Starting phenix.real_space_refine on Sat May 24 22:11:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8whv_37549/05_2025/8whv_37549.cif Found real_map, /net/cci-nas-00/data/ceres_data/8whv_37549/05_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_37549/05_2025/8whv_37549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8whv_37549/05_2025/8whv_37549.map" model { file = "/net/cci-nas-00/data/ceres_data/8whv_37549/05_2025/8whv_37549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8whv_37549/05_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-5687/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: 15.51, per 1000 atoms: 0.60 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: 6.78 Conformation dependent library (CDL) restraints added in 3.2 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: 3.42 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: 10.43 Time building geometry restraints manager: 7.93 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: 4.200 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: 1.050 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 58.760 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.180 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.020 ------------------------------------------------------------------------------- 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 : 2.808 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: 0.3381 time to fit residues: 149.5068 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 : 3.142 ------------------------------------------------------------------------------- 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 = 0.132904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.102490 restraints weight = 45897.357| |-----------------------------------------------------------------------------| r_work (start): 0.3487 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: 0.7861 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 3.26822 ( 54) hydrogen bonds : bond 0.04292 ( 848) hydrogen bonds : angle 6.06199 ( 2280) SS BOND : bond 0.00463 ( 39) SS BOND : angle 1.67859 ( 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 : 2.827 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: -0.1538 (OUTLIER) cc_final: -0.3389 (m90) REVERT: A 988 GLU cc_start: 0.8453 (tp30) cc_final: 0.8202 (tp30) REVERT: A 994 ASP cc_start: 0.8437 (t70) cc_final: 0.8169 (t0) REVERT: B 43 PHE cc_start: 0.8823 (t80) cc_final: 0.8471 (t80) REVERT: B 334 ASN cc_start: 0.6689 (OUTLIER) cc_final: 0.6361 (p0) REVERT: B 360 ASN cc_start: 0.8239 (t0) cc_final: 0.7998 (t0) REVERT: B 369 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.7322 (t80) REVERT: B 389 ASP cc_start: 0.7563 (m-30) cc_final: 0.7295 (m-30) REVERT: B 421 TYR cc_start: 0.8992 (m-10) cc_final: 0.8753 (m-10) REVERT: B 495 TYR cc_start: 0.7309 (OUTLIER) cc_final: 0.6348 (t80) REVERT: B 505 HIS cc_start: -0.1883 (OUTLIER) cc_final: -0.3300 (m90) REVERT: B 581 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8123 (p) REVERT: B 988 GLU cc_start: 0.8837 (tp30) cc_final: 0.8612 (tp30) REVERT: B 994 ASP cc_start: 0.8564 (t70) cc_final: 0.8201 (t0) REVERT: C 53 ASP cc_start: 0.8014 (t0) cc_final: 0.7751 (t0) REVERT: C 134 GLN cc_start: 0.6664 (OUTLIER) cc_final: 0.6219 (tm-30) REVERT: C 214 ARG cc_start: 0.3623 (OUTLIER) cc_final: 0.3307 (ptt90) REVERT: C 334 ASN cc_start: 0.6812 (OUTLIER) cc_final: 0.6458 (p0) REVERT: C 421 TYR cc_start: 0.8643 (m-10) cc_final: 0.8369 (m-10) REVERT: C 424 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7380 (tptm) REVERT: C 505 HIS cc_start: -0.1317 (OUTLIER) cc_final: -0.2693 (m90) REVERT: C 780 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8403 (tt0) REVERT: C 994 ASP cc_start: 0.8241 (t70) cc_final: 0.7888 (t0) outliers start: 98 outliers final: 46 residues processed: 309 average time/residue: 0.3177 time to fit residues: 164.4729 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 : 2.725 ------------------------------------------------------------------------------- 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: 10.0000 chunk 254 optimal weight: 2.9990 chunk 154 optimal weight: 0.4980 chunk 266 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 78 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 228 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3943 r_free = 0.3943 target = 0.133850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.103436 restraints weight = 45764.844| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.32 r_work: 0.3369 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 26523 Z= 0.143 Angle : 0.712 15.073 36231 Z= 0.349 Chirality : 0.052 0.648 4254 Planarity : 0.004 0.045 4557 Dihedral : 10.744 101.163 4792 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.74 % Favored : 93.16 % Rotamer: Outliers : 4.00 % Allowed : 19.78 % 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: -1.73 (0.15), residues: 3159 helix: 0.58 (0.21), residues: 678 sheet: -0.87 (0.20), residues: 645 loop : -2.02 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 633 HIS 0.002 0.000 HIS B 339 PHE 0.026 0.001 PHE A 133 TYR 0.023 0.001 TYR B 501 ARG 0.003 0.000 ARG A 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00825 ( 48) link_NAG-ASN : angle 3.48076 ( 144) link_BETA1-4 : bond 0.00554 ( 18) link_BETA1-4 : angle 2.97934 ( 54) hydrogen bonds : bond 0.04187 ( 848) hydrogen bonds : angle 5.86780 ( 2280) SS BOND : bond 0.00511 ( 39) SS BOND : angle 2.39179 ( 78) covalent geometry : bond 0.00317 (26418) covalent geometry : angle 0.66096 (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 343 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 232 time to evaluate : 2.770 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: 0.7086 (OUTLIER) cc_final: 0.6743 (ptmm) REVERT: A 369 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.7180 (t80) REVERT: A 505 HIS cc_start: -0.2034 (OUTLIER) cc_final: -0.4009 (m90) REVERT: A 988 GLU cc_start: 0.8431 (tp30) cc_final: 0.8205 (tp30) REVERT: B 43 PHE cc_start: 0.8869 (t80) cc_final: 0.8588 (t80) REVERT: B 200 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.7324 (t80) REVERT: B 360 ASN cc_start: 0.8306 (t0) cc_final: 0.8104 (t0) REVERT: B 369 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.7297 (t80) REVERT: B 402 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.7704 (pp) REVERT: B 495 TYR cc_start: 0.7181 (OUTLIER) cc_final: 0.6104 (t80) REVERT: B 581 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.8016 (p) REVERT: B 856 ASN cc_start: 0.7838 (m110) cc_final: 0.7289 (m110) REVERT: B 988 GLU cc_start: 0.8800 (tp30) cc_final: 0.8579 (tp30) REVERT: B 994 ASP cc_start: 0.8574 (t70) cc_final: 0.8204 (t0) REVERT: C 53 ASP cc_start: 0.8013 (t0) cc_final: 0.7792 (t0) REVERT: C 66 HIS cc_start: 0.8083 (OUTLIER) cc_final: 0.7075 (m-70) REVERT: C 134 GLN cc_start: 0.6561 (OUTLIER) cc_final: 0.6185 (tm-30) REVERT: C 334 ASN cc_start: 0.6716 (OUTLIER) cc_final: 0.6436 (p0) REVERT: C 402 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8216 (pp) REVERT: C 403 LYS cc_start: 0.7235 (ttmt) cc_final: 0.6870 (mttt) REVERT: C 421 TYR cc_start: 0.8674 (m-80) cc_final: 0.8349 (m-10) REVERT: C 495 TYR cc_start: 0.7389 (OUTLIER) cc_final: 0.6191 (t80) REVERT: C 505 HIS cc_start: -0.1899 (OUTLIER) cc_final: -0.3789 (m90) REVERT: C 578 ASP cc_start: 0.8052 (t70) cc_final: 0.7573 (t70) outliers start: 111 outliers final: 53 residues processed: 322 average time/residue: 0.3171 time to fit residues: 171.2292 Evaluate side-chains 259 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 192 time to evaluate : 2.802 ------------------------------------------------------------------------------- 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 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 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: 7.9990 chunk 32 optimal weight: 7.9990 chunk 250 optimal weight: 8.9990 chunk 87 optimal weight: 0.6980 chunk 289 optimal weight: 4.9990 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: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 ** C 121 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 = 0.3852 r_free = 0.3852 target = 0.127617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.096151 restraints weight = 47192.782| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.36 r_work: 0.3229 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 26523 Z= 0.254 Angle : 0.767 15.212 36231 Z= 0.380 Chirality : 0.052 0.668 4254 Planarity : 0.005 0.051 4557 Dihedral : 8.849 93.970 4788 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.79 % Favored : 92.12 % Rotamer: Outliers : 4.94 % Allowed : 19.86 % Favored : 75.21 % 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: -1.81 (0.15), residues: 3159 helix: 0.52 (0.21), residues: 690 sheet: -1.16 (0.20), residues: 648 loop : -1.98 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 452 HIS 0.005 0.001 HIS C1064 PHE 0.019 0.002 PHE B 133 TYR 0.031 0.002 TYR C 501 ARG 0.019 0.001 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00639 ( 48) link_NAG-ASN : angle 3.52618 ( 144) link_BETA1-4 : bond 0.00423 ( 18) link_BETA1-4 : angle 2.72500 ( 54) hydrogen bonds : bond 0.04459 ( 848) hydrogen bonds : angle 5.85278 ( 2280) SS BOND : bond 0.00594 ( 39) SS BOND : angle 2.75893 ( 78) covalent geometry : bond 0.00599 (26418) covalent geometry : angle 0.71793 (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 366 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 229 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8051 (t0) cc_final: 0.7814 (t0) REVERT: A 129 LYS cc_start: 0.7061 (OUTLIER) cc_final: 0.6763 (ptpt) REVERT: A 200 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.7086 (m-80) REVERT: A 369 TYR cc_start: 0.7775 (OUTLIER) cc_final: 0.6985 (t80) REVERT: A 505 HIS cc_start: -0.2615 (OUTLIER) cc_final: -0.4470 (m90) REVERT: A 917 TYR cc_start: 0.8882 (m-10) cc_final: 0.8653 (m-80) REVERT: A 988 GLU cc_start: 0.8650 (tp30) cc_final: 0.8249 (tp30) REVERT: B 134 GLN cc_start: 0.6714 (OUTLIER) cc_final: 0.6434 (tm-30) REVERT: B 200 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.7340 (t80) REVERT: B 369 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7491 (t80) REVERT: B 402 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.7899 (pp) REVERT: B 495 TYR cc_start: 0.7315 (OUTLIER) cc_final: 0.6019 (t80) REVERT: B 505 HIS cc_start: -0.1702 (OUTLIER) cc_final: -0.3317 (m90) REVERT: B 552 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8486 (mt) REVERT: B 867 ASP cc_start: 0.8628 (t0) cc_final: 0.8334 (t0) REVERT: B 988 GLU cc_start: 0.8823 (tp30) cc_final: 0.8562 (tp30) REVERT: C 66 HIS cc_start: 0.8467 (OUTLIER) cc_final: 0.7043 (m-70) REVERT: C 127 PHE cc_start: 0.6650 (t80) cc_final: 0.6434 (t80) REVERT: C 200 TYR cc_start: 0.7553 (OUTLIER) cc_final: 0.6722 (m-80) REVERT: C 334 ASN cc_start: 0.6714 (OUTLIER) cc_final: 0.6365 (p0) REVERT: C 402 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8183 (pp) REVERT: C 421 TYR cc_start: 0.8749 (m-10) cc_final: 0.8435 (m-10) REVERT: C 424 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7480 (tptm) REVERT: C 495 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.6155 (t80) REVERT: C 505 HIS cc_start: -0.2130 (OUTLIER) cc_final: -0.3518 (m90) REVERT: C 552 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8394 (mt) REVERT: C 578 ASP cc_start: 0.8204 (t70) cc_final: 0.7437 (t70) REVERT: C 994 ASP cc_start: 0.8448 (t70) cc_final: 0.8147 (t0) outliers start: 137 outliers final: 81 residues processed: 337 average time/residue: 0.3348 time to fit residues: 185.8926 Evaluate side-chains 291 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 191 time to evaluate : 2.728 ------------------------------------------------------------------------------- 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 134 GLN 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 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 581 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 697 MET 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 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 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 595 VAL 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 714 ILE 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 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 286 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 334 ASN Chi-restraints excluded: chain C residue 343 ASN 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 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 973 ILE 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: 3.9990 chunk 222 optimal weight: 0.2980 chunk 2 optimal weight: 4.9990 chunk 278 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 chunk 239 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 287 optimal weight: 7.9990 chunk 186 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 556 ASN B 628 GLN C 334 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.129011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.098276 restraints weight = 45848.242| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.27 r_work: 0.3284 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 26523 Z= 0.145 Angle : 0.682 14.744 36231 Z= 0.336 Chirality : 0.050 0.641 4254 Planarity : 0.004 0.039 4557 Dihedral : 8.322 91.226 4787 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.90 % Favored : 93.00 % Rotamer: Outliers : 4.61 % Allowed : 20.14 % Favored : 75.24 % 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: -1.66 (0.15), residues: 3159 helix: 0.71 (0.21), residues: 690 sheet: -0.99 (0.20), residues: 618 loop : -1.93 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 452 HIS 0.003 0.001 HIS B 339 PHE 0.021 0.001 PHE B 43 TYR 0.025 0.001 TYR B 501 ARG 0.007 0.000 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00610 ( 48) link_NAG-ASN : angle 3.42458 ( 144) link_BETA1-4 : bond 0.00443 ( 18) link_BETA1-4 : angle 2.49837 ( 54) hydrogen bonds : bond 0.03925 ( 848) hydrogen bonds : angle 5.76081 ( 2280) SS BOND : bond 0.00401 ( 39) SS BOND : angle 2.25371 ( 78) covalent geometry : bond 0.00339 (26418) covalent geometry : angle 0.63387 (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 357 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 229 time to evaluate : 2.637 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 53 ASP cc_start: 0.8016 (t0) cc_final: 0.7793 (t0) REVERT: A 200 TYR cc_start: 0.7634 (OUTLIER) cc_final: 0.7032 (m-80) REVERT: A 324 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7475 (tm-30) REVERT: A 366 SER cc_start: 0.8426 (m) cc_final: 0.8112 (p) REVERT: A 369 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.7043 (t80) REVERT: A 495 TYR cc_start: 0.7316 (OUTLIER) cc_final: 0.6076 (t80) REVERT: A 505 HIS cc_start: -0.2599 (OUTLIER) cc_final: -0.4750 (m90) REVERT: A 858 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7292 (mt) REVERT: A 988 GLU cc_start: 0.8570 (tp30) cc_final: 0.8221 (tp30) REVERT: B 200 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.7405 (t80) REVERT: B 369 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.7439 (t80) REVERT: B 402 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.7741 (pp) REVERT: B 495 TYR cc_start: 0.7339 (OUTLIER) cc_final: 0.5896 (t80) REVERT: B 552 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8443 (mt) REVERT: B 823 PHE cc_start: 0.7878 (m-80) cc_final: 0.7420 (m-10) REVERT: B 867 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8294 (t0) REVERT: B 988 GLU cc_start: 0.8829 (tp30) cc_final: 0.8595 (tp30) REVERT: B 994 ASP cc_start: 0.8600 (t70) cc_final: 0.8327 (t0) REVERT: C 66 HIS cc_start: 0.8392 (OUTLIER) cc_final: 0.6885 (m-70) REVERT: C 200 TYR cc_start: 0.7388 (OUTLIER) cc_final: 0.7155 (t80) REVERT: C 346 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7552 (tpt170) REVERT: C 402 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8204 (pp) REVERT: C 421 TYR cc_start: 0.8709 (m-80) cc_final: 0.8305 (m-10) REVERT: C 424 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7435 (tptm) REVERT: C 495 TYR cc_start: 0.7442 (OUTLIER) cc_final: 0.6250 (t80) REVERT: C 505 HIS cc_start: -0.2078 (OUTLIER) cc_final: -0.3462 (m90) REVERT: C 552 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8402 (mt) REVERT: C 578 ASP cc_start: 0.8191 (t70) cc_final: 0.7723 (t70) REVERT: C 994 ASP cc_start: 0.8323 (t70) cc_final: 0.7992 (t0) outliers start: 128 outliers final: 69 residues processed: 331 average time/residue: 0.3382 time to fit residues: 184.6293 Evaluate side-chains 291 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 202 time to evaluate : 2.848 ------------------------------------------------------------------------------- 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 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 581 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 624 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 858 LEU 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 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 134 GLN 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 620 VAL 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 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 947 LYS 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 134 GLN Chi-restraints excluded: chain C residue 200 TYR 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 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 878 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1039 ARG 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: 4.9990 chunk 134 optimal weight: 8.9990 chunk 232 optimal weight: 3.9990 chunk 237 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 21 optimal weight: 0.0980 chunk 262 optimal weight: 7.9990 chunk 233 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 556 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN C 556 ASN C1054 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.130799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.100107 restraints weight = 46156.183| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.31 r_work: 0.3301 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2559 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= 0.127 Angle : 0.666 14.558 36231 Z= 0.326 Chirality : 0.049 0.634 4254 Planarity : 0.004 0.040 4557 Dihedral : 7.953 88.793 4786 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.58 % Favored : 93.32 % Rotamer: Outliers : 4.43 % Allowed : 21.19 % Favored : 74.38 % 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: 0.88 (0.21), residues: 690 sheet: -1.03 (0.21), residues: 624 loop : -1.83 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 452 HIS 0.003 0.000 HIS B 49 PHE 0.021 0.001 PHE B 43 TYR 0.028 0.001 TYR B 501 ARG 0.006 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00593 ( 48) link_NAG-ASN : angle 3.38090 ( 144) link_BETA1-4 : bond 0.00423 ( 18) link_BETA1-4 : angle 2.28593 ( 54) hydrogen bonds : bond 0.03720 ( 848) hydrogen bonds : angle 5.60280 ( 2280) SS BOND : bond 0.00453 ( 39) SS BOND : angle 1.91466 ( 78) covalent geometry : bond 0.00290 (26418) covalent geometry : angle 0.62102 (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 358 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 235 time to evaluate : 3.017 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: 0.8035 (t0) cc_final: 0.7806 (t0) REVERT: A 131 CYS cc_start: 0.4138 (t) cc_final: 0.3617 (t) REVERT: A 134 GLN cc_start: 0.6889 (tm-30) cc_final: 0.6583 (tm-30) REVERT: A 160 TYR cc_start: 0.6146 (p90) cc_final: 0.5914 (p90) REVERT: A 200 TYR cc_start: 0.7634 (OUTLIER) cc_final: 0.6926 (m-80) REVERT: A 324 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: A 366 SER cc_start: 0.8429 (m) cc_final: 0.8089 (p) REVERT: A 369 TYR cc_start: 0.7696 (OUTLIER) cc_final: 0.7022 (t80) REVERT: A 495 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.6005 (t80) REVERT: A 505 HIS cc_start: -0.2189 (OUTLIER) cc_final: -0.4489 (m90) REVERT: A 816 SER cc_start: 0.9316 (OUTLIER) cc_final: 0.8915 (m) REVERT: A 988 GLU cc_start: 0.8576 (tp30) cc_final: 0.8244 (tp30) REVERT: B 131 CYS cc_start: 0.2982 (t) cc_final: 0.2549 (t) REVERT: B 200 TYR cc_start: 0.7624 (OUTLIER) cc_final: 0.7318 (t80) REVERT: B 369 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7412 (t80) REVERT: B 383 SER cc_start: 0.8775 (t) cc_final: 0.8191 (p) REVERT: B 402 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.7732 (pp) REVERT: B 495 TYR cc_start: 0.7323 (OUTLIER) cc_final: 0.5825 (t80) REVERT: B 552 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8428 (mt) REVERT: B 823 PHE cc_start: 0.7846 (m-80) cc_final: 0.7423 (m-10) REVERT: B 867 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8315 (t0) REVERT: B 988 GLU cc_start: 0.8830 (tp30) cc_final: 0.8605 (tp30) REVERT: B 994 ASP cc_start: 0.8578 (t70) cc_final: 0.8294 (t0) REVERT: B 1050 MET cc_start: 0.8101 (mtm) cc_final: 0.7841 (mtm) REVERT: C 66 HIS cc_start: 0.8265 (OUTLIER) cc_final: 0.6681 (m-70) REVERT: C 127 PHE cc_start: 0.6245 (t80) cc_final: 0.5962 (t80) REVERT: C 131 CYS cc_start: 0.2866 (t) cc_final: 0.2523 (t) REVERT: C 346 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7492 (tpt170) REVERT: C 402 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8338 (pp) REVERT: C 421 TYR cc_start: 0.8719 (m-80) cc_final: 0.8286 (m-10) REVERT: C 424 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7438 (tptm) REVERT: C 495 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.6187 (t80) REVERT: C 505 HIS cc_start: -0.1854 (OUTLIER) cc_final: -0.3515 (m90) REVERT: C 552 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8410 (mt) REVERT: C 578 ASP cc_start: 0.8146 (t70) cc_final: 0.7675 (t70) REVERT: C 994 ASP cc_start: 0.8308 (t70) cc_final: 0.7906 (t0) REVERT: C 998 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8943 (m) outliers start: 123 outliers final: 72 residues processed: 336 average time/residue: 0.3508 time to fit residues: 198.7762 Evaluate side-chains 303 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 211 time to evaluate : 2.666 ------------------------------------------------------------------------------- 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 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 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 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 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 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 591 SER Chi-restraints excluded: chain B residue 595 VAL 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 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 66 HIS Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 208 THR 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 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 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 878 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1039 ARG 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: 3.9990 chunk 267 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 19 optimal weight: 0.0970 chunk 304 optimal weight: 0.7980 chunk 110 optimal weight: 0.0570 chunk 307 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 170 optimal weight: 0.4980 overall best weight: 0.4896 ------------------------------------------------------------------------------- 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 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 628 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.131726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.101160 restraints weight = 45761.599| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.31 r_work: 0.3330 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26523 Z= 0.118 Angle : 0.656 14.497 36231 Z= 0.319 Chirality : 0.049 0.634 4254 Planarity : 0.004 0.039 4557 Dihedral : 7.671 86.282 4786 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.74 % Favored : 93.16 % Rotamer: Outliers : 4.43 % Allowed : 21.05 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.15), residues: 3159 helix: 0.97 (0.21), residues: 690 sheet: -0.93 (0.21), residues: 612 loop : -1.78 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 452 HIS 0.003 0.000 HIS B 339 PHE 0.026 0.001 PHE B 43 TYR 0.029 0.001 TYR B 501 ARG 0.004 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 48) link_NAG-ASN : angle 3.37015 ( 144) link_BETA1-4 : bond 0.00506 ( 18) link_BETA1-4 : angle 2.15728 ( 54) hydrogen bonds : bond 0.03592 ( 848) hydrogen bonds : angle 5.48747 ( 2280) SS BOND : bond 0.00344 ( 39) SS BOND : angle 1.81920 ( 78) covalent geometry : bond 0.00271 (26418) covalent geometry : angle 0.61127 (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: 123 poor density : 237 time to evaluate : 2.913 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 134 GLN cc_start: 0.6734 (tm-30) cc_final: 0.6486 (tm-30) REVERT: A 200 TYR cc_start: 0.7594 (OUTLIER) cc_final: 0.6861 (m-80) REVERT: A 324 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7589 (tm-30) REVERT: A 369 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.6897 (t80) REVERT: A 495 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.6003 (t80) REVERT: A 505 HIS cc_start: -0.2017 (OUTLIER) cc_final: -0.4349 (m90) REVERT: A 816 SER cc_start: 0.9308 (OUTLIER) cc_final: 0.8906 (m) REVERT: A 988 GLU cc_start: 0.8593 (tp30) cc_final: 0.8353 (tp30) REVERT: B 40 ASP cc_start: 0.8366 (m-30) cc_final: 0.8144 (m-30) REVERT: B 131 CYS cc_start: 0.2480 (t) cc_final: 0.2067 (t) REVERT: B 200 TYR cc_start: 0.7573 (OUTLIER) cc_final: 0.7238 (t80) REVERT: B 367 VAL cc_start: 0.9071 (m) cc_final: 0.8793 (p) REVERT: B 369 TYR cc_start: 0.7919 (OUTLIER) cc_final: 0.7438 (t80) REVERT: B 383 SER cc_start: 0.8751 (t) cc_final: 0.8173 (p) REVERT: B 402 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.7678 (pp) REVERT: B 495 TYR cc_start: 0.7316 (OUTLIER) cc_final: 0.5666 (t80) REVERT: B 552 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8202 (mt) REVERT: B 823 PHE cc_start: 0.7871 (m-80) cc_final: 0.7484 (m-10) REVERT: B 867 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8259 (t0) REVERT: B 994 ASP cc_start: 0.8554 (t70) cc_final: 0.8197 (t0) REVERT: B 998 THR cc_start: 0.9433 (OUTLIER) cc_final: 0.9155 (m) REVERT: B 1019 ARG cc_start: 0.8270 (tpt170) cc_final: 0.7920 (tpp-160) REVERT: C 66 HIS cc_start: 0.8180 (OUTLIER) cc_final: 0.6599 (m-70) REVERT: C 131 CYS cc_start: 0.2949 (t) cc_final: 0.2469 (t) REVERT: C 421 TYR cc_start: 0.8747 (m-80) cc_final: 0.8255 (m-10) REVERT: C 424 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7445 (tptm) REVERT: C 495 TYR cc_start: 0.7471 (OUTLIER) cc_final: 0.6254 (t80) REVERT: C 505 HIS cc_start: -0.1848 (OUTLIER) cc_final: -0.3575 (m90) REVERT: C 552 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8443 (mt) REVERT: C 578 ASP cc_start: 0.8092 (t70) cc_final: 0.7604 (t70) REVERT: C 902 MET cc_start: 0.9004 (tpt) cc_final: 0.8675 (tpt) REVERT: C 994 ASP cc_start: 0.8280 (t70) cc_final: 0.7868 (t0) REVERT: C 1039 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8934 (ptm160) outliers start: 123 outliers final: 73 residues processed: 340 average time/residue: 0.3259 time to fit residues: 183.6591 Evaluate side-chains 303 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 211 time to evaluate : 2.727 ------------------------------------------------------------------------------- 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 135 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 220 PHE 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 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 642 VAL 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 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 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 PHE 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 591 SER Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 697 MET 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 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 66 HIS 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 512 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 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 878 LEU Chi-restraints excluded: chain C residue 1039 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 194 optimal weight: 3.9990 chunk 234 optimal weight: 0.0980 chunk 244 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 274 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 315 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 147 optimal weight: 8.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B1036 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.130203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.099589 restraints weight = 45947.359| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.30 r_work: 0.3310 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 26523 Z= 0.151 Angle : 0.682 14.356 36231 Z= 0.332 Chirality : 0.049 0.637 4254 Planarity : 0.004 0.052 4557 Dihedral : 7.613 85.749 4786 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.46 % Favored : 93.45 % Rotamer: Outliers : 4.04 % Allowed : 21.51 % Favored : 74.45 % 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: -1.37 (0.15), residues: 3159 helix: 0.87 (0.21), residues: 705 sheet: -0.63 (0.21), residues: 576 loop : -1.79 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP C 633 HIS 0.003 0.001 HIS B 339 PHE 0.029 0.001 PHE A 133 TYR 0.028 0.001 TYR B 501 ARG 0.004 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00574 ( 48) link_NAG-ASN : angle 3.37168 ( 144) link_BETA1-4 : bond 0.00452 ( 18) link_BETA1-4 : angle 2.10029 ( 54) hydrogen bonds : bond 0.03735 ( 848) hydrogen bonds : angle 5.40139 ( 2280) SS BOND : bond 0.00396 ( 39) SS BOND : angle 2.04832 ( 78) covalent geometry : bond 0.00356 (26418) covalent geometry : angle 0.63831 (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 332 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 220 time to evaluate : 2.899 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 134 GLN cc_start: 0.6693 (tm-30) cc_final: 0.6363 (tm-30) REVERT: A 160 TYR cc_start: 0.6074 (p90) cc_final: 0.5783 (p90) REVERT: A 200 TYR cc_start: 0.7578 (OUTLIER) cc_final: 0.6801 (m-80) REVERT: A 324 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7596 (tm-30) REVERT: A 369 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.6906 (t80) REVERT: A 402 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.7935 (pp) REVERT: A 403 LYS cc_start: 0.7191 (ttmt) cc_final: 0.6615 (mmmm) REVERT: A 495 TYR cc_start: 0.7293 (OUTLIER) cc_final: 0.5914 (t80) REVERT: A 505 HIS cc_start: -0.1882 (OUTLIER) cc_final: -0.4573 (m90) REVERT: A 816 SER cc_start: 0.9319 (OUTLIER) cc_final: 0.8920 (m) REVERT: A 988 GLU cc_start: 0.8633 (tp30) cc_final: 0.8304 (tp30) REVERT: B 40 ASP cc_start: 0.8374 (m-30) cc_final: 0.8138 (m-30) REVERT: B 200 TYR cc_start: 0.7523 (OUTLIER) cc_final: 0.7185 (t80) REVERT: B 367 VAL cc_start: 0.9055 (m) cc_final: 0.8781 (p) REVERT: B 369 TYR cc_start: 0.7867 (OUTLIER) cc_final: 0.7406 (t80) REVERT: B 383 SER cc_start: 0.8757 (t) cc_final: 0.8186 (p) REVERT: B 392 PHE cc_start: 0.8696 (m-80) cc_final: 0.8339 (m-80) REVERT: B 402 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.7755 (pp) REVERT: B 495 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.5870 (t80) REVERT: B 552 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8498 (mt) REVERT: B 587 ILE cc_start: 0.8625 (mm) cc_final: 0.8413 (mm) REVERT: B 823 PHE cc_start: 0.7887 (m-80) cc_final: 0.7458 (m-80) REVERT: B 867 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8240 (t0) REVERT: B 994 ASP cc_start: 0.8569 (t70) cc_final: 0.8126 (t0) REVERT: B 998 THR cc_start: 0.9506 (OUTLIER) cc_final: 0.9235 (m) REVERT: B 1019 ARG cc_start: 0.8410 (tpt170) cc_final: 0.7908 (tpp-160) REVERT: C 66 HIS cc_start: 0.8222 (OUTLIER) cc_final: 0.6601 (m-70) REVERT: C 127 PHE cc_start: 0.6316 (t80) cc_final: 0.6109 (t80) REVERT: C 131 CYS cc_start: 0.2686 (t) cc_final: 0.2238 (t) REVERT: C 134 GLN cc_start: 0.6861 (tm-30) cc_final: 0.6535 (tm-30) REVERT: C 200 TYR cc_start: 0.7415 (OUTLIER) cc_final: 0.6620 (m-80) REVERT: C 265 TYR cc_start: 0.8112 (t80) cc_final: 0.7485 (m-80) REVERT: C 421 TYR cc_start: 0.8794 (m-80) cc_final: 0.8292 (m-10) REVERT: C 424 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7463 (tptm) REVERT: C 495 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.6113 (t80) REVERT: C 505 HIS cc_start: -0.1727 (OUTLIER) cc_final: -0.3663 (m90) REVERT: C 552 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8484 (mt) REVERT: C 578 ASP cc_start: 0.8056 (t70) cc_final: 0.7612 (t70) REVERT: C 628 GLN cc_start: 0.8285 (pt0) cc_final: 0.8002 (pt0) REVERT: C 994 ASP cc_start: 0.8215 (t70) cc_final: 0.7792 (t0) outliers start: 112 outliers final: 69 residues processed: 312 average time/residue: 0.3385 time to fit residues: 173.8308 Evaluate side-chains 298 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 209 time to evaluate : 2.863 ------------------------------------------------------------------------------- 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 135 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 220 PHE 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 402 ILE 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 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 632 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 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 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 PHE 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 591 SER Chi-restraints excluded: chain B residue 595 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 66 HIS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 220 PHE 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 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 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 747 THR 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 878 LEU Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1122 VAL 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: 0.2980 chunk 255 optimal weight: 4.9990 chunk 170 optimal weight: 0.9980 chunk 293 optimal weight: 0.6980 chunk 168 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 221 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 228 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN C 628 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.131431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.100731 restraints weight = 45992.801| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.32 r_work: 0.3327 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26523 Z= 0.127 Angle : 0.664 14.238 36231 Z= 0.322 Chirality : 0.049 0.625 4254 Planarity : 0.004 0.038 4557 Dihedral : 7.476 83.472 4786 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.65 % Favored : 93.29 % Rotamer: Outliers : 3.39 % Allowed : 22.34 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.15), residues: 3159 helix: 0.91 (0.21), residues: 705 sheet: -0.82 (0.21), residues: 609 loop : -1.73 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP C 633 HIS 0.003 0.000 HIS B 339 PHE 0.028 0.001 PHE B 43 TYR 0.026 0.001 TYR B 501 ARG 0.008 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00555 ( 48) link_NAG-ASN : angle 3.36073 ( 144) link_BETA1-4 : bond 0.00488 ( 18) link_BETA1-4 : angle 2.04620 ( 54) hydrogen bonds : bond 0.03613 ( 848) hydrogen bonds : angle 5.33867 ( 2280) SS BOND : bond 0.00339 ( 39) SS BOND : angle 1.94727 ( 78) covalent geometry : bond 0.00297 (26418) covalent geometry : angle 0.61997 (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 321 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 227 time to evaluate : 2.713 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: 0.6920 (tm-30) cc_final: 0.6589 (tm-30) REVERT: A 160 TYR cc_start: 0.6044 (p90) cc_final: 0.5753 (p90) REVERT: A 200 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.6808 (m-80) REVERT: A 324 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: A 403 LYS cc_start: 0.7132 (ttmt) cc_final: 0.6644 (mmmm) REVERT: A 495 TYR cc_start: 0.7336 (OUTLIER) cc_final: 0.5845 (t80) REVERT: A 505 HIS cc_start: -0.1801 (OUTLIER) cc_final: -0.4485 (m90) REVERT: A 816 SER cc_start: 0.9234 (OUTLIER) cc_final: 0.8936 (m) REVERT: A 858 LEU cc_start: 0.7140 (mt) cc_final: 0.6932 (mt) REVERT: A 988 GLU cc_start: 0.8594 (tp30) cc_final: 0.8378 (tp30) REVERT: B 40 ASP cc_start: 0.8337 (m-30) cc_final: 0.8095 (m-30) REVERT: B 134 GLN cc_start: 0.6486 (tm-30) cc_final: 0.5202 (tm-30) REVERT: B 135 PHE cc_start: 0.3744 (OUTLIER) cc_final: 0.3476 (p90) REVERT: B 200 TYR cc_start: 0.7587 (OUTLIER) cc_final: 0.7256 (t80) REVERT: B 367 VAL cc_start: 0.8998 (m) cc_final: 0.8714 (p) REVERT: B 369 TYR cc_start: 0.7875 (OUTLIER) cc_final: 0.7461 (t80) REVERT: B 383 SER cc_start: 0.8829 (t) cc_final: 0.8270 (p) REVERT: B 392 PHE cc_start: 0.8672 (m-80) cc_final: 0.8321 (m-80) REVERT: B 402 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.7742 (pp) REVERT: B 495 TYR cc_start: 0.7388 (OUTLIER) cc_final: 0.5822 (t80) REVERT: B 552 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8323 (mt) REVERT: B 823 PHE cc_start: 0.7909 (m-80) cc_final: 0.7575 (m-80) REVERT: B 856 ASN cc_start: 0.7748 (m-40) cc_final: 0.7095 (m110) REVERT: B 867 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8312 (t0) REVERT: B 994 ASP cc_start: 0.8535 (t70) cc_final: 0.8086 (t0) REVERT: B 998 THR cc_start: 0.9452 (OUTLIER) cc_final: 0.9192 (m) REVERT: B 1019 ARG cc_start: 0.8361 (tpt170) cc_final: 0.7918 (tpp-160) REVERT: C 66 HIS cc_start: 0.8166 (OUTLIER) cc_final: 0.6541 (m-70) REVERT: C 127 PHE cc_start: 0.6276 (t80) cc_final: 0.6059 (t80) REVERT: C 134 GLN cc_start: 0.6705 (tm-30) cc_final: 0.6438 (tm-30) REVERT: C 265 TYR cc_start: 0.8072 (t80) cc_final: 0.7442 (m-80) REVERT: C 421 TYR cc_start: 0.8792 (m-80) cc_final: 0.8208 (m-10) REVERT: C 424 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7468 (tptm) REVERT: C 495 TYR cc_start: 0.7488 (OUTLIER) cc_final: 0.6168 (t80) REVERT: C 505 HIS cc_start: -0.1670 (OUTLIER) cc_final: -0.3656 (m90) REVERT: C 552 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8431 (mt) REVERT: C 578 ASP cc_start: 0.8085 (t70) cc_final: 0.7358 (t70) REVERT: C 628 GLN cc_start: 0.8242 (pt0) cc_final: 0.7928 (pt0) REVERT: C 994 ASP cc_start: 0.8219 (t70) cc_final: 0.7813 (t0) REVERT: C 1039 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8927 (ptm160) outliers start: 94 outliers final: 69 residues processed: 304 average time/residue: 0.3309 time to fit residues: 165.4530 Evaluate side-chains 300 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 212 time to evaluate : 2.700 ------------------------------------------------------------------------------- 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 135 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 220 PHE 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 552 LEU Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 632 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 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 135 PHE 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 552 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 699 LEU 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 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 110 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 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 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 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1039 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 151 optimal weight: 3.9990 chunk 211 optimal weight: 0.5980 chunk 302 optimal weight: 0.0070 chunk 188 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 229 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- 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 487 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.131720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.101079 restraints weight = 45722.115| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.31 r_work: 0.3328 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26523 Z= 0.127 Angle : 0.670 14.098 36231 Z= 0.324 Chirality : 0.048 0.620 4254 Planarity : 0.004 0.042 4557 Dihedral : 7.397 81.976 4786 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.55 % Favored : 93.38 % Rotamer: Outliers : 3.53 % Allowed : 22.31 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.15), residues: 3159 helix: 0.97 (0.21), residues: 705 sheet: -0.83 (0.21), residues: 612 loop : -1.71 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 633 HIS 0.003 0.000 HIS B 339 PHE 0.033 0.001 PHE A 133 TYR 0.027 0.001 TYR B 501 ARG 0.007 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00570 ( 48) link_NAG-ASN : angle 3.40264 ( 144) link_BETA1-4 : bond 0.00479 ( 18) link_BETA1-4 : angle 2.00351 ( 54) hydrogen bonds : bond 0.03574 ( 848) hydrogen bonds : angle 5.28781 ( 2280) SS BOND : bond 0.00346 ( 39) SS BOND : angle 2.00234 ( 78) covalent geometry : bond 0.00297 (26418) covalent geometry : angle 0.62575 (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 327 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 229 time to evaluate : 2.889 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 134 GLN cc_start: 0.6814 (tm-30) cc_final: 0.6527 (tm-30) REVERT: A 160 TYR cc_start: 0.6080 (p90) cc_final: 0.5763 (p90) REVERT: A 200 TYR cc_start: 0.7559 (OUTLIER) cc_final: 0.6807 (m-80) REVERT: A 324 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7733 (tm-30) REVERT: A 402 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8176 (pp) REVERT: A 505 HIS cc_start: -0.1661 (OUTLIER) cc_final: -0.3852 (m90) REVERT: B 40 ASP cc_start: 0.8349 (m-30) cc_final: 0.8103 (m-30) REVERT: B 134 GLN cc_start: 0.6554 (tm-30) cc_final: 0.6200 (tm-30) REVERT: B 200 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.7173 (t80) REVERT: B 367 VAL cc_start: 0.8979 (m) cc_final: 0.8700 (p) REVERT: B 369 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.7460 (t80) REVERT: B 383 SER cc_start: 0.8882 (t) cc_final: 0.8310 (p) REVERT: B 392 PHE cc_start: 0.8660 (m-80) cc_final: 0.8303 (m-80) REVERT: B 402 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.7772 (pp) REVERT: B 495 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.5780 (t80) REVERT: B 552 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8123 (mt) REVERT: B 823 PHE cc_start: 0.7895 (m-80) cc_final: 0.7573 (m-80) REVERT: B 856 ASN cc_start: 0.7731 (m-40) cc_final: 0.7117 (m-40) REVERT: B 867 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8276 (t0) REVERT: B 994 ASP cc_start: 0.8537 (t70) cc_final: 0.8092 (t0) REVERT: B 998 THR cc_start: 0.9447 (OUTLIER) cc_final: 0.9191 (m) REVERT: B 1019 ARG cc_start: 0.8297 (tpt170) cc_final: 0.7907 (tpp-160) REVERT: C 66 HIS cc_start: 0.8134 (OUTLIER) cc_final: 0.6514 (m-70) REVERT: C 127 PHE cc_start: 0.6323 (t80) cc_final: 0.6013 (t80) REVERT: C 129 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.6724 (ptmt) REVERT: C 134 GLN cc_start: 0.6638 (tm-30) cc_final: 0.6338 (tm-30) REVERT: C 265 TYR cc_start: 0.8076 (t80) cc_final: 0.7491 (m-80) REVERT: C 421 TYR cc_start: 0.8825 (m-80) cc_final: 0.8213 (m-10) REVERT: C 424 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7463 (tptm) REVERT: C 495 TYR cc_start: 0.7507 (OUTLIER) cc_final: 0.6096 (t80) REVERT: C 505 HIS cc_start: -0.1700 (OUTLIER) cc_final: -0.4537 (m90) REVERT: C 552 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8365 (mt) REVERT: C 578 ASP cc_start: 0.8096 (t70) cc_final: 0.7374 (t70) REVERT: C 994 ASP cc_start: 0.8202 (t70) cc_final: 0.7826 (t0) REVERT: C 1039 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8933 (ptm160) outliers start: 98 outliers final: 72 residues processed: 312 average time/residue: 0.3383 time to fit residues: 173.5629 Evaluate side-chains 299 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 209 time to evaluate : 3.061 ------------------------------------------------------------------------------- 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 135 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 220 PHE 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 402 ILE 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 617 CYS Chi-restraints excluded: chain A residue 619 GLU 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 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 90 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 135 PHE 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 552 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 699 LEU 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 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 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 135 PHE 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 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 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 752 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1039 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 102 optimal weight: 1.9990 chunk 272 optimal weight: 0.3980 chunk 203 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 182 optimal weight: 8.9990 chunk 284 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 151 optimal weight: 0.3980 chunk 286 optimal weight: 0.0070 chunk 122 optimal weight: 1.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN C 628 GLN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.132497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.101562 restraints weight = 46161.117| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.35 r_work: 0.3351 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26523 Z= 0.121 Angle : 0.672 14.034 36231 Z= 0.326 Chirality : 0.049 0.612 4254 Planarity : 0.004 0.040 4557 Dihedral : 7.294 80.509 4786 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.43 % Favored : 93.51 % Rotamer: Outliers : 3.46 % Allowed : 22.45 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.15), residues: 3159 helix: 0.99 (0.21), residues: 711 sheet: -0.74 (0.21), residues: 615 loop : -1.66 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 633 HIS 0.003 0.000 HIS B 339 PHE 0.041 0.001 PHE B 133 TYR 0.028 0.001 TYR B 501 ARG 0.007 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 48) link_NAG-ASN : angle 3.50362 ( 144) link_BETA1-4 : bond 0.00493 ( 18) link_BETA1-4 : angle 1.98535 ( 54) hydrogen bonds : bond 0.03503 ( 848) hydrogen bonds : angle 5.26276 ( 2280) SS BOND : bond 0.00406 ( 39) SS BOND : angle 2.07989 ( 78) covalent geometry : bond 0.00283 (26418) covalent geometry : angle 0.62509 (35955) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10643.46 seconds wall clock time: 186 minutes 17.23 seconds (11177.23 seconds total)