mmmt) REVERT: D 153 LYS cc_start: 0.4590 (ptmt) cc_final: 0.4241 (ttmt) REVERT: D 186 TYR cc_start: 0.4632 (m-80) cc_final: 0.4056 (m-80) REVERT: D 188 LEU cc_start: 0.1104 (OUTLIER) cc_final: 0.0879 (tt) REVERT: E 34 MET cc_start: 0.4851 (ptp) cc_final: 0.4405 (mmp) REVERT: E 58 LYS cc_start: 0.3462 (OUTLIER) cc_final: 0.3209 (mmmm) REVERT: F 110 MET cc_start: 0.3605 (mtt) cc_final: 0.2602 (tpp) REVERT: F 150 CYS cc_start: 0.0224 (OUTLIER) cc_final: -0.0968 (t) REVERT: G 183 LYS cc_start: 0.2443 (ptmt) cc_final: 0.2228 (mmmt) REVERT: H 11 MET cc_start: 0.2393 (ttp) cc_final: 0.2110 (ttm) REVERT: H 47 ILE cc_start: 0.5632 (pt) cc_final: 0.5352 (mp) REVERT: I 27 GLN cc_start: 0.3893 (mt0) cc_final: 0.3678 (mp10) REVERT: I 89 LEU cc_start: 0.3081 (OUTLIER) cc_final: 0.2448 (tt) outliers start: 90 outliers final: 65 residues processed: 281 average time/residue: 0.5359 time to fit residues: 189.0211 Evaluate side-chains 271 residues out of total 3795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 191 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 54 GLN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 150 CYS Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 178 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 209 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 259 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 176 optimal weight: 0.6980 chunk 207 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 45 optimal weight: 0.0570 overall best weight: 1.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 487 ASN B 556 ASN B 675 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 ASN ** I 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.228069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.161924 restraints weight = 46239.198| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 5.13 r_work: 0.3346 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35268 Z= 0.126 Angle : 0.626 19.846 48081 Z= 0.313 Chirality : 0.049 1.057 5514 Planarity : 0.004 0.052 6135 Dihedral : 6.249 116.025 5424 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.28 % Favored : 96.69 % Rotamer: Outliers : 2.29 % Allowed : 16.26 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.13), residues: 4296 helix: 1.58 (0.20), residues: 700 sheet: 0.75 (0.13), residues: 1380 loop : -1.31 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 983 TYR 0.029 0.001 TYR E 155 PHE 0.030 0.001 PHE A 135 TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00280 (35184) covalent geometry : angle 0.59398 (47877) SS BOND : bond 0.00508 ( 48) SS BOND : angle 1.59736 ( 96) hydrogen bonds : bond 0.05338 ( 1343) hydrogen bonds : angle 5.33353 ( 3834) link_BETA1-4 : bond 0.00491 ( 12) link_BETA1-4 : angle 1.83479 ( 36) link_NAG-ASN : bond 0.00617 ( 24) link_NAG-ASN : angle 4.70093 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26942.64 seconds wall clock time: 455 minutes 0.58 seconds (27300.58 seconds total)