Starting phenix.real_space_refine on Sun Jun 22 13:47:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8whv_37549/06_2025/8whv_37549.cif Found real_map, /net/cci-nas-00/data/ceres_data/8whv_37549/06_2025/8whv_37549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8whv_37549/06_2025/8whv_37549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8whv_37549/06_2025/8whv_37549.map" model { file = "/net/cci-nas-00/data/ceres_data/8whv_37549/06_2025/8whv_37549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8whv_37549/06_2025/8whv_37549.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.079 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 114 5.16 5 C 16458 2.51 5 N 4197 2.21 5 O 5049 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25818 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 16.36, per 1000 atoms: 0.63 Number of scatterers: 25818 At special positions: 0 Unit cell: (144, 144, 170, 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 114 16.00 O 5049 8.00 N 4197 7.00 C 16458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " 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 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " 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 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " BMA D 2 " " NAG E 1 " - " BMA E 2 " " NAG F 1 " - " BMA F 2 " " NAG G 1 " - " BMA G 2 " " NAG H 1 " - " BMA H 2 " " NAG I 1 " - " BMA I 2 " " NAG J 1 " - " BMA J 2 " " NAG K 1 " - " BMA K 2 " " NAG L 1 " - " BMA L 2 " " NAG M 1 " - " BMA M 2 " " NAG N 1 " - " BMA N 2 " " NAG O 1 " - " BMA O 2 " " NAG P 1 " - " BMA P 2 " " NAG Q 1 " - " BMA Q 2 " " NAG R 1 " - " BMA R 2 " " NAG S 1 " - " BMA S 2 " " NAG T 1 " - " BMA T 2 " " NAG U 1 " - " BMA U 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 61 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 234 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 234 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG D 1 " - " ASN A 354 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN B 354 " " NAG K 1 " - " ASN B 282 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN C 354 " " NAG Q 1 " - " ASN C 282 " " NAG R 1 " - " ASN C1134 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C1098 " Time building additional restraints: 7.20 Conformation dependent library (CDL) restraints added in 3.5 seconds 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5958 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 52 sheets defined 24.5% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.34 Creating SS restraints... Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.543A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.759A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.883A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.603A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 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 758 through 783 removed outlier: 4.044A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.704A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.575A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 884 removed outlier: 3.581A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.746A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 Processing helix chain 'A' and resid 965 through 968 removed outlier: 3.674A pdb=" N SER A 968 " --> pdb=" O GLN A 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 965 through 968' Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.670A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.038A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 301 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.578A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.931A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.519A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 616 through 626 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.973A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.791A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 869 through 882 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.707A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 937 " --> pdb=" O LYS B 933 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 Processing helix chain 'B' and resid 965 through 968 removed outlier: 3.773A pdb=" N SER B 968 " --> pdb=" O GLN B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 965 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.597A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.149A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 300 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.814A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.695A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.850A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.581A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 616 through 626 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.871A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.783A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE C 823 " --> pdb=" O GLU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 868 through 884 removed outlier: 3.615A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.758A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER C 937 " --> pdb=" O LYS C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 964 Processing helix chain 'C' and resid 965 through 967 No H-bonds generated for 'chain 'C' and resid 965 through 967' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.544A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.026A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.056A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR A 95 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.710A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.903A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 7.058A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.979A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.720A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.019A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 575 through 577 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.114A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 713 through 715 removed outlier: 3.780A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.206A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.249A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.053A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASP B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR B 95 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC2, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.594A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.912A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.506A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR B 167 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.102A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 326 removed outlier: 6.934A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.716A 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 removed outlier: 3.820A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.038A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 713 through 715 removed outlier: 3.794A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.270A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.248A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'C' and resid 26 through 30 removed outlier: 3.523A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N THR C 95 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.635A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.072A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 116 through 118 removed outlier: 3.583A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.094A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 326 removed outlier: 6.941A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.578A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA C 435 " --> pdb=" O PHE C 375 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.706A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.722A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.099A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 713 through 715 removed outlier: 3.723A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.266A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.196A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'C' and resid 1094 through 1097 848 hydrogen bonds defined for protein. 2280 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.67 Time building geometry restraints manager: 8.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4166 1.32 - 1.44: 7487 1.44 - 1.57: 14624 1.57 - 1.69: 0 1.69 - 1.82: 141 Bond restraints: 26418 Sorted by residual: bond pdb=" CA THR C 208 " pdb=" C THR C 208 " ideal model delta sigma weight residual 1.523 1.469 0.054 1.00e-02 1.00e+04 2.96e+01 bond pdb=" CA THR B 208 " pdb=" C THR B 208 " ideal model delta sigma weight residual 1.520 1.463 0.057 1.18e-02 7.18e+03 2.33e+01 bond pdb=" CA SER B 305 " pdb=" CB SER B 305 " ideal model delta sigma weight residual 1.533 1.459 0.074 1.66e-02 3.63e+03 2.00e+01 bond pdb=" N GLN C 506 " pdb=" CA GLN C 506 " ideal model delta sigma weight residual 1.453 1.490 -0.037 8.30e-03 1.45e+04 1.95e+01 bond pdb=" CA SER C 305 " pdb=" CB SER C 305 " ideal model delta sigma weight residual 1.533 1.461 0.072 1.65e-02 3.67e+03 1.89e+01 ... (remaining 26413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 35149 2.72 - 5.44: 709 5.44 - 8.17: 86 8.17 - 10.89: 7 10.89 - 13.61: 4 Bond angle restraints: 35955 Sorted by residual: angle pdb=" N THR C 302 " pdb=" CA THR C 302 " pdb=" C THR C 302 " ideal model delta sigma weight residual 113.55 102.10 11.45 1.26e+00 6.30e-01 8.25e+01 angle pdb=" N THR B 302 " pdb=" CA THR B 302 " pdb=" C THR B 302 " ideal model delta sigma weight residual 114.04 102.96 11.08 1.24e+00 6.50e-01 7.99e+01 angle pdb=" N THR A 302 " pdb=" CA THR A 302 " pdb=" C THR A 302 " ideal model delta sigma weight residual 114.04 103.44 10.60 1.24e+00 6.50e-01 7.31e+01 angle pdb=" N GLY C 213 " pdb=" CA GLY C 213 " pdb=" C GLY C 213 " ideal model delta sigma weight residual 115.32 105.78 9.54 1.31e+00 5.83e-01 5.30e+01 angle pdb=" N LEU B 303 " pdb=" CA LEU B 303 " pdb=" C LEU B 303 " ideal model delta sigma weight residual 112.93 104.80 8.13 1.12e+00 7.97e-01 5.27e+01 ... (remaining 35950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.54: 15049 24.54 - 49.09: 1146 49.09 - 73.63: 132 73.63 - 98.18: 120 98.18 - 122.72: 110 Dihedral angle restraints: 16557 sinusoidal: 7281 harmonic: 9276 Sorted by residual: dihedral pdb=" CA ILE C 210 " pdb=" C ILE C 210 " pdb=" N ILE C 212 " pdb=" CA ILE C 212 " ideal model delta harmonic sigma weight residual 180.00 57.28 122.72 0 5.00e+00 4.00e-02 6.02e+02 dihedral pdb=" CA ILE B 210 " pdb=" C ILE B 210 " pdb=" N ILE B 212 " pdb=" CA ILE B 212 " ideal model delta harmonic sigma weight residual 180.00 75.51 104.49 0 5.00e+00 4.00e-02 4.37e+02 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 41.22 51.78 1 1.00e+01 1.00e-02 3.66e+01 ... (remaining 16554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.195: 4214 0.195 - 0.390: 37 0.390 - 0.586: 0 0.586 - 0.781: 0 0.781 - 0.976: 3 Chirality restraints: 4254 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-01 2.50e+01 2.38e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.43 -0.97 2.00e-01 2.50e+01 2.37e+01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.27e+01 ... (remaining 4251 not shown) Planarity restraints: 4605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 34 " -0.534 9.50e-02 1.11e+02 2.39e-01 3.50e+01 pdb=" NE ARG B 34 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG B 34 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 34 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 34 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 34 " 0.500 9.50e-02 1.11e+02 2.24e-01 3.07e+01 pdb=" NE ARG A 34 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 34 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 34 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 34 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 509 " -0.418 9.50e-02 1.11e+02 1.87e-01 2.14e+01 pdb=" NE ARG B 509 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG B 509 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 509 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 509 " -0.014 2.00e-02 2.50e+03 ... (remaining 4602 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 308 2.56 - 3.15: 21048 3.15 - 3.73: 39185 3.73 - 4.32: 55959 4.32 - 4.90: 93131 Nonbonded interactions: 209631 Sorted by model distance: nonbonded pdb=" CD1 ILE B 210 " pdb=" CA GLY B 213 " model vdw 1.979 3.860 nonbonded pdb=" OH TYR B 837 " pdb=" O CYS C 590 " model vdw 2.086 3.040 nonbonded pdb=" CD1 ILE B 210 " pdb=" O ILE B 212 " model vdw 2.097 3.460 nonbonded pdb=" O CYS A 590 " pdb=" OH TYR C 837 " model vdw 2.105 3.040 nonbonded pdb=" OH TYR A 837 " pdb=" O CYS B 590 " model vdw 2.121 3.040 ... (remaining 209626 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: 0.08 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' 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: 2.140 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: 0.020 Extract box with map and model: 1.070 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 63.070 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.140 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 : 0.005 0.076 26523 Z= 0.290 Angle : 0.960 15.001 36231 Z= 0.540 Chirality : 0.060 0.976 4254 Planarity : 0.008 0.239 4557 Dihedral : 20.849 122.721 10482 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.14 % Favored : 91.71 % Rotamer: Outliers : 1.19 % Allowed : 21.08 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.15), residues: 3159 helix: 0.04 (0.21), residues: 672 sheet: -1.19 (0.20), residues: 645 loop : -2.10 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP B 633 HIS 0.007 0.001 HIS A 505 PHE 0.024 0.002 PHE A 759 TYR 0.029 0.002 TYR C 501 ARG 0.004 0.001 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00657 ( 48) link_NAG-ASN : angle 3.75817 ( 144) link_BETA1-4 : bond 0.00511 ( 18) link_BETA1-4 : angle 2.26525 ( 54) hydrogen bonds : bond 0.19655 ( 848) hydrogen bonds : angle 8.31691 ( 2280) SS BOND : bond 0.00511 ( 39) SS BOND : angle 1.93810 ( 78) covalent geometry : bond 0.00508 (26418) covalent geometry : angle 0.92492 (35955) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 3.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7926 (t0) cc_final: 0.7585 (t0) REVERT: A 505 HIS cc_start: -0.2529 (OUTLIER) cc_final: -0.4119 (m-70) REVERT: B 32 PHE cc_start: 0.8522 (m-10) cc_final: 0.8174 (m-10) REVERT: B 43 PHE cc_start: 0.8892 (t80) cc_final: 0.8534 (t80) REVERT: B 389 ASP cc_start: 0.7473 (m-30) cc_final: 0.7207 (m-30) REVERT: B 505 HIS cc_start: -0.2396 (OUTLIER) cc_final: -0.3892 (m90) REVERT: B 641 ASN cc_start: 0.8081 (m-40) cc_final: 0.7832 (p0) REVERT: B 856 ASN cc_start: 0.7889 (m-40) cc_final: 0.7534 (p0) REVERT: B 994 ASP cc_start: 0.8652 (t70) cc_final: 0.8239 (t0) REVERT: C 214 ARG cc_start: 0.2202 (OUTLIER) cc_final: 0.1213 (ppt90) REVERT: C 505 HIS cc_start: -0.2607 (OUTLIER) cc_final: -0.3994 (m-70) REVERT: C 508 TYR cc_start: 0.8430 (m-80) cc_final: 0.8051 (m-80) outliers start: 33 outliers final: 15 residues processed: 267 average time/residue: 0.3831 time to fit residues: 169.7977 Evaluate side-chains 212 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 249 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 185 optimal weight: 0.9980 chunk 288 optimal weight: 0.2980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS B 81 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 505 HIS C 675 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.132905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.102478 restraints weight = 45897.340| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.30 r_work: 0.3359 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26523 Z= 0.154 Angle : 0.751 15.401 36231 Z= 0.363 Chirality : 0.052 0.666 4254 Planarity : 0.005 0.046 4557 Dihedral : 14.858 109.127 4802 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.28 % Favored : 92.62 % Rotamer: Outliers : 3.53 % Allowed : 18.88 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.15), residues: 3159 helix: 0.33 (0.21), residues: 684 sheet: -1.07 (0.20), residues: 678 loop : -2.03 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 633 HIS 0.003 0.001 HIS A 505 PHE 0.014 0.002 PHE B 759 TYR 0.024 0.001 TYR C 501 ARG 0.005 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00666 ( 48) link_NAG-ASN : angle 3.62323 ( 144) link_BETA1-4 : bond 0.00554 ( 18) link_BETA1-4 : angle 3.26817 ( 54) hydrogen bonds : bond 0.04292 ( 848) hydrogen bonds : angle 6.06200 ( 2280) SS BOND : bond 0.00463 ( 39) SS BOND : angle 1.67860 ( 78) covalent geometry : bond 0.00352 (26418) covalent geometry : angle 0.70282 (35955) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 227 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 HIS cc_start: -0.1536 (OUTLIER) cc_final: -0.3388 (m90) REVERT: A 988 GLU cc_start: 0.8451 (tp30) cc_final: 0.8201 (tp30) REVERT: A 994 ASP cc_start: 0.8438 (t70) cc_final: 0.8170 (t0) REVERT: B 43 PHE cc_start: 0.8822 (t80) cc_final: 0.8469 (t80) REVERT: B 334 ASN cc_start: 0.6694 (OUTLIER) cc_final: 0.6367 (p0) REVERT: B 360 ASN cc_start: 0.8237 (t0) cc_final: 0.7998 (t0) REVERT: B 369 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.7320 (t80) REVERT: B 389 ASP cc_start: 0.7563 (m-30) cc_final: 0.7296 (m-30) REVERT: B 421 TYR cc_start: 0.8992 (m-10) cc_final: 0.8752 (m-10) REVERT: B 495 TYR cc_start: 0.7310 (OUTLIER) cc_final: 0.6351 (t80) REVERT: B 505 HIS cc_start: -0.1883 (OUTLIER) cc_final: -0.3298 (m90) REVERT: B 581 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8122 (p) REVERT: B 988 GLU cc_start: 0.8836 (tp30) cc_final: 0.8611 (tp30) REVERT: B 994 ASP cc_start: 0.8565 (t70) cc_final: 0.8202 (t0) REVERT: C 53 ASP cc_start: 0.8010 (t0) cc_final: 0.7747 (t0) REVERT: C 134 GLN cc_start: 0.6664 (OUTLIER) cc_final: 0.6220 (tm-30) REVERT: C 214 ARG cc_start: 0.3622 (OUTLIER) cc_final: 0.3306 (ptt90) REVERT: C 334 ASN cc_start: 0.6817 (OUTLIER) cc_final: 0.6462 (p0) REVERT: C 421 TYR cc_start: 0.8643 (m-10) cc_final: 0.8368 (m-10) REVERT: C 424 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7381 (tptm) REVERT: C 505 HIS cc_start: -0.1314 (OUTLIER) cc_final: -0.2690 (m90) REVERT: C 780 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8401 (tt0) REVERT: C 994 ASP cc_start: 0.8244 (t70) cc_final: 0.7890 (t0) outliers start: 98 outliers final: 46 residues processed: 309 average time/residue: 0.3196 time to fit residues: 166.3525 Evaluate side-chains 249 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 192 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 77 optimal weight: 8.9990 chunk 254 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 266 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 78 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 228 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.133547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.103179 restraints weight = 45761.026| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.30 r_work: 0.3368 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 26523 Z= 0.138 Angle : 0.712 15.120 36231 Z= 0.348 Chirality : 0.052 0.649 4254 Planarity : 0.004 0.044 4557 Dihedral : 10.845 100.850 4792 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.74 % Favored : 93.16 % Rotamer: Outliers : 4.07 % Allowed : 19.71 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.15), residues: 3159 helix: 0.58 (0.21), residues: 678 sheet: -0.92 (0.20), residues: 651 loop : -2.02 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 633 HIS 0.002 0.000 HIS B 339 PHE 0.029 0.001 PHE A 133 TYR 0.024 0.001 TYR B 501 ARG 0.003 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00824 ( 48) link_NAG-ASN : angle 3.49652 ( 144) link_BETA1-4 : bond 0.00545 ( 18) link_BETA1-4 : angle 2.97810 ( 54) hydrogen bonds : bond 0.04160 ( 848) hydrogen bonds : angle 5.87825 ( 2280) SS BOND : bond 0.00557 ( 39) SS BOND : angle 2.37730 ( 78) covalent geometry : bond 0.00311 (26418) covalent geometry : angle 0.66039 (35955) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 231 time to evaluate : 2.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6774 (ptmm) REVERT: A 369 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.7191 (t80) REVERT: A 505 HIS cc_start: -0.2018 (OUTLIER) cc_final: -0.4001 (m90) REVERT: A 988 GLU cc_start: 0.8431 (tp30) cc_final: 0.8205 (tp30) REVERT: B 43 PHE cc_start: 0.8870 (t80) cc_final: 0.8586 (t80) REVERT: B 200 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.7382 (t80) REVERT: B 360 ASN cc_start: 0.8304 (t0) cc_final: 0.8098 (t0) REVERT: B 369 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.7292 (t80) REVERT: B 402 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.7713 (pp) REVERT: B 495 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.6126 (t80) REVERT: B 581 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.8023 (p) REVERT: B 856 ASN cc_start: 0.7844 (m110) cc_final: 0.7287 (m110) REVERT: B 988 GLU cc_start: 0.8798 (tp30) cc_final: 0.8581 (tp30) REVERT: B 994 ASP cc_start: 0.8576 (t70) cc_final: 0.8205 (t0) REVERT: C 53 ASP cc_start: 0.8011 (t0) cc_final: 0.7790 (t0) REVERT: C 66 HIS cc_start: 0.8090 (OUTLIER) cc_final: 0.7082 (m-70) REVERT: C 134 GLN cc_start: 0.6585 (OUTLIER) cc_final: 0.6199 (tm-30) REVERT: C 334 ASN cc_start: 0.6725 (OUTLIER) cc_final: 0.6443 (p0) REVERT: C 402 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8231 (pp) REVERT: C 421 TYR cc_start: 0.8672 (m-80) cc_final: 0.8342 (m-10) REVERT: C 495 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.6236 (t80) REVERT: C 505 HIS cc_start: -0.1884 (OUTLIER) cc_final: -0.3105 (m90) REVERT: C 578 ASP cc_start: 0.8057 (t70) cc_final: 0.7584 (t70) outliers start: 113 outliers final: 55 residues processed: 322 average time/residue: 0.3279 time to fit residues: 177.3273 Evaluate side-chains 267 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 198 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 88 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 250 optimal weight: 8.9990 chunk 87 optimal weight: 0.6980 chunk 289 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 804 GLN B 965 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.130070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.099136 restraints weight = 46303.790| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.31 r_work: 0.3295 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 26523 Z= 0.187 Angle : 0.709 15.072 36231 Z= 0.349 Chirality : 0.051 0.650 4254 Planarity : 0.004 0.043 4557 Dihedral : 8.779 93.080 4788 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.44 % Favored : 92.50 % Rotamer: Outliers : 4.65 % Allowed : 19.93 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.15), residues: 3159 helix: 0.69 (0.21), residues: 690 sheet: -1.05 (0.20), residues: 642 loop : -1.93 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 633 HIS 0.003 0.001 HIS C1064 PHE 0.021 0.002 PHE B 133 TYR 0.023 0.001 TYR B 265 ARG 0.015 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00641 ( 48) link_NAG-ASN : angle 3.46877 ( 144) link_BETA1-4 : bond 0.00443 ( 18) link_BETA1-4 : angle 2.77224 ( 54) hydrogen bonds : bond 0.04040 ( 848) hydrogen bonds : angle 5.74251 ( 2280) SS BOND : bond 0.00478 ( 39) SS BOND : angle 2.32129 ( 78) covalent geometry : bond 0.00441 (26418) covalent geometry : angle 0.65943 (35955) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 233 time to evaluate : 7.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8065 (t0) cc_final: 0.7850 (t0) REVERT: A 129 LYS cc_start: 0.6989 (OUTLIER) cc_final: 0.6722 (ptmm) REVERT: A 200 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.7076 (m-80) REVERT: A 366 SER cc_start: 0.8508 (m) cc_final: 0.8197 (p) REVERT: A 369 TYR cc_start: 0.7781 (OUTLIER) cc_final: 0.7027 (t80) REVERT: A 505 HIS cc_start: -0.2078 (OUTLIER) cc_final: -0.4289 (m90) REVERT: A 823 PHE cc_start: 0.7985 (m-10) cc_final: 0.7776 (m-10) REVERT: A 988 GLU cc_start: 0.8525 (tp30) cc_final: 0.8253 (tp30) REVERT: B 43 PHE cc_start: 0.8961 (t80) cc_final: 0.8746 (t80) REVERT: B 134 GLN cc_start: 0.6704 (OUTLIER) cc_final: 0.6310 (tm-30) REVERT: B 200 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.7369 (t80) REVERT: B 360 ASN cc_start: 0.8379 (t0) cc_final: 0.8148 (t0) REVERT: B 369 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.7429 (t80) REVERT: B 402 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.7814 (pp) REVERT: B 495 TYR cc_start: 0.7258 (OUTLIER) cc_final: 0.6070 (t80) REVERT: B 552 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8397 (mt) REVERT: B 581 THR cc_start: 0.8383 (OUTLIER) cc_final: 0.8065 (p) REVERT: B 867 ASP cc_start: 0.8627 (t0) cc_final: 0.8330 (t0) REVERT: B 988 GLU cc_start: 0.8818 (tp30) cc_final: 0.8596 (tp30) REVERT: C 66 HIS cc_start: 0.8321 (OUTLIER) cc_final: 0.7026 (m-70) REVERT: C 200 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.6648 (m-80) REVERT: C 346 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7621 (tpt170) REVERT: C 402 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8168 (pp) REVERT: C 421 TYR cc_start: 0.8696 (m-80) cc_final: 0.8348 (m-10) REVERT: C 424 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7440 (tptm) REVERT: C 495 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.6211 (t80) REVERT: C 505 HIS cc_start: -0.1971 (OUTLIER) cc_final: -0.3321 (m90) REVERT: C 552 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8369 (mt) REVERT: C 578 ASP cc_start: 0.8168 (t70) cc_final: 0.7705 (t70) REVERT: C 994 ASP cc_start: 0.8386 (t70) cc_final: 0.8148 (t0) REVERT: C 1076 THR cc_start: 0.7555 (OUTLIER) cc_final: 0.7337 (m) outliers start: 129 outliers final: 75 residues processed: 337 average time/residue: 0.3683 time to fit residues: 209.9672 Evaluate side-chains 299 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 204 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 208 optimal weight: 4.9990 chunk 222 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 278 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 168 optimal weight: 4.9990 chunk 239 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 287 optimal weight: 9.9990 chunk 186 optimal weight: 0.4980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.129579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.098497 restraints weight = 46617.165| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.34 r_work: 0.3271 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 26523 Z= 0.180 Angle : 0.683 14.797 36231 Z= 0.337 Chirality : 0.050 0.647 4254 Planarity : 0.004 0.039 4557 Dihedral : 8.208 91.266 4787 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.93 % Favored : 92.97 % Rotamer: Outliers : 5.19 % Allowed : 19.89 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.15), residues: 3159 helix: 0.78 (0.21), residues: 690 sheet: -1.07 (0.20), residues: 651 loop : -1.87 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 452 HIS 0.004 0.001 HIS B 339 PHE 0.018 0.002 PHE A 43 TYR 0.030 0.001 TYR B 501 ARG 0.005 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00628 ( 48) link_NAG-ASN : angle 3.43266 ( 144) link_BETA1-4 : bond 0.00428 ( 18) link_BETA1-4 : angle 2.43089 ( 54) hydrogen bonds : bond 0.03997 ( 848) hydrogen bonds : angle 5.69249 ( 2280) SS BOND : bond 0.00511 ( 39) SS BOND : angle 2.12380 ( 78) covalent geometry : bond 0.00423 (26418) covalent geometry : angle 0.63624 (35955) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 240 time to evaluate : 3.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8040 (t0) cc_final: 0.7819 (t0) REVERT: A 129 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6799 (ptmm) REVERT: A 200 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.7089 (m-80) REVERT: A 324 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: A 366 SER cc_start: 0.8451 (m) cc_final: 0.8137 (p) REVERT: A 369 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.7088 (t80) REVERT: A 495 TYR cc_start: 0.7115 (OUTLIER) cc_final: 0.5930 (t80) REVERT: A 505 HIS cc_start: -0.2395 (OUTLIER) cc_final: -0.4582 (m90) REVERT: A 858 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7357 (mt) REVERT: A 988 GLU cc_start: 0.8608 (tp30) cc_final: 0.8230 (tp30) REVERT: B 200 TYR cc_start: 0.7693 (OUTLIER) cc_final: 0.7422 (t80) REVERT: B 360 ASN cc_start: 0.8414 (t0) cc_final: 0.8192 (t0) REVERT: B 369 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.7442 (t80) REVERT: B 402 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.7736 (pp) REVERT: B 495 TYR cc_start: 0.7322 (OUTLIER) cc_final: 0.5691 (t80) REVERT: B 552 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8421 (mt) REVERT: B 628 GLN cc_start: 0.8245 (pt0) cc_final: 0.8026 (pt0) REVERT: B 823 PHE cc_start: 0.7881 (m-80) cc_final: 0.7422 (m-10) REVERT: B 867 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8282 (t0) REVERT: B 988 GLU cc_start: 0.8836 (tp30) cc_final: 0.8600 (tp30) REVERT: B 994 ASP cc_start: 0.8626 (t70) cc_final: 0.8354 (t0) REVERT: C 66 HIS cc_start: 0.8389 (OUTLIER) cc_final: 0.6945 (m-70) REVERT: C 127 PHE cc_start: 0.6331 (t80) cc_final: 0.5936 (t80) REVERT: C 129 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7271 (ptmm) REVERT: C 200 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.7108 (t80) REVERT: C 229 LEU cc_start: 0.6776 (OUTLIER) cc_final: 0.6524 (mp) REVERT: C 346 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7589 (tpt170) REVERT: C 402 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8217 (pp) REVERT: C 421 TYR cc_start: 0.8716 (m-80) cc_final: 0.8303 (m-10) REVERT: C 424 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7423 (tptm) REVERT: C 495 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.6167 (t80) REVERT: C 505 HIS cc_start: -0.1918 (OUTLIER) cc_final: -0.3389 (m90) REVERT: C 552 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8428 (mt) REVERT: C 578 ASP cc_start: 0.8100 (t70) cc_final: 0.7647 (t70) REVERT: C 745 ASP cc_start: 0.7507 (p0) cc_final: 0.7306 (t0) REVERT: C 867 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8269 (t0) REVERT: C 994 ASP cc_start: 0.8369 (t70) cc_final: 0.7962 (t0) REVERT: C 998 THR cc_start: 0.9231 (OUTLIER) cc_final: 0.8977 (m) outliers start: 144 outliers final: 84 residues processed: 356 average time/residue: 0.3490 time to fit residues: 207.5377 Evaluate side-chains 317 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 208 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 300 optimal weight: 0.6980 chunk 274 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 232 optimal weight: 0.0030 chunk 237 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 262 optimal weight: 7.9990 chunk 233 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN C 556 ASN C 628 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.130823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.100173 restraints weight = 45920.697| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.30 r_work: 0.3318 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26523 Z= 0.124 Angle : 0.662 14.490 36231 Z= 0.324 Chirality : 0.049 0.631 4254 Planarity : 0.004 0.040 4557 Dihedral : 7.900 88.080 4786 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.58 % Favored : 93.32 % Rotamer: Outliers : 4.76 % Allowed : 21.01 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.15), residues: 3159 helix: 0.91 (0.21), residues: 690 sheet: -1.01 (0.21), residues: 624 loop : -1.82 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 452 HIS 0.002 0.000 HIS B 339 PHE 0.020 0.001 PHE B 43 TYR 0.021 0.001 TYR B 170 ARG 0.005 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00592 ( 48) link_NAG-ASN : angle 3.37554 ( 144) link_BETA1-4 : bond 0.00493 ( 18) link_BETA1-4 : angle 2.27977 ( 54) hydrogen bonds : bond 0.03701 ( 848) hydrogen bonds : angle 5.58128 ( 2280) SS BOND : bond 0.00343 ( 39) SS BOND : angle 2.00164 ( 78) covalent geometry : bond 0.00284 (26418) covalent geometry : angle 0.61652 (35955) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 238 time to evaluate : 2.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8057 (t0) cc_final: 0.7843 (t0) REVERT: A 129 LYS cc_start: 0.7005 (OUTLIER) cc_final: 0.6688 (ptmm) REVERT: A 131 CYS cc_start: 0.4225 (t) cc_final: 0.3736 (t) REVERT: A 134 GLN cc_start: 0.6731 (tm-30) cc_final: 0.6464 (tm-30) REVERT: A 200 TYR cc_start: 0.7640 (OUTLIER) cc_final: 0.6938 (m-80) REVERT: A 324 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7569 (tm-30) REVERT: A 366 SER cc_start: 0.8449 (m) cc_final: 0.8132 (p) REVERT: A 369 TYR cc_start: 0.7671 (OUTLIER) cc_final: 0.7021 (t80) REVERT: A 495 TYR cc_start: 0.7106 (OUTLIER) cc_final: 0.5961 (t80) REVERT: A 505 HIS cc_start: -0.2200 (OUTLIER) cc_final: -0.4507 (m90) REVERT: A 816 SER cc_start: 0.9308 (OUTLIER) cc_final: 0.8887 (m) REVERT: A 988 GLU cc_start: 0.8596 (tp30) cc_final: 0.8333 (tp30) REVERT: B 131 CYS cc_start: 0.3190 (t) cc_final: 0.2764 (t) REVERT: B 200 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.7331 (t80) REVERT: B 369 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.7421 (t80) REVERT: B 383 SER cc_start: 0.8788 (t) cc_final: 0.8217 (p) REVERT: B 402 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.7766 (pp) REVERT: B 421 TYR cc_start: 0.8901 (m-10) cc_final: 0.8330 (m-10) REVERT: B 495 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.5769 (t80) REVERT: B 552 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8400 (mt) REVERT: B 628 GLN cc_start: 0.8241 (pt0) cc_final: 0.7961 (pt0) REVERT: B 823 PHE cc_start: 0.7821 (m-80) cc_final: 0.7396 (m-10) REVERT: B 856 ASN cc_start: 0.7946 (m110) cc_final: 0.7344 (m110) REVERT: B 867 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8289 (t0) REVERT: B 988 GLU cc_start: 0.8834 (tp30) cc_final: 0.8622 (tp30) REVERT: B 994 ASP cc_start: 0.8599 (t70) cc_final: 0.8249 (t0) REVERT: B 998 THR cc_start: 0.9456 (OUTLIER) cc_final: 0.9172 (m) REVERT: C 66 HIS cc_start: 0.8295 (OUTLIER) cc_final: 0.6801 (m-70) REVERT: C 129 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.6632 (ptmm) REVERT: C 131 CYS cc_start: 0.3033 (t) cc_final: 0.2381 (t) REVERT: C 200 TYR cc_start: 0.7335 (OUTLIER) cc_final: 0.7093 (t80) REVERT: C 229 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6664 (mp) REVERT: C 346 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7536 (tpt170) REVERT: C 402 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8312 (pp) REVERT: C 421 TYR cc_start: 0.8706 (m-80) cc_final: 0.8291 (m-10) REVERT: C 424 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7432 (tptm) REVERT: C 495 TYR cc_start: 0.7479 (OUTLIER) cc_final: 0.6262 (t80) REVERT: C 505 HIS cc_start: -0.1980 (OUTLIER) cc_final: -0.3605 (m90) REVERT: C 552 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8369 (mt) REVERT: C 578 ASP cc_start: 0.8121 (t70) cc_final: 0.7633 (t70) REVERT: C 867 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8209 (t0) REVERT: C 902 MET cc_start: 0.9018 (tpt) cc_final: 0.8677 (tpt) REVERT: C 994 ASP cc_start: 0.8322 (t70) cc_final: 0.8002 (t0) outliers start: 132 outliers final: 80 residues processed: 343 average time/residue: 0.3339 time to fit residues: 190.2929 Evaluate side-chains 324 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 219 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 229 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 267 optimal weight: 3.9990 chunk 76 optimal weight: 30.0000 chunk 19 optimal weight: 2.9990 chunk 304 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 307 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 907 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.127872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.096853 restraints weight = 46316.518| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 3.32 r_work: 0.3250 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 26523 Z= 0.201 Angle : 0.707 14.544 36231 Z= 0.346 Chirality : 0.050 0.660 4254 Planarity : 0.004 0.038 4557 Dihedral : 7.862 87.456 4786 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.06 % Favored : 92.85 % Rotamer: Outliers : 4.94 % Allowed : 21.05 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.15), residues: 3159 helix: 0.82 (0.21), residues: 690 sheet: -1.02 (0.20), residues: 648 loop : -1.83 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 452 HIS 0.004 0.001 HIS B 339 PHE 0.026 0.002 PHE B 43 TYR 0.024 0.001 TYR B 265 ARG 0.004 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00581 ( 48) link_NAG-ASN : angle 3.42157 ( 144) link_BETA1-4 : bond 0.00430 ( 18) link_BETA1-4 : angle 2.17969 ( 54) hydrogen bonds : bond 0.04020 ( 848) hydrogen bonds : angle 5.55808 ( 2280) SS BOND : bond 0.00645 ( 39) SS BOND : angle 2.22264 ( 78) covalent geometry : bond 0.00477 (26418) covalent geometry : angle 0.66247 (35955) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 223 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.6560 (tm-30) cc_final: 0.6326 (tm-30) REVERT: A 200 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.6927 (m-80) REVERT: A 324 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7499 (tm-30) REVERT: A 369 TYR cc_start: 0.7661 (OUTLIER) cc_final: 0.6974 (t80) REVERT: A 495 TYR cc_start: 0.7166 (OUTLIER) cc_final: 0.6079 (t80) REVERT: A 505 HIS cc_start: -0.2137 (OUTLIER) cc_final: -0.4196 (m90) REVERT: A 578 ASP cc_start: 0.8224 (t70) cc_final: 0.7678 (t0) REVERT: A 816 SER cc_start: 0.9299 (OUTLIER) cc_final: 0.8893 (m) REVERT: A 988 GLU cc_start: 0.8646 (tp30) cc_final: 0.8279 (tp30) REVERT: B 40 ASP cc_start: 0.8448 (m-30) cc_final: 0.8230 (m-30) REVERT: B 200 TYR cc_start: 0.7643 (OUTLIER) cc_final: 0.7364 (t80) REVERT: B 369 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7466 (t80) REVERT: B 383 SER cc_start: 0.8838 (t) cc_final: 0.8253 (p) REVERT: B 402 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.7782 (pp) REVERT: B 495 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.5656 (t80) REVERT: B 552 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8528 (mt) REVERT: B 628 GLN cc_start: 0.8229 (pt0) cc_final: 0.7978 (pt0) REVERT: B 823 PHE cc_start: 0.7904 (m-80) cc_final: 0.7418 (m-80) REVERT: B 856 ASN cc_start: 0.7976 (m110) cc_final: 0.7383 (m110) REVERT: B 867 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8310 (t0) REVERT: B 988 GLU cc_start: 0.8861 (tp30) cc_final: 0.8621 (tp30) REVERT: B 1019 ARG cc_start: 0.8369 (tpt170) cc_final: 0.7906 (tpp-160) REVERT: C 66 HIS cc_start: 0.8422 (OUTLIER) cc_final: 0.6801 (m-70) REVERT: C 127 PHE cc_start: 0.6332 (t80) cc_final: 0.6086 (t80) REVERT: C 129 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.6970 (ptmt) REVERT: C 131 CYS cc_start: 0.2872 (t) cc_final: 0.2292 (t) REVERT: C 200 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.7254 (t80) REVERT: C 421 TYR cc_start: 0.8746 (m-80) cc_final: 0.8299 (m-10) REVERT: C 424 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7473 (tptm) REVERT: C 495 TYR cc_start: 0.7438 (OUTLIER) cc_final: 0.6196 (t80) REVERT: C 505 HIS cc_start: -0.2127 (OUTLIER) cc_final: -0.3901 (m90) REVERT: C 552 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8468 (mt) REVERT: C 578 ASP cc_start: 0.8167 (t70) cc_final: 0.7444 (t70) REVERT: C 628 GLN cc_start: 0.8142 (pt0) cc_final: 0.7886 (pt0) REVERT: C 867 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8281 (t0) REVERT: C 998 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.9020 (m) outliers start: 137 outliers final: 84 residues processed: 335 average time/residue: 0.3313 time to fit residues: 183.9292 Evaluate side-chains 311 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 206 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 194 optimal weight: 1.9990 chunk 234 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 274 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 315 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.128426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.098085 restraints weight = 45587.983| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.20 r_work: 0.3284 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 26523 Z= 0.234 Angle : 0.737 14.415 36231 Z= 0.363 Chirality : 0.051 0.662 4254 Planarity : 0.004 0.037 4557 Dihedral : 7.928 87.836 4786 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.31 % Favored : 92.62 % Rotamer: Outliers : 4.58 % Allowed : 21.69 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.15), residues: 3159 helix: 0.53 (0.20), residues: 708 sheet: -0.90 (0.21), residues: 621 loop : -1.92 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 452 HIS 0.004 0.001 HIS B 339 PHE 0.026 0.002 PHE B 43 TYR 0.026 0.002 TYR C 265 ARG 0.005 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 48) link_NAG-ASN : angle 3.44103 ( 144) link_BETA1-4 : bond 0.00419 ( 18) link_BETA1-4 : angle 2.09618 ( 54) hydrogen bonds : bond 0.04138 ( 848) hydrogen bonds : angle 5.63063 ( 2280) SS BOND : bond 0.00530 ( 39) SS BOND : angle 2.42248 ( 78) covalent geometry : bond 0.00558 (26418) covalent geometry : angle 0.69365 (35955) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 218 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.6787 (tm-30) cc_final: 0.6508 (tm-30) REVERT: A 200 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.7136 (m-80) REVERT: A 324 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7552 (tm-30) REVERT: A 389 ASP cc_start: 0.8619 (m-30) cc_final: 0.8400 (t0) REVERT: A 495 TYR cc_start: 0.7324 (OUTLIER) cc_final: 0.5988 (t80) REVERT: A 505 HIS cc_start: -0.1809 (OUTLIER) cc_final: -0.4165 (m90) REVERT: A 578 ASP cc_start: 0.8244 (t70) cc_final: 0.7713 (t0) REVERT: A 816 SER cc_start: 0.9328 (OUTLIER) cc_final: 0.8968 (m) REVERT: A 858 LEU cc_start: 0.7973 (mt) cc_final: 0.7754 (mt) REVERT: A 988 GLU cc_start: 0.8684 (tp30) cc_final: 0.8282 (tp30) REVERT: B 40 ASP cc_start: 0.8340 (m-30) cc_final: 0.8129 (m-30) REVERT: B 369 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.7570 (t80) REVERT: B 402 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.7830 (pp) REVERT: B 495 TYR cc_start: 0.7414 (OUTLIER) cc_final: 0.5740 (t80) REVERT: B 508 TYR cc_start: 0.8350 (m-80) cc_final: 0.7814 (m-80) REVERT: B 552 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8630 (mt) REVERT: B 823 PHE cc_start: 0.7906 (m-80) cc_final: 0.7387 (m-80) REVERT: B 856 ASN cc_start: 0.8094 (m110) cc_final: 0.7491 (m110) REVERT: B 867 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8328 (t0) REVERT: B 988 GLU cc_start: 0.8835 (tp30) cc_final: 0.8623 (tp30) REVERT: C 66 HIS cc_start: 0.8479 (OUTLIER) cc_final: 0.6671 (m-70) REVERT: C 127 PHE cc_start: 0.6650 (t80) cc_final: 0.6404 (t80) REVERT: C 129 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.6880 (ptmt) REVERT: C 134 GLN cc_start: 0.6881 (tm-30) cc_final: 0.6571 (tm-30) REVERT: C 200 TYR cc_start: 0.7608 (OUTLIER) cc_final: 0.7213 (t80) REVERT: C 421 TYR cc_start: 0.8815 (m-80) cc_final: 0.8378 (m-10) REVERT: C 424 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7524 (tptm) REVERT: C 495 TYR cc_start: 0.7473 (OUTLIER) cc_final: 0.6210 (t80) REVERT: C 505 HIS cc_start: -0.2837 (OUTLIER) cc_final: -0.4221 (m90) REVERT: C 552 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8523 (mt) REVERT: C 578 ASP cc_start: 0.8110 (t70) cc_final: 0.7500 (t70) REVERT: C 628 GLN cc_start: 0.8242 (pt0) cc_final: 0.7860 (pt0) REVERT: C 867 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8315 (t0) REVERT: C 998 THR cc_start: 0.9275 (OUTLIER) cc_final: 0.9055 (m) outliers start: 127 outliers final: 86 residues processed: 325 average time/residue: 0.3454 time to fit residues: 187.8858 Evaluate side-chains 308 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 203 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 217 optimal weight: 2.9990 chunk 255 optimal weight: 0.0270 chunk 170 optimal weight: 1.9990 chunk 293 optimal weight: 0.6980 chunk 168 optimal weight: 1.9990 chunk 281 optimal weight: 0.6980 chunk 181 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 221 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 787 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN C 901 GLN ** C1002 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 = 0.3920 r_free = 0.3920 target = 0.130924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.101003 restraints weight = 45382.988| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.17 r_work: 0.3340 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 26523 Z= 0.139 Angle : 0.690 14.266 36231 Z= 0.338 Chirality : 0.049 0.646 4254 Planarity : 0.004 0.037 4557 Dihedral : 7.689 84.786 4786 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.55 % Favored : 93.38 % Rotamer: Outliers : 4.11 % Allowed : 22.02 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.15), residues: 3159 helix: 0.66 (0.20), residues: 708 sheet: -0.81 (0.21), residues: 612 loop : -1.84 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 452 HIS 0.003 0.000 HIS B 339 PHE 0.044 0.001 PHE B 133 TYR 0.021 0.001 TYR B 170 ARG 0.006 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 48) link_NAG-ASN : angle 3.42370 ( 144) link_BETA1-4 : bond 0.00510 ( 18) link_BETA1-4 : angle 2.01707 ( 54) hydrogen bonds : bond 0.03779 ( 848) hydrogen bonds : angle 5.55482 ( 2280) SS BOND : bond 0.00375 ( 39) SS BOND : angle 2.27773 ( 78) covalent geometry : bond 0.00324 (26418) covalent geometry : angle 0.64507 (35955) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 233 time to evaluate : 3.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.6731 (tm-30) cc_final: 0.6516 (tm-30) REVERT: A 200 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.6993 (m-80) REVERT: A 324 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: A 495 TYR cc_start: 0.7289 (OUTLIER) cc_final: 0.6055 (t80) REVERT: A 505 HIS cc_start: -0.1544 (OUTLIER) cc_final: -0.4013 (m90) REVERT: A 578 ASP cc_start: 0.8156 (t70) cc_final: 0.7657 (t0) REVERT: A 816 SER cc_start: 0.9287 (OUTLIER) cc_final: 0.8927 (m) REVERT: A 988 GLU cc_start: 0.8577 (tp30) cc_final: 0.8266 (tp30) REVERT: B 40 ASP cc_start: 0.8273 (m-30) cc_final: 0.8040 (m-30) REVERT: B 96 GLU cc_start: 0.5745 (mt-10) cc_final: 0.5484 (mp0) REVERT: B 200 TYR cc_start: 0.7582 (OUTLIER) cc_final: 0.7367 (t80) REVERT: B 367 VAL cc_start: 0.9055 (m) cc_final: 0.8800 (p) REVERT: B 369 TYR cc_start: 0.7851 (OUTLIER) cc_final: 0.7413 (t80) REVERT: B 402 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.7790 (pp) REVERT: B 495 TYR cc_start: 0.7395 (OUTLIER) cc_final: 0.5875 (t80) REVERT: B 552 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8551 (mt) REVERT: B 823 PHE cc_start: 0.7836 (m-80) cc_final: 0.7336 (m-80) REVERT: B 856 ASN cc_start: 0.8021 (m110) cc_final: 0.7467 (m110) REVERT: B 867 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8291 (t0) REVERT: B 988 GLU cc_start: 0.8810 (tp30) cc_final: 0.8609 (tp30) REVERT: B 994 ASP cc_start: 0.8656 (t70) cc_final: 0.8374 (t0) REVERT: B 1019 ARG cc_start: 0.8336 (tpt170) cc_final: 0.7887 (tpp-160) REVERT: C 66 HIS cc_start: 0.8346 (OUTLIER) cc_final: 0.6628 (m-70) REVERT: C 127 PHE cc_start: 0.6520 (t80) cc_final: 0.6304 (t80) REVERT: C 129 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.6723 (ptmm) REVERT: C 134 GLN cc_start: 0.6359 (tm-30) cc_final: 0.6106 (tm-30) REVERT: C 200 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.7180 (t80) REVERT: C 421 TYR cc_start: 0.8821 (m-80) cc_final: 0.8222 (m-10) REVERT: C 424 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7508 (tptm) REVERT: C 495 TYR cc_start: 0.7586 (OUTLIER) cc_final: 0.6320 (t80) REVERT: C 501 TYR cc_start: 0.5026 (m-10) cc_final: 0.4809 (m-10) REVERT: C 505 HIS cc_start: -0.2698 (OUTLIER) cc_final: -0.4103 (m90) REVERT: C 552 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8553 (mt) REVERT: C 578 ASP cc_start: 0.8090 (t70) cc_final: 0.7489 (t70) REVERT: C 867 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8251 (t0) REVERT: C 998 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.9005 (m) outliers start: 114 outliers final: 69 residues processed: 328 average time/residue: 0.3428 time to fit residues: 187.4665 Evaluate side-chains 292 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 203 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 151 optimal weight: 6.9990 chunk 211 optimal weight: 7.9990 chunk 302 optimal weight: 0.8980 chunk 188 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 238 optimal weight: 0.0040 chunk 94 optimal weight: 0.6980 chunk 229 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN C 628 GLN C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.131877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.102089 restraints weight = 45188.454| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 3.16 r_work: 0.3353 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26523 Z= 0.134 Angle : 0.708 15.642 36231 Z= 0.345 Chirality : 0.049 0.635 4254 Planarity : 0.004 0.037 4557 Dihedral : 7.555 83.516 4786 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.68 % Favored : 93.26 % Rotamer: Outliers : 3.50 % Allowed : 22.49 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.15), residues: 3159 helix: 0.72 (0.20), residues: 708 sheet: -0.86 (0.21), residues: 615 loop : -1.82 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 452 HIS 0.003 0.000 HIS B 339 PHE 0.030 0.001 PHE B 43 TYR 0.028 0.001 TYR A 917 ARG 0.005 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00537 ( 48) link_NAG-ASN : angle 3.43919 ( 144) link_BETA1-4 : bond 0.00491 ( 18) link_BETA1-4 : angle 1.99293 ( 54) hydrogen bonds : bond 0.03702 ( 848) hydrogen bonds : angle 5.46079 ( 2280) SS BOND : bond 0.00413 ( 39) SS BOND : angle 2.69387 ( 78) covalent geometry : bond 0.00313 (26418) covalent geometry : angle 0.66009 (35955) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 212 time to evaluate : 2.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7584 (OUTLIER) cc_final: 0.6852 (m-80) REVERT: A 324 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7647 (tm-30) REVERT: A 495 TYR cc_start: 0.7293 (OUTLIER) cc_final: 0.5993 (t80) REVERT: A 501 TYR cc_start: 0.5539 (m-80) cc_final: 0.5324 (m-80) REVERT: A 505 HIS cc_start: -0.1631 (OUTLIER) cc_final: -0.4034 (m90) REVERT: A 578 ASP cc_start: 0.8138 (t70) cc_final: 0.7650 (t0) REVERT: A 988 GLU cc_start: 0.8591 (tp30) cc_final: 0.8287 (tp30) REVERT: B 40 ASP cc_start: 0.8237 (m-30) cc_final: 0.7990 (m-30) REVERT: B 134 GLN cc_start: 0.6450 (tm-30) cc_final: 0.6140 (tm-30) REVERT: B 200 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.7226 (t80) REVERT: B 367 VAL cc_start: 0.9013 (m) cc_final: 0.8752 (p) REVERT: B 369 TYR cc_start: 0.7783 (OUTLIER) cc_final: 0.7456 (t80) REVERT: B 402 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.7786 (pp) REVERT: B 495 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.5863 (t80) REVERT: B 552 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8541 (mt) REVERT: B 823 PHE cc_start: 0.7805 (m-80) cc_final: 0.7322 (m-80) REVERT: B 856 ASN cc_start: 0.7958 (m110) cc_final: 0.7443 (m110) REVERT: B 867 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8270 (t0) REVERT: B 902 MET cc_start: 0.8947 (tpt) cc_final: 0.8386 (tpt) REVERT: B 994 ASP cc_start: 0.8628 (t70) cc_final: 0.8348 (t0) REVERT: B 1019 ARG cc_start: 0.8304 (tpt170) cc_final: 0.7924 (tpp-160) REVERT: C 66 HIS cc_start: 0.8341 (OUTLIER) cc_final: 0.6613 (m-70) REVERT: C 127 PHE cc_start: 0.6495 (t80) cc_final: 0.6285 (t80) REVERT: C 129 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.6945 (ptmt) REVERT: C 134 GLN cc_start: 0.6468 (tm-30) cc_final: 0.6197 (tm-30) REVERT: C 421 TYR cc_start: 0.8801 (m-80) cc_final: 0.8195 (m-10) REVERT: C 424 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7515 (tptm) REVERT: C 495 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.6343 (t80) REVERT: C 505 HIS cc_start: -0.2284 (OUTLIER) cc_final: -0.3970 (m90) REVERT: C 552 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8565 (mt) REVERT: C 578 ASP cc_start: 0.8072 (t70) cc_final: 0.7486 (t70) REVERT: C 628 GLN cc_start: 0.8076 (pt0) cc_final: 0.7769 (pt0) REVERT: C 867 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8218 (t0) REVERT: C 998 THR cc_start: 0.9242 (OUTLIER) cc_final: 0.9023 (m) outliers start: 97 outliers final: 69 residues processed: 292 average time/residue: 0.3433 time to fit residues: 165.1998 Evaluate side-chains 285 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 198 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 102 optimal weight: 4.9990 chunk 272 optimal weight: 7.9990 chunk 203 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 182 optimal weight: 0.1980 chunk 284 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 286 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.130734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.100826 restraints weight = 45373.440| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 3.16 r_work: 0.3334 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26523 Z= 0.161 Angle : 0.718 14.120 36231 Z= 0.351 Chirality : 0.050 0.638 4254 Planarity : 0.004 0.037 4557 Dihedral : 7.482 83.132 4786 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.58 % Favored : 93.35 % Rotamer: Outliers : 3.57 % Allowed : 22.59 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.15), residues: 3159 helix: 0.73 (0.20), residues: 708 sheet: -0.90 (0.21), residues: 612 loop : -1.82 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 452 HIS 0.004 0.001 HIS B 339 PHE 0.029 0.001 PHE B 43 TYR 0.027 0.001 TYR A 917 ARG 0.006 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 48) link_NAG-ASN : angle 3.48293 ( 144) link_BETA1-4 : bond 0.00459 ( 18) link_BETA1-4 : angle 1.98834 ( 54) hydrogen bonds : bond 0.03790 ( 848) hydrogen bonds : angle 5.44063 ( 2280) SS BOND : bond 0.00441 ( 39) SS BOND : angle 2.54982 ( 78) covalent geometry : bond 0.00382 (26418) covalent geometry : angle 0.67192 (35955) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11430.99 seconds wall clock time: 199 minutes 59.40 seconds (11999.40 seconds total)