Starting phenix.real_space_refine on Sat May 24 23:25:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x4z_38056/05_2025/8x4z_38056.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x4z_38056/05_2025/8x4z_38056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x4z_38056/05_2025/8x4z_38056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x4z_38056/05_2025/8x4z_38056.map" model { file = "/net/cci-nas-00/data/ceres_data/8x4z_38056/05_2025/8x4z_38056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x4z_38056/05_2025/8x4z_38056.cif" } resolution = 3.49 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= 0.071 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 16473 2.51 5 N 4200 2.21 5 O 5052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25839 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1008} 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: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1008} 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: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1008} 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: 14.91, per 1000 atoms: 0.58 Number of scatterers: 25839 At special positions: 0 Unit cell: (144.56, 144.56, 170.56, 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 5052 8.00 N 4200 7.00 C 16473 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.04 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " BMA D 2 " " NAG E 1 " - " BMA E 2 " " NAG F 1 " - " BMA F 2 " " NAG G 1 " - " BMA G 2 " " NAG H 1 " - " BMA H 2 " " NAG I 1 " - " BMA I 2 " " NAG J 1 " - " BMA J 2 " " NAG K 1 " - " BMA K 2 " " NAG L 1 " - " BMA L 2 " " NAG M 1 " - " BMA M 2 " " NAG N 1 " - " BMA N 2 " " NAG O 1 " - " BMA O 2 " " NAG P 1 " - " BMA P 2 " " NAG Q 1 " - " BMA Q 2 " " NAG R 1 " - " BMA R 2 " " NAG S 1 " - " BMA S 2 " " NAG T 1 " - " BMA T 2 " " NAG U 1 " - " BMA U 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 61 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 234 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 234 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG D 1 " - " ASN A 354 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN B 354 " " NAG K 1 " - " ASN B 282 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN C 354 " " NAG Q 1 " - " ASN C 282 " " NAG R 1 " - " ASN C1134 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C1098 " Time building additional restraints: 7.19 Conformation dependent library (CDL) restraints added in 3.9 seconds 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5964 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 53 sheets defined 25.0% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.534A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 4.112A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 617 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 760 through 783 Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.645A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.618A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 881 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.357A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.752A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.613A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.001A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1144 removed outlier: 4.444A pdb=" N LEU A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1139 through 1144' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.050A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 618 through 627 removed outlier: 3.785A pdb=" N HIS B 625 " --> pdb=" O SER B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.623A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.702A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 868 through 881 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.333A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.729A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.121A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1144 removed outlier: 4.390A pdb=" N LEU B1143 " --> pdb=" O ASP B1139 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1139 through 1144' Processing helix chain 'C' and resid 212 through 216 removed outlier: 3.792A pdb=" N ASP C 215 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE C 216 " --> pdb=" O GLY C 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 212 through 216' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.844A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.894A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 617 through 627 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: 3.825A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.682A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE C 823 " --> pdb=" O GLU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.676A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 884 removed outlier: 3.629A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.826A 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 912 through 919 removed outlier: 4.319A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.763A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.041A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1144 removed outlier: 4.322A pdb=" N LEU C1143 " --> pdb=" O ASP C1139 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1139 through 1144' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.310A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASP A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR A 95 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.894A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 170 removed outlier: 4.903A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.663A 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: 7.151A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 326 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.561A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.501A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 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 473 through 474 removed outlier: 3.821A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.905A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 575 through 577 removed outlier: 3.638A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.375A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 713 through 715 removed outlier: 3.519A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.174A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.240A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.313A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR B 95 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC3, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.651A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 167 through 169 removed outlier: 3.529A pdb=" N THR B 167 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.116A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 326 removed outlier: 6.878A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.548A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.820A 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: 3.979A 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: 6.184A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.702A 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: 3.774A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.601A 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 722 Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 722 removed outlier: 7.168A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.388A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 787 through 788 removed outlier: 3.538A pdb=" N ILE B 788 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'B' and resid 1095 through 1097 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.285A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N THR C 95 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.483A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.672A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.682A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.121A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.986A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.599A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA C 435 " --> pdb=" O PHE C 375 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.912A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.017A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 575 through 577 removed outlier: 3.611A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.195A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 713 through 715 removed outlier: 3.507A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.595A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.348A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 867 hydrogen bonds defined for protein. 2382 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.21 Time building geometry restraints manager: 8.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8139 1.35 - 1.47: 6784 1.47 - 1.59: 11374 1.59 - 1.71: 1 1.71 - 1.83: 141 Bond restraints: 26439 Sorted by residual: bond pdb=" CG PRO B 217 " pdb=" CD PRO B 217 " ideal model delta sigma weight residual 1.503 1.269 0.234 3.40e-02 8.65e+02 4.72e+01 bond pdb=" N PRO B 217 " pdb=" CD PRO B 217 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.38e+01 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" CB PRO B 217 " pdb=" CG PRO B 217 " ideal model delta sigma weight residual 1.492 1.656 -0.164 5.00e-02 4.00e+02 1.08e+01 bond pdb=" N PRO B 217 " pdb=" CA PRO B 217 " ideal model delta sigma weight residual 1.466 1.428 0.038 1.21e-02 6.83e+03 9.89e+00 ... (remaining 26434 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.52: 35672 3.52 - 7.03: 288 7.03 - 10.55: 18 10.55 - 14.07: 3 14.07 - 17.58: 4 Bond angle restraints: 35985 Sorted by residual: angle pdb=" CA PRO B 217 " pdb=" N PRO B 217 " pdb=" CD PRO B 217 " ideal model delta sigma weight residual 112.00 94.42 17.58 1.40e+00 5.10e-01 1.58e+02 angle pdb=" N PRO B 217 " pdb=" CD PRO B 217 " pdb=" CG PRO B 217 " ideal model delta sigma weight residual 103.20 90.91 12.29 1.50e+00 4.44e-01 6.71e+01 angle pdb=" C ASN A1074 " pdb=" N PHE A1075 " pdb=" CA PHE A1075 " ideal model delta sigma weight residual 121.90 114.96 6.94 1.26e+00 6.30e-01 3.04e+01 angle pdb=" C ASN C1074 " pdb=" N PHE C1075 " pdb=" CA PHE C1075 " ideal model delta sigma weight residual 121.90 115.10 6.80 1.26e+00 6.30e-01 2.91e+01 angle pdb=" N GLN B 218 " pdb=" CA GLN B 218 " pdb=" C GLN B 218 " ideal model delta sigma weight residual 114.39 107.23 7.16 1.45e+00 4.76e-01 2.44e+01 ... (remaining 35980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.98: 14713 22.98 - 45.96: 1396 45.96 - 68.94: 198 68.94 - 91.92: 143 91.92 - 114.90: 119 Dihedral angle restraints: 16569 sinusoidal: 7284 harmonic: 9285 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 13.03 79.97 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 159.12 -66.12 1 1.00e+01 1.00e-02 5.71e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 29.34 63.66 1 1.00e+01 1.00e-02 5.34e+01 ... (remaining 16566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 4225 0.175 - 0.349: 32 0.349 - 0.524: 0 0.524 - 0.698: 0 0.698 - 0.873: 3 Chirality restraints: 4260 Sorted by residual: 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 -1.53 -0.87 2.00e-01 2.50e+01 1.91e+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 -1.54 -0.86 2.00e-01 2.50e+01 1.86e+01 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 -1.57 -0.83 2.00e-01 2.50e+01 1.74e+01 ... (remaining 4257 not shown) Planarity restraints: 4608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 216 " 0.143 5.00e-02 4.00e+02 1.94e-01 5.99e+01 pdb=" N PRO B 217 " -0.333 5.00e-02 4.00e+02 pdb=" CA PRO B 217 " 0.109 5.00e-02 4.00e+02 pdb=" CD PRO B 217 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 208 " -0.069 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO C 209 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 371 " -0.018 2.00e-02 2.50e+03 2.82e-02 1.39e+01 pdb=" CG PHE B 371 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE B 371 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 371 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 371 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 PHE B 371 " 0.028 2.00e-02 2.50e+03 pdb=" CZ PHE B 371 " -0.055 2.00e-02 2.50e+03 ... (remaining 4605 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 495 2.66 - 3.22: 24264 3.22 - 3.78: 38661 3.78 - 4.34: 52485 4.34 - 4.90: 87510 Nonbonded interactions: 203415 Sorted by model distance: nonbonded pdb=" O CYS A 590 " pdb=" OH TYR C 837 " model vdw 2.094 3.040 nonbonded pdb=" OH TYR B 837 " pdb=" O CYS C 590 " model vdw 2.123 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.154 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.162 3.040 nonbonded pdb=" OH TYR A 837 " pdb=" O CYS B 590 " model vdw 2.173 3.040 ... (remaining 203410 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 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: 0.980 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 60.920 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.160 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 0.234 26544 Z= 0.225 Angle : 0.859 17.583 36261 Z= 0.426 Chirality : 0.057 0.873 4260 Planarity : 0.006 0.194 4560 Dihedral : 21.367 114.901 10488 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.65 % Favored : 92.25 % Rotamer: Outliers : 0.50 % Allowed : 26.46 % Favored : 73.04 % 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: -1.62 (0.15), residues: 3162 helix: 0.71 (0.20), residues: 726 sheet: -0.92 (0.21), residues: 588 loop : -1.96 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP B 633 HIS 0.005 0.001 HIS B 505 PHE 0.055 0.002 PHE B 371 TYR 0.037 0.002 TYR B 170 ARG 0.006 0.001 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00622 ( 48) link_NAG-ASN : angle 3.53852 ( 144) link_BETA1-4 : bond 0.00421 ( 18) link_BETA1-4 : angle 2.15881 ( 54) hydrogen bonds : bond 0.19109 ( 863) hydrogen bonds : angle 7.88534 ( 2382) SS BOND : bond 0.00524 ( 39) SS BOND : angle 1.65900 ( 78) covalent geometry : bond 0.00496 (26439) covalent geometry : angle 0.82443 (35985) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 2.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.8209 (mtp180) cc_final: 0.7947 (mtp85) REVERT: A 904 TYR cc_start: 0.8310 (m-10) cc_final: 0.7640 (m-10) REVERT: B 173 GLN cc_start: 0.7369 (mm-40) cc_final: 0.6432 (tt0) REVERT: B 400 PHE cc_start: 0.8467 (p90) cc_final: 0.8200 (p90) REVERT: B 495 TYR cc_start: 0.4840 (t80) cc_final: 0.4581 (t80) REVERT: B 1130 ILE cc_start: 0.9052 (mm) cc_final: 0.8773 (mt) REVERT: C 127 PHE cc_start: 0.6561 (t80) cc_final: 0.6277 (t80) REVERT: C 495 TYR cc_start: 0.5331 (OUTLIER) cc_final: 0.4463 (t80) REVERT: C 677 GLN cc_start: 0.6318 (OUTLIER) cc_final: 0.5924 (pm20) REVERT: C 1130 ILE cc_start: 0.8981 (mm) cc_final: 0.8754 (mt) outliers start: 14 outliers final: 9 residues processed: 227 average time/residue: 0.3301 time to fit residues: 124.4853 Evaluate side-chains 203 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 192 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 677 GLN Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 856 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.8980 chunk 241 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 249 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 288 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 955 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 207 HIS C 360 ASN C 370 ASN C 394 ASN C 439 ASN C 613 GLN C 677 GLN C 957 GLN C1002 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.121187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.090683 restraints weight = 55110.131| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.42 r_work: 0.3261 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26544 Z= 0.142 Angle : 0.748 14.293 36261 Z= 0.351 Chirality : 0.052 0.624 4260 Planarity : 0.005 0.115 4560 Dihedral : 13.358 107.176 4791 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.96 % Favored : 92.95 % Rotamer: Outliers : 4.28 % Allowed : 23.11 % Favored : 72.61 % 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: -1.40 (0.15), residues: 3162 helix: 1.13 (0.21), residues: 708 sheet: -0.69 (0.20), residues: 627 loop : -1.95 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 353 HIS 0.003 0.001 HIS C 207 PHE 0.022 0.001 PHE B 456 TYR 0.021 0.001 TYR B1067 ARG 0.006 0.001 ARG A 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00592 ( 48) link_NAG-ASN : angle 3.41802 ( 144) link_BETA1-4 : bond 0.00421 ( 18) link_BETA1-4 : angle 3.34341 ( 54) hydrogen bonds : bond 0.04269 ( 863) hydrogen bonds : angle 5.79056 ( 2382) SS BOND : bond 0.00339 ( 39) SS BOND : angle 1.44417 ( 78) covalent geometry : bond 0.00319 (26439) covalent geometry : angle 0.70410 (35985) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 213 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: A 97 LYS cc_start: 0.5092 (OUTLIER) cc_final: 0.4408 (pttp) REVERT: A 298 GLU cc_start: 0.8593 (tt0) cc_final: 0.8388 (mm-30) REVERT: A 636 TYR cc_start: 0.7464 (t80) cc_final: 0.7153 (t80) REVERT: A 904 TYR cc_start: 0.8374 (m-10) cc_final: 0.7750 (m-10) REVERT: A 998 THR cc_start: 0.9502 (OUTLIER) cc_final: 0.9269 (m) REVERT: B 173 GLN cc_start: 0.7339 (mm-40) cc_final: 0.6390 (tt0) REVERT: B 495 TYR cc_start: 0.4805 (t80) cc_final: 0.4586 (t80) REVERT: B 558 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8431 (mmmt) REVERT: B 788 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8994 (mt) REVERT: B 979 ASP cc_start: 0.8523 (t0) cc_final: 0.8287 (t0) REVERT: B 1130 ILE cc_start: 0.9093 (mm) cc_final: 0.8840 (mt) REVERT: C 127 PHE cc_start: 0.6826 (t80) cc_final: 0.6290 (t80) REVERT: C 339 HIS cc_start: 0.7909 (t-90) cc_final: 0.7568 (t70) REVERT: C 495 TYR cc_start: 0.5586 (OUTLIER) cc_final: 0.4480 (t80) REVERT: C 523 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7728 (p) REVERT: C 1130 ILE cc_start: 0.9019 (mm) cc_final: 0.8815 (mt) outliers start: 119 outliers final: 53 residues processed: 317 average time/residue: 0.3261 time to fit residues: 172.5303 Evaluate side-chains 244 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 186 time to evaluate : 2.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 50 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 266 optimal weight: 6.9990 chunk 283 optimal weight: 0.3980 chunk 107 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 272 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 151 optimal weight: 0.1980 chunk 153 optimal weight: 0.0270 chunk 224 optimal weight: 0.7980 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 394 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 GLN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.121337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.090959 restraints weight = 55140.156| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.41 r_work: 0.3260 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26544 Z= 0.123 Angle : 0.701 14.180 36261 Z= 0.331 Chirality : 0.050 0.616 4260 Planarity : 0.004 0.077 4560 Dihedral : 10.259 101.766 4780 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.70 % Favored : 93.17 % Rotamer: Outliers : 3.74 % Allowed : 23.40 % Favored : 72.86 % 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: -1.31 (0.15), residues: 3162 helix: 1.17 (0.20), residues: 714 sheet: -0.62 (0.20), residues: 657 loop : -1.91 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 353 HIS 0.004 0.001 HIS C 207 PHE 0.027 0.001 PHE C 541 TYR 0.016 0.001 TYR B1067 ARG 0.005 0.000 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00592 ( 48) link_NAG-ASN : angle 3.32987 ( 144) link_BETA1-4 : bond 0.00390 ( 18) link_BETA1-4 : angle 3.11446 ( 54) hydrogen bonds : bond 0.04055 ( 863) hydrogen bonds : angle 5.43894 ( 2382) SS BOND : bond 0.00358 ( 39) SS BOND : angle 1.32445 ( 78) covalent geometry : bond 0.00277 (26439) covalent geometry : angle 0.65764 (35985) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 198 time to evaluate : 2.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5070 (OUTLIER) cc_final: 0.4336 (pttp) REVERT: A 374 PHE cc_start: 0.6217 (m-10) cc_final: 0.5339 (m-10) REVERT: A 904 TYR cc_start: 0.8371 (m-10) cc_final: 0.7731 (m-10) REVERT: A 998 THR cc_start: 0.9492 (OUTLIER) cc_final: 0.9253 (m) REVERT: B 173 GLN cc_start: 0.7361 (mm-40) cc_final: 0.7067 (tp40) REVERT: B 495 TYR cc_start: 0.4782 (t80) cc_final: 0.4475 (t80) REVERT: B 759 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.7594 (t80) REVERT: B 788 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.9003 (mt) REVERT: B 979 ASP cc_start: 0.8603 (t0) cc_final: 0.8296 (t0) REVERT: B 1130 ILE cc_start: 0.9144 (mm) cc_final: 0.8889 (mt) REVERT: C 127 PHE cc_start: 0.6729 (t80) cc_final: 0.6156 (t80) REVERT: C 393 THR cc_start: 0.7260 (OUTLIER) cc_final: 0.6848 (t) REVERT: C 495 TYR cc_start: 0.5472 (OUTLIER) cc_final: 0.4405 (t80) REVERT: C 523 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7577 (p) REVERT: C 759 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7434 (t80) REVERT: C 957 GLN cc_start: 0.8643 (tt0) cc_final: 0.8169 (tm-30) REVERT: C 1029 MET cc_start: 0.9237 (tpp) cc_final: 0.8912 (tpp) REVERT: C 1130 ILE cc_start: 0.9114 (mm) cc_final: 0.8891 (mt) outliers start: 104 outliers final: 51 residues processed: 288 average time/residue: 0.3235 time to fit residues: 155.3794 Evaluate side-chains 238 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 179 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 288 optimal weight: 5.9990 chunk 252 optimal weight: 0.2980 chunk 313 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 63 optimal weight: 0.0060 chunk 101 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 237 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 254 optimal weight: 10.0000 chunk 263 optimal weight: 9.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN A1071 GLN B 121 ASN B 394 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 677 GLN C1054 GLN C1071 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.119483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.088865 restraints weight = 55739.821| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.42 r_work: 0.3226 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26544 Z= 0.142 Angle : 0.684 14.164 36261 Z= 0.326 Chirality : 0.049 0.604 4260 Planarity : 0.004 0.051 4560 Dihedral : 8.293 96.094 4778 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.96 % Favored : 92.92 % Rotamer: Outliers : 5.08 % Allowed : 22.53 % Favored : 72.39 % 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: -1.24 (0.15), residues: 3162 helix: 1.21 (0.20), residues: 714 sheet: -0.54 (0.20), residues: 639 loop : -1.86 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 353 HIS 0.003 0.001 HIS C 207 PHE 0.019 0.001 PHE C 59 TYR 0.016 0.001 TYR C1067 ARG 0.005 0.000 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 48) link_NAG-ASN : angle 3.36189 ( 144) link_BETA1-4 : bond 0.00335 ( 18) link_BETA1-4 : angle 2.79331 ( 54) hydrogen bonds : bond 0.03999 ( 863) hydrogen bonds : angle 5.23512 ( 2382) SS BOND : bond 0.00332 ( 39) SS BOND : angle 1.38034 ( 78) covalent geometry : bond 0.00329 (26439) covalent geometry : angle 0.64010 (35985) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 187 time to evaluate : 2.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5157 (OUTLIER) cc_final: 0.4332 (pttp) REVERT: A 357 ARG cc_start: 0.8022 (ptm160) cc_final: 0.7685 (mtp-110) REVERT: A 495 TYR cc_start: 0.6004 (OUTLIER) cc_final: 0.5093 (t80) REVERT: A 636 TYR cc_start: 0.7436 (OUTLIER) cc_final: 0.7061 (t80) REVERT: A 759 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7658 (t80) REVERT: A 904 TYR cc_start: 0.8352 (m-10) cc_final: 0.7699 (m-10) REVERT: A 957 GLN cc_start: 0.8717 (tt0) cc_final: 0.8400 (tm-30) REVERT: A 998 THR cc_start: 0.9510 (OUTLIER) cc_final: 0.9267 (m) REVERT: A 1029 MET cc_start: 0.9217 (tpp) cc_final: 0.8605 (ttm) REVERT: B 173 GLN cc_start: 0.7356 (mm-40) cc_final: 0.7065 (tp40) REVERT: B 465 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6839 (pt0) REVERT: B 495 TYR cc_start: 0.4899 (t80) cc_final: 0.4589 (t80) REVERT: B 558 LYS cc_start: 0.8730 (mmtt) cc_final: 0.8389 (mmmt) REVERT: B 759 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7596 (t80) REVERT: B 788 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8991 (mt) REVERT: B 979 ASP cc_start: 0.8582 (t0) cc_final: 0.8311 (t0) REVERT: B 1130 ILE cc_start: 0.9244 (mm) cc_final: 0.9006 (mt) REVERT: C 127 PHE cc_start: 0.7010 (t80) cc_final: 0.6432 (t80) REVERT: C 430 THR cc_start: 0.8455 (m) cc_final: 0.8111 (p) REVERT: C 495 TYR cc_start: 0.5490 (OUTLIER) cc_final: 0.4444 (t80) REVERT: C 523 THR cc_start: 0.8013 (OUTLIER) cc_final: 0.7650 (p) REVERT: C 677 GLN cc_start: 0.6341 (pt0) cc_final: 0.6108 (pm20) REVERT: C 759 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7559 (t80) REVERT: C 957 GLN cc_start: 0.8661 (tt0) cc_final: 0.8118 (tm-30) REVERT: C 1029 MET cc_start: 0.9242 (tpp) cc_final: 0.8884 (ttm) REVERT: C 1130 ILE cc_start: 0.9182 (mm) cc_final: 0.8965 (mt) outliers start: 141 outliers final: 69 residues processed: 314 average time/residue: 0.3149 time to fit residues: 166.8873 Evaluate side-chains 250 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 170 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 223 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 220 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 305 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 211 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 chunk 307 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 306 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.116942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.086408 restraints weight = 55448.876| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.41 r_work: 0.3183 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 26544 Z= 0.172 Angle : 0.689 15.034 36261 Z= 0.332 Chirality : 0.049 0.587 4260 Planarity : 0.004 0.047 4560 Dihedral : 7.869 92.391 4778 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.27 % Favored : 92.63 % Rotamer: Outliers : 4.46 % Allowed : 23.79 % Favored : 71.74 % 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: -1.24 (0.15), residues: 3162 helix: 1.27 (0.21), residues: 708 sheet: -0.62 (0.20), residues: 657 loop : -1.85 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 353 HIS 0.004 0.001 HIS B 519 PHE 0.026 0.001 PHE A 342 TYR 0.017 0.001 TYR A 265 ARG 0.003 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 48) link_NAG-ASN : angle 3.34520 ( 144) link_BETA1-4 : bond 0.00411 ( 18) link_BETA1-4 : angle 2.36991 ( 54) hydrogen bonds : bond 0.04118 ( 863) hydrogen bonds : angle 5.15422 ( 2382) SS BOND : bond 0.00390 ( 39) SS BOND : angle 1.48949 ( 78) covalent geometry : bond 0.00405 (26439) covalent geometry : angle 0.64866 (35985) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 189 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5272 (OUTLIER) cc_final: 0.4303 (pttp) REVERT: A 237 ARG cc_start: 0.7803 (mtp180) cc_final: 0.7563 (mtp180) REVERT: A 357 ARG cc_start: 0.8085 (ptm160) cc_final: 0.7721 (mtp-110) REVERT: A 495 TYR cc_start: 0.6028 (OUTLIER) cc_final: 0.5123 (t80) REVERT: A 759 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7789 (t80) REVERT: A 904 TYR cc_start: 0.8445 (m-10) cc_final: 0.7920 (m-10) REVERT: A 957 GLN cc_start: 0.8699 (tt0) cc_final: 0.8189 (tm-30) REVERT: A 998 THR cc_start: 0.9513 (OUTLIER) cc_final: 0.9275 (m) REVERT: A 1029 MET cc_start: 0.9257 (tpp) cc_final: 0.8693 (ttm) REVERT: B 173 GLN cc_start: 0.7388 (mm-40) cc_final: 0.7083 (tp40) REVERT: B 430 THR cc_start: 0.8609 (m) cc_final: 0.8264 (p) REVERT: B 465 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6798 (pt0) REVERT: B 957 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7697 (tm-30) REVERT: B 979 ASP cc_start: 0.8630 (t0) cc_final: 0.8366 (t0) REVERT: B 981 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8686 (mp) REVERT: B 1130 ILE cc_start: 0.9325 (mm) cc_final: 0.9096 (mt) REVERT: C 127 PHE cc_start: 0.7080 (t80) cc_final: 0.6508 (t80) REVERT: C 233 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7292 (pt) REVERT: C 393 THR cc_start: 0.7051 (OUTLIER) cc_final: 0.6572 (t) REVERT: C 430 THR cc_start: 0.8450 (m) cc_final: 0.8097 (p) REVERT: C 495 TYR cc_start: 0.5559 (OUTLIER) cc_final: 0.4418 (t80) REVERT: C 523 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7877 (p) REVERT: C 759 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7763 (t80) REVERT: C 957 GLN cc_start: 0.8730 (tt0) cc_final: 0.8172 (tm-30) REVERT: C 1029 MET cc_start: 0.9275 (tpp) cc_final: 0.8942 (ttm) REVERT: C 1130 ILE cc_start: 0.9292 (mm) cc_final: 0.9062 (mt) outliers start: 124 outliers final: 79 residues processed: 304 average time/residue: 0.3341 time to fit residues: 169.1326 Evaluate side-chains 264 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 174 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 235 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 307 optimal weight: 0.0970 chunk 12 optimal weight: 0.1980 chunk 195 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 236 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 chunk 172 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.119210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.088961 restraints weight = 54994.693| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.41 r_work: 0.3234 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26544 Z= 0.108 Angle : 0.652 13.887 36261 Z= 0.312 Chirality : 0.048 0.590 4260 Planarity : 0.004 0.053 4560 Dihedral : 7.453 89.756 4776 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.45 % Favored : 93.45 % Rotamer: Outliers : 3.60 % Allowed : 24.91 % Favored : 71.49 % 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: -1.11 (0.15), residues: 3162 helix: 1.39 (0.20), residues: 711 sheet: -0.57 (0.20), residues: 660 loop : -1.78 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 353 HIS 0.002 0.000 HIS C 49 PHE 0.028 0.001 PHE A 371 TYR 0.014 0.001 TYR B1067 ARG 0.005 0.000 ARG C 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 48) link_NAG-ASN : angle 3.34666 ( 144) link_BETA1-4 : bond 0.00469 ( 18) link_BETA1-4 : angle 2.29549 ( 54) hydrogen bonds : bond 0.03671 ( 863) hydrogen bonds : angle 5.01358 ( 2382) SS BOND : bond 0.00320 ( 39) SS BOND : angle 1.12894 ( 78) covalent geometry : bond 0.00241 (26439) covalent geometry : angle 0.61093 (35985) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 192 time to evaluate : 2.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5034 (OUTLIER) cc_final: 0.4006 (pttp) REVERT: A 127 PHE cc_start: 0.6482 (t80) cc_final: 0.5983 (t80) REVERT: A 237 ARG cc_start: 0.7814 (mtp180) cc_final: 0.7557 (mtp180) REVERT: A 357 ARG cc_start: 0.8087 (ptm160) cc_final: 0.7448 (ptm160) REVERT: A 495 TYR cc_start: 0.6183 (OUTLIER) cc_final: 0.5178 (t80) REVERT: A 532 ASN cc_start: 0.8301 (t0) cc_final: 0.8035 (t0) REVERT: A 636 TYR cc_start: 0.7454 (OUTLIER) cc_final: 0.7109 (t80) REVERT: A 904 TYR cc_start: 0.8309 (m-10) cc_final: 0.7786 (m-10) REVERT: A 957 GLN cc_start: 0.8680 (tt0) cc_final: 0.8176 (tm-30) REVERT: A 998 THR cc_start: 0.9479 (OUTLIER) cc_final: 0.9232 (m) REVERT: A 1029 MET cc_start: 0.9192 (tpp) cc_final: 0.8736 (ttm) REVERT: B 127 PHE cc_start: 0.6970 (OUTLIER) cc_final: 0.6544 (m-80) REVERT: B 173 GLN cc_start: 0.7358 (mm-40) cc_final: 0.7075 (tp40) REVERT: B 188 ASN cc_start: 0.7343 (OUTLIER) cc_final: 0.5629 (p0) REVERT: B 237 ARG cc_start: 0.8332 (mtp85) cc_final: 0.8074 (mtp85) REVERT: B 430 THR cc_start: 0.8286 (m) cc_final: 0.7906 (p) REVERT: B 558 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8403 (mmmt) REVERT: B 957 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7616 (tm-30) REVERT: B 979 ASP cc_start: 0.8616 (t0) cc_final: 0.8336 (t0) REVERT: B 1130 ILE cc_start: 0.9313 (mm) cc_final: 0.9092 (mt) REVERT: C 127 PHE cc_start: 0.6997 (t80) cc_final: 0.6442 (t80) REVERT: C 160 TYR cc_start: 0.7035 (p90) cc_final: 0.6802 (p90) REVERT: C 233 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7217 (pt) REVERT: C 393 THR cc_start: 0.6761 (OUTLIER) cc_final: 0.6397 (t) REVERT: C 430 THR cc_start: 0.8209 (m) cc_final: 0.7735 (p) REVERT: C 495 TYR cc_start: 0.5542 (OUTLIER) cc_final: 0.4429 (t80) REVERT: C 523 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7831 (p) REVERT: C 759 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7577 (t80) REVERT: C 957 GLN cc_start: 0.8688 (tt0) cc_final: 0.8168 (tm-30) REVERT: C 1029 MET cc_start: 0.9222 (tpp) cc_final: 0.8930 (ttm) REVERT: C 1130 ILE cc_start: 0.9255 (mm) cc_final: 0.9037 (mt) outliers start: 100 outliers final: 53 residues processed: 275 average time/residue: 0.3314 time to fit residues: 150.6796 Evaluate side-chains 238 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 174 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 136 optimal weight: 9.9990 chunk 19 optimal weight: 0.0670 chunk 172 optimal weight: 0.7980 chunk 222 optimal weight: 0.0980 chunk 75 optimal weight: 30.0000 chunk 193 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 285 optimal weight: 6.9990 chunk 240 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.119614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.089438 restraints weight = 55465.436| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.42 r_work: 0.3239 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 26544 Z= 0.106 Angle : 0.645 15.592 36261 Z= 0.308 Chirality : 0.048 0.584 4260 Planarity : 0.004 0.049 4560 Dihedral : 7.234 87.449 4776 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.36 % Favored : 93.55 % Rotamer: Outliers : 3.60 % Allowed : 25.20 % Favored : 71.20 % 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: -0.97 (0.15), residues: 3162 helix: 1.55 (0.20), residues: 708 sheet: -0.51 (0.20), residues: 660 loop : -1.68 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 353 HIS 0.002 0.000 HIS B1048 PHE 0.020 0.001 PHE A 456 TYR 0.014 0.001 TYR A 265 ARG 0.004 0.000 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00500 ( 48) link_NAG-ASN : angle 3.29082 ( 144) link_BETA1-4 : bond 0.00431 ( 18) link_BETA1-4 : angle 2.07813 ( 54) hydrogen bonds : bond 0.03529 ( 863) hydrogen bonds : angle 4.87329 ( 2382) SS BOND : bond 0.00328 ( 39) SS BOND : angle 1.06261 ( 78) covalent geometry : bond 0.00240 (26439) covalent geometry : angle 0.60610 (35985) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 187 time to evaluate : 2.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.6480 (t80) cc_final: 0.5986 (t80) REVERT: A 237 ARG cc_start: 0.7779 (mtp180) cc_final: 0.7543 (mtp85) REVERT: A 357 ARG cc_start: 0.8098 (ptm160) cc_final: 0.7887 (ttp-110) REVERT: A 495 TYR cc_start: 0.6210 (OUTLIER) cc_final: 0.5216 (t80) REVERT: A 532 ASN cc_start: 0.8308 (t0) cc_final: 0.8047 (t0) REVERT: A 636 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.7235 (t80) REVERT: A 904 TYR cc_start: 0.8349 (m-10) cc_final: 0.7805 (m-10) REVERT: A 957 GLN cc_start: 0.8656 (tt0) cc_final: 0.8148 (tm-30) REVERT: A 998 THR cc_start: 0.9460 (OUTLIER) cc_final: 0.9207 (m) REVERT: A 1029 MET cc_start: 0.9208 (tpp) cc_final: 0.8785 (ttm) REVERT: B 127 PHE cc_start: 0.6901 (OUTLIER) cc_final: 0.6452 (m-80) REVERT: B 173 GLN cc_start: 0.7321 (mm-40) cc_final: 0.7062 (tp40) REVERT: B 188 ASN cc_start: 0.7232 (OUTLIER) cc_final: 0.5663 (p0) REVERT: B 296 LEU cc_start: 0.8348 (pp) cc_final: 0.8145 (tp) REVERT: B 430 THR cc_start: 0.8122 (m) cc_final: 0.7816 (p) REVERT: B 449 TYR cc_start: 0.7841 (p90) cc_final: 0.7141 (m-80) REVERT: B 558 LYS cc_start: 0.8688 (mmtt) cc_final: 0.8367 (mmmt) REVERT: B 957 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7627 (tm-30) REVERT: B 979 ASP cc_start: 0.8596 (t0) cc_final: 0.8293 (t0) REVERT: B 981 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8739 (mp) REVERT: C 127 PHE cc_start: 0.7044 (t80) cc_final: 0.6476 (t80) REVERT: C 160 TYR cc_start: 0.7067 (p90) cc_final: 0.6735 (p90) REVERT: C 233 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7283 (pt) REVERT: C 393 THR cc_start: 0.6740 (OUTLIER) cc_final: 0.6327 (t) REVERT: C 495 TYR cc_start: 0.5533 (OUTLIER) cc_final: 0.4418 (t80) REVERT: C 523 THR cc_start: 0.8101 (OUTLIER) cc_final: 0.7818 (p) REVERT: C 759 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7559 (t80) REVERT: C 957 GLN cc_start: 0.8671 (tt0) cc_final: 0.8142 (tm-30) REVERT: C 1029 MET cc_start: 0.9223 (tpp) cc_final: 0.8952 (ttm) REVERT: C 1130 ILE cc_start: 0.9241 (mm) cc_final: 0.9034 (mt) outliers start: 100 outliers final: 62 residues processed: 274 average time/residue: 0.3268 time to fit residues: 150.5512 Evaluate side-chains 244 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 171 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 137 optimal weight: 0.9990 chunk 295 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 258 optimal weight: 8.9990 chunk 224 optimal weight: 3.9990 chunk 180 optimal weight: 0.2980 chunk 102 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 210 optimal weight: 0.2980 chunk 245 optimal weight: 0.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 613 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.119607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.089477 restraints weight = 55168.977| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.40 r_work: 0.3243 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 26544 Z= 0.108 Angle : 0.643 15.297 36261 Z= 0.307 Chirality : 0.048 0.575 4260 Planarity : 0.004 0.055 4560 Dihedral : 7.094 86.071 4776 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.36 % Favored : 93.55 % Rotamer: Outliers : 3.28 % Allowed : 25.70 % Favored : 71.02 % 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: -0.89 (0.15), residues: 3162 helix: 1.76 (0.21), residues: 687 sheet: -0.48 (0.20), residues: 660 loop : -1.64 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP C 633 HIS 0.002 0.000 HIS C 207 PHE 0.019 0.001 PHE A 456 TYR 0.013 0.001 TYR B1067 ARG 0.003 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 48) link_NAG-ASN : angle 3.23231 ( 144) link_BETA1-4 : bond 0.00429 ( 18) link_BETA1-4 : angle 2.04210 ( 54) hydrogen bonds : bond 0.03470 ( 863) hydrogen bonds : angle 4.84100 ( 2382) SS BOND : bond 0.00352 ( 39) SS BOND : angle 1.24767 ( 78) covalent geometry : bond 0.00248 (26439) covalent geometry : angle 0.60456 (35985) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 178 time to evaluate : 2.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5162 (OUTLIER) cc_final: 0.4187 (pttp) REVERT: A 127 PHE cc_start: 0.6523 (t80) cc_final: 0.6089 (t80) REVERT: A 190 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8278 (mtt-85) REVERT: A 237 ARG cc_start: 0.7755 (mtp180) cc_final: 0.7541 (mtp85) REVERT: A 338 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7712 (m-80) REVERT: A 357 ARG cc_start: 0.8094 (ptm160) cc_final: 0.7847 (ttp-110) REVERT: A 495 TYR cc_start: 0.6207 (OUTLIER) cc_final: 0.5181 (t80) REVERT: A 532 ASN cc_start: 0.8300 (t0) cc_final: 0.8033 (t0) REVERT: A 558 LYS cc_start: 0.9078 (mmmt) cc_final: 0.8737 (mmmt) REVERT: A 636 TYR cc_start: 0.7513 (OUTLIER) cc_final: 0.7249 (t80) REVERT: A 957 GLN cc_start: 0.8659 (tt0) cc_final: 0.8150 (tm-30) REVERT: A 998 THR cc_start: 0.9450 (OUTLIER) cc_final: 0.9195 (m) REVERT: A 1029 MET cc_start: 0.9199 (tpp) cc_final: 0.8769 (ttm) REVERT: B 173 GLN cc_start: 0.7286 (mm-40) cc_final: 0.7057 (tp40) REVERT: B 449 TYR cc_start: 0.7907 (p90) cc_final: 0.7200 (m-80) REVERT: B 558 LYS cc_start: 0.8697 (mmtt) cc_final: 0.8372 (mmmt) REVERT: B 900 MET cc_start: 0.9167 (mtp) cc_final: 0.8899 (mtp) REVERT: B 957 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7598 (tm-30) REVERT: B 979 ASP cc_start: 0.8589 (t0) cc_final: 0.8296 (t0) REVERT: B 981 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8737 (mp) REVERT: C 127 PHE cc_start: 0.7159 (t80) cc_final: 0.6733 (t80) REVERT: C 160 TYR cc_start: 0.6878 (p90) cc_final: 0.6616 (p90) REVERT: C 233 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.6957 (pt) REVERT: C 393 THR cc_start: 0.6722 (OUTLIER) cc_final: 0.6300 (t) REVERT: C 495 TYR cc_start: 0.5589 (OUTLIER) cc_final: 0.4498 (t80) REVERT: C 523 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7805 (p) REVERT: C 759 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7617 (t80) REVERT: C 957 GLN cc_start: 0.8655 (tt0) cc_final: 0.8131 (tm-30) REVERT: C 1029 MET cc_start: 0.9200 (tpp) cc_final: 0.8924 (ttm) REVERT: C 1130 ILE cc_start: 0.9243 (mm) cc_final: 0.9037 (mt) outliers start: 91 outliers final: 60 residues processed: 256 average time/residue: 0.3387 time to fit residues: 143.7556 Evaluate side-chains 242 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 170 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 185 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 233 optimal weight: 0.6980 chunk 264 optimal weight: 0.9980 chunk 188 optimal weight: 0.8980 chunk 192 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 180 optimal weight: 0.6980 chunk 166 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.119413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.089218 restraints weight = 55471.847| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.42 r_work: 0.3237 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26544 Z= 0.110 Angle : 0.642 14.712 36261 Z= 0.306 Chirality : 0.047 0.569 4260 Planarity : 0.004 0.054 4560 Dihedral : 7.010 83.627 4775 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.33 % Favored : 93.58 % Rotamer: Outliers : 3.10 % Allowed : 25.92 % Favored : 70.99 % 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: -0.84 (0.15), residues: 3162 helix: 1.86 (0.21), residues: 669 sheet: -0.48 (0.20), residues: 660 loop : -1.59 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 353 HIS 0.004 0.000 HIS C 207 PHE 0.020 0.001 PHE A 456 TYR 0.014 0.001 TYR A 265 ARG 0.005 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 48) link_NAG-ASN : angle 3.21713 ( 144) link_BETA1-4 : bond 0.00413 ( 18) link_BETA1-4 : angle 1.99895 ( 54) hydrogen bonds : bond 0.03484 ( 863) hydrogen bonds : angle 4.81553 ( 2382) SS BOND : bond 0.00389 ( 39) SS BOND : angle 1.13331 ( 78) covalent geometry : bond 0.00256 (26439) covalent geometry : angle 0.60419 (35985) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 173 time to evaluate : 3.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5179 (OUTLIER) cc_final: 0.4194 (pttp) REVERT: A 127 PHE cc_start: 0.6493 (t80) cc_final: 0.6082 (t80) REVERT: A 160 TYR cc_start: 0.6826 (p90) cc_final: 0.6610 (p90) REVERT: A 237 ARG cc_start: 0.7780 (mtp180) cc_final: 0.7556 (mtp85) REVERT: A 338 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7739 (m-80) REVERT: A 495 TYR cc_start: 0.6190 (OUTLIER) cc_final: 0.5149 (t80) REVERT: A 558 LYS cc_start: 0.9008 (mmmt) cc_final: 0.8710 (mmmt) REVERT: A 636 TYR cc_start: 0.7486 (OUTLIER) cc_final: 0.7222 (t80) REVERT: A 957 GLN cc_start: 0.8661 (tt0) cc_final: 0.8157 (tm-30) REVERT: A 998 THR cc_start: 0.9444 (OUTLIER) cc_final: 0.9190 (m) REVERT: A 1029 MET cc_start: 0.9205 (tpp) cc_final: 0.8767 (ttm) REVERT: B 173 GLN cc_start: 0.7304 (mm-40) cc_final: 0.7070 (tp40) REVERT: B 449 TYR cc_start: 0.7922 (p90) cc_final: 0.7219 (m-80) REVERT: B 558 LYS cc_start: 0.8707 (mmtt) cc_final: 0.8383 (mmmt) REVERT: B 900 MET cc_start: 0.9186 (mtp) cc_final: 0.8892 (mtp) REVERT: B 957 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7660 (tm-30) REVERT: B 981 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8749 (mp) REVERT: C 127 PHE cc_start: 0.7179 (t80) cc_final: 0.6763 (t80) REVERT: C 160 TYR cc_start: 0.6863 (p90) cc_final: 0.6590 (p90) REVERT: C 346 ARG cc_start: 0.8685 (ttm110) cc_final: 0.8371 (tpt170) REVERT: C 393 THR cc_start: 0.6740 (OUTLIER) cc_final: 0.6247 (t) REVERT: C 495 TYR cc_start: 0.5613 (OUTLIER) cc_final: 0.4527 (t80) REVERT: C 523 THR cc_start: 0.8083 (OUTLIER) cc_final: 0.7788 (p) REVERT: C 759 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7615 (t80) REVERT: C 850 ILE cc_start: 0.4270 (OUTLIER) cc_final: 0.3542 (mm) REVERT: C 957 GLN cc_start: 0.8671 (tt0) cc_final: 0.8170 (tm-30) REVERT: C 1029 MET cc_start: 0.9210 (tpp) cc_final: 0.8925 (ttm) outliers start: 86 outliers final: 65 residues processed: 246 average time/residue: 0.3472 time to fit residues: 142.8974 Evaluate side-chains 248 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 172 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 156 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 181 optimal weight: 9.9990 chunk 289 optimal weight: 0.9990 chunk 286 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 143 optimal weight: 10.0000 chunk 225 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.117919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.087759 restraints weight = 55260.611| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.39 r_work: 0.3213 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26544 Z= 0.127 Angle : 0.652 14.863 36261 Z= 0.312 Chirality : 0.047 0.559 4260 Planarity : 0.004 0.059 4560 Dihedral : 7.010 83.290 4775 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 2.99 % Allowed : 26.21 % Favored : 70.81 % 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: -0.88 (0.15), residues: 3162 helix: 1.66 (0.21), residues: 690 sheet: -0.53 (0.20), residues: 660 loop : -1.56 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 353 HIS 0.005 0.001 HIS C 954 PHE 0.026 0.001 PHE B 456 TYR 0.015 0.001 TYR A 265 ARG 0.006 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 48) link_NAG-ASN : angle 3.22616 ( 144) link_BETA1-4 : bond 0.00360 ( 18) link_BETA1-4 : angle 1.94800 ( 54) hydrogen bonds : bond 0.03658 ( 863) hydrogen bonds : angle 4.82836 ( 2382) SS BOND : bond 0.00364 ( 39) SS BOND : angle 1.24058 ( 78) covalent geometry : bond 0.00300 (26439) covalent geometry : angle 0.61470 (35985) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 175 time to evaluate : 3.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.5299 (OUTLIER) cc_final: 0.4196 (pttp) REVERT: A 127 PHE cc_start: 0.6678 (t80) cc_final: 0.6452 (t80) REVERT: A 218 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.8035 (pm20) REVERT: A 237 ARG cc_start: 0.7823 (mtp180) cc_final: 0.7523 (mtp180) REVERT: A 338 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.7747 (m-80) REVERT: A 346 ARG cc_start: 0.8383 (ttp-110) cc_final: 0.8067 (tpt170) REVERT: A 495 TYR cc_start: 0.6176 (OUTLIER) cc_final: 0.5173 (t80) REVERT: A 558 LYS cc_start: 0.8962 (mmmt) cc_final: 0.8697 (mmmt) REVERT: A 904 TYR cc_start: 0.8409 (m-10) cc_final: 0.7866 (m-10) REVERT: A 957 GLN cc_start: 0.8668 (tt0) cc_final: 0.8163 (tm-30) REVERT: A 998 THR cc_start: 0.9458 (OUTLIER) cc_final: 0.9208 (m) REVERT: A 1029 MET cc_start: 0.9222 (tpp) cc_final: 0.8765 (ttm) REVERT: B 173 GLN cc_start: 0.7477 (mm-40) cc_final: 0.7205 (tp40) REVERT: B 383 SER cc_start: 0.8840 (t) cc_final: 0.8591 (p) REVERT: B 449 TYR cc_start: 0.7867 (p90) cc_final: 0.7277 (m-80) REVERT: B 900 MET cc_start: 0.9164 (mtp) cc_final: 0.8932 (mtp) REVERT: B 957 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7640 (tm-30) REVERT: B 981 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8868 (mp) REVERT: C 119 ILE cc_start: 0.8910 (mt) cc_final: 0.8665 (tt) REVERT: C 127 PHE cc_start: 0.7324 (t80) cc_final: 0.6931 (t80) REVERT: C 160 TYR cc_start: 0.6963 (p90) cc_final: 0.6695 (p90) REVERT: C 346 ARG cc_start: 0.8646 (ttm110) cc_final: 0.8299 (tpt170) REVERT: C 393 THR cc_start: 0.6898 (OUTLIER) cc_final: 0.6437 (t) REVERT: C 495 TYR cc_start: 0.5806 (OUTLIER) cc_final: 0.4670 (t80) REVERT: C 523 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7852 (p) REVERT: C 759 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7714 (t80) REVERT: C 850 ILE cc_start: 0.4272 (OUTLIER) cc_final: 0.3554 (mm) REVERT: C 957 GLN cc_start: 0.8549 (tt0) cc_final: 0.8163 (tm-30) REVERT: C 1029 MET cc_start: 0.9240 (tpp) cc_final: 0.8927 (ttm) outliers start: 83 outliers final: 64 residues processed: 249 average time/residue: 0.3340 time to fit residues: 137.2468 Evaluate side-chains 245 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 170 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 157 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 258 optimal weight: 0.0670 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 288 optimal weight: 10.0000 chunk 301 optimal weight: 7.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN C 339 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.118053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.087944 restraints weight = 55073.236| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.39 r_work: 0.3217 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26544 Z= 0.117 Angle : 0.646 14.274 36261 Z= 0.308 Chirality : 0.048 0.554 4260 Planarity : 0.004 0.054 4560 Dihedral : 6.950 82.616 4775 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.42 % Favored : 93.45 % Rotamer: Outliers : 2.99 % Allowed : 26.10 % Favored : 70.91 % 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: -0.86 (0.15), residues: 3162 helix: 1.67 (0.21), residues: 690 sheet: -0.51 (0.20), residues: 660 loop : -1.55 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 353 HIS 0.003 0.000 HIS C 207 PHE 0.020 0.001 PHE B 456 TYR 0.014 0.001 TYR A 265 ARG 0.003 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00473 ( 48) link_NAG-ASN : angle 3.20787 ( 144) link_BETA1-4 : bond 0.00399 ( 18) link_BETA1-4 : angle 1.93713 ( 54) hydrogen bonds : bond 0.03570 ( 863) hydrogen bonds : angle 4.83076 ( 2382) SS BOND : bond 0.00340 ( 39) SS BOND : angle 1.12756 ( 78) covalent geometry : bond 0.00278 (26439) covalent geometry : angle 0.60868 (35985) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10223.18 seconds wall clock time: 178 minutes 57.14 seconds (10737.14 seconds total)