Starting phenix.real_space_refine on Sat May 24 21:24:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x55_38063/05_2025/8x55_38063.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x55_38063/05_2025/8x55_38063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x55_38063/05_2025/8x55_38063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x55_38063/05_2025/8x55_38063.map" model { file = "/net/cci-nas-00/data/ceres_data/8x55_38063/05_2025/8x55_38063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x55_38063/05_2025/8x55_38063.cif" } resolution = 3.75 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= 0.003 sd= 0.063 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 16422 2.51 5 N 4197 2.21 5 O 5016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25749 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8318 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 8318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8318 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 8318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8318 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 16.44, per 1000 atoms: 0.64 Number of scatterers: 25749 At special positions: 0 Unit cell: (146.64, 140.4, 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 5016 8.00 N 4197 7.00 C 16422 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=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 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=2.05 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=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " BMA D 2 " " NAG E 1 " - " BMA E 2 " " NAG F 1 " - " BMA F 2 " " NAG G 1 " - " BMA G 2 " " NAG H 1 " - " BMA H 2 " " NAG I 1 " - " BMA I 2 " " NAG J 1 " - " BMA J 2 " " NAG K 1 " - " BMA K 2 " " NAG L 1 " - " BMA L 2 " " NAG M 1 " - " BMA M 2 " " NAG N 1 " - " BMA N 2 " " NAG O 1 " - " BMA O 2 " " NAG P 1 " - " BMA P 2 " " NAG Q 1 " - " BMA Q 2 " " NAG R 1 " - " BMA R 2 " NAG-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 282 " " NAG E 1 " - " ASN A1134 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN B 282 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN C 282 " " NAG O 1 " - " ASN C1134 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C1098 " Time building additional restraints: 6.15 Conformation dependent library (CDL) restraints added in 3.1 seconds 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5958 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 54 sheets defined 26.3% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.50 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 349 through 353 removed outlier: 3.713A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.804A 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 616 through 627 removed outlier: 3.692A pdb=" N VAL A 620 " --> pdb=" O ASN A 616 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 840 through 844 removed outlier: 4.350A pdb=" N ILE A 844 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 868 through 884 removed outlier: 3.577A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.271A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.646A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (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: 3.620A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.119A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1144 removed outlier: 4.589A pdb=" N LEU A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) removed outlier: 4.067A 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 349 through 353 removed outlier: 3.757A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.538A pdb=" N VAL B 407 " --> pdb=" O LYS B 403 " (cutoff:3.500A) removed outlier: 3.790A 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 502 through 506 Processing helix chain 'B' and resid 616 through 626 removed outlier: 3.583A pdb=" N VAL B 620 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.528A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 844 removed outlier: 4.195A pdb=" N ILE B 844 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 868 through 884 removed outlier: 3.508A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) 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: 4.380A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.798A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.634A 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: 5.567A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1144 removed outlier: 4.536A pdb=" N LEU B1143 " --> pdb=" O ASP B1139 " (cutoff:3.500A) removed outlier: 3.908A 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 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.826A 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: 3.738A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 616 through 626 removed outlier: 3.673A pdb=" N VAL C 620 " --> pdb=" O ASN C 616 " (cutoff:3.500A) 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 760 through 783 Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.672A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 844 removed outlier: 4.190A pdb=" N ILE C 844 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 868 through 884 removed outlier: 3.550A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.507A 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: 4.322A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.662A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 964 Processing helix chain 'C' and resid 965 through 968 Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.261A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1144 removed outlier: 4.549A pdb=" N LEU C1143 " --> pdb=" O ASP C1139 " (cutoff:3.500A) removed outlier: 4.097A 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: 7.177A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASP A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR A 95 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.650A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.625A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 7.157A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 326 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.653A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 6.650A 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: 6.873A 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: 3.962A 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: 6.831A 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 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.332A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.184A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 713 through 715 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.235A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.332A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.708A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.156A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASP B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR B 95 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC5, first strand: chain 'B' and resid 50 through 55 Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.582A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 116 through 118 removed outlier: 4.873A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.118A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 324 through 326 removed outlier: 4.041A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.542A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.750A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 451 through 454 removed outlier: 3.945A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.916A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.847A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 713 through 715 Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.612A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.428A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.701A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.204A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR C 95 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.554A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.586A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 316 removed outlier: 5.148A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.729A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.787A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.862A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.372A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 713 through 715 Processing sheet with id=AF6, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.215A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.278A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.726A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1094 through 1097 913 hydrogen bonds defined for protein. 2481 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.09 Time building geometry restraints manager: 7.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8116 1.34 - 1.47: 6730 1.47 - 1.59: 11360 1.59 - 1.72: 2 1.72 - 1.85: 141 Bond restraints: 26349 Sorted by residual: bond pdb=" CG PRO A 209 " pdb=" CD PRO A 209 " ideal model delta sigma weight residual 1.503 1.215 0.288 3.40e-02 8.65e+02 7.15e+01 bond pdb=" N PRO A 209 " pdb=" CD PRO A 209 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.99e+01 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" CB PRO A 209 " pdb=" CG PRO A 209 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.30e+00 bond pdb=" CA THR A 430 " pdb=" CB THR A 430 " ideal model delta sigma weight residual 1.526 1.567 -0.041 1.53e-02 4.27e+03 7.21e+00 ... (remaining 26344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 35570 3.63 - 7.26: 268 7.26 - 10.89: 14 10.89 - 14.52: 1 14.52 - 18.15: 3 Bond angle restraints: 35856 Sorted by residual: angle pdb=" CA PRO A 209 " pdb=" N PRO A 209 " pdb=" CD PRO A 209 " ideal model delta sigma weight residual 112.00 93.85 18.15 1.40e+00 5.10e-01 1.68e+02 angle pdb=" N PRO A 209 " pdb=" CD PRO A 209 " pdb=" CG PRO A 209 " ideal model delta sigma weight residual 103.20 88.35 14.85 1.50e+00 4.44e-01 9.81e+01 angle pdb=" C ASN B1074 " pdb=" N PHE B1075 " pdb=" CA PHE B1075 " ideal model delta sigma weight residual 122.44 115.35 7.09 1.19e+00 7.06e-01 3.55e+01 angle pdb=" C ASN C1074 " pdb=" N PHE C1075 " pdb=" CA PHE C1075 " ideal model delta sigma weight residual 122.44 115.39 7.05 1.19e+00 7.06e-01 3.51e+01 angle pdb=" CA PRO A 463 " pdb=" N PRO A 463 " pdb=" CD PRO A 463 " ideal model delta sigma weight residual 112.00 104.34 7.66 1.40e+00 5.10e-01 3.00e+01 ... (remaining 35851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.03: 14640 23.03 - 46.05: 1400 46.05 - 69.08: 178 69.08 - 92.11: 122 92.11 - 115.13: 106 Dihedral angle restraints: 16446 sinusoidal: 7170 harmonic: 9276 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual 93.00 7.99 85.01 1 1.00e+01 1.00e-02 8.77e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual 93.00 23.16 69.84 1 1.00e+01 1.00e-02 6.29e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual 93.00 25.27 67.73 1 1.00e+01 1.00e-02 5.96e+01 ... (remaining 16443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.174: 4184 0.174 - 0.349: 34 0.349 - 0.523: 0 0.523 - 0.697: 0 0.697 - 0.872: 3 Chirality restraints: 4221 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-01 2.50e+01 1.90e+01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-01 2.50e+01 1.88e+01 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-01 2.50e+01 1.88e+01 ... (remaining 4218 not shown) Planarity restraints: 4599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 208 " 0.151 5.00e-02 4.00e+02 2.05e-01 6.74e+01 pdb=" N PRO A 209 " -0.353 5.00e-02 4.00e+02 pdb=" CA PRO A 209 " 0.119 5.00e-02 4.00e+02 pdb=" CD PRO A 209 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " 0.076 5.00e-02 4.00e+02 1.10e-01 1.92e+01 pdb=" N PRO A 463 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 81 " 0.059 5.00e-02 4.00e+02 8.84e-02 1.25e+01 pdb=" N PRO A 82 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.048 5.00e-02 4.00e+02 ... (remaining 4596 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 451 2.64 - 3.21: 24084 3.21 - 3.77: 38977 3.77 - 4.34: 53693 4.34 - 4.90: 87066 Nonbonded interactions: 204271 Sorted by model distance: nonbonded pdb=" OH TYR B 837 " pdb=" O CYS C 590 " model vdw 2.075 3.040 nonbonded pdb=" O CYS A 590 " pdb=" OH TYR C 837 " model vdw 2.092 3.040 nonbonded pdb=" OH TYR A 837 " pdb=" O CYS B 590 " model vdw 2.120 3.040 nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.166 3.040 nonbonded pdb=" NE2 GLN C 804 " pdb=" OE1 GLN C 935 " model vdw 2.166 3.120 ... (remaining 204266 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' } 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 group one per residue 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: 2.160 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: 0.290 Extract box with map and model: 0.910 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 58.910 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 0.288 26448 Z= 0.214 Angle : 0.853 18.148 36114 Z= 0.430 Chirality : 0.056 0.872 4221 Planarity : 0.007 0.205 4554 Dihedral : 20.861 115.132 10371 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.38 % Favored : 92.50 % Rotamer: Outliers : 0.40 % Allowed : 27.06 % Favored : 72.54 % 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: -1.54 (0.15), residues: 3159 helix: 0.70 (0.20), residues: 690 sheet: -0.98 (0.20), residues: 696 loop : -1.80 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP B 633 HIS 0.007 0.001 HIS B 505 PHE 0.037 0.002 PHE B 135 TYR 0.022 0.001 TYR A 904 ARG 0.007 0.001 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00577 ( 45) link_NAG-ASN : angle 3.68017 ( 135) link_BETA1-4 : bond 0.00448 ( 15) link_BETA1-4 : angle 2.34911 ( 45) hydrogen bonds : bond 0.20178 ( 913) hydrogen bonds : angle 8.20371 ( 2481) SS BOND : bond 0.00554 ( 39) SS BOND : angle 2.07987 ( 78) covalent geometry : bond 0.00480 (26349) covalent geometry : angle 0.81555 (35856) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 732 THR cc_start: 0.9071 (m) cc_final: 0.8602 (p) REVERT: A 1002 GLN cc_start: 0.8361 (tt0) cc_final: 0.7990 (tt0) REVERT: B 127 PHE cc_start: 0.8200 (t80) cc_final: 0.7835 (t80) REVERT: B 699 LEU cc_start: 0.8269 (mp) cc_final: 0.7997 (mp) REVERT: C 508 TYR cc_start: 0.8148 (m-80) cc_final: 0.7624 (m-10) outliers start: 11 outliers final: 9 residues processed: 210 average time/residue: 0.3509 time to fit residues: 120.8851 Evaluate side-chains 188 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 179 time to evaluate : 2.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 346 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 chunk 82 optimal weight: 0.7980 chunk 162 optimal weight: 7.9990 chunk 128 optimal weight: 0.1980 chunk 249 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 chunk 288 optimal weight: 8.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN A 644 GLN B 774 GLN B 804 GLN B 965 GLN B1064 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.100067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.071162 restraints weight = 76421.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.073718 restraints weight = 41309.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.075422 restraints weight = 28156.071| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 26448 Z= 0.242 Angle : 0.787 14.175 36114 Z= 0.382 Chirality : 0.052 0.626 4221 Planarity : 0.006 0.116 4554 Dihedral : 14.310 108.399 4668 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.85 % Favored : 92.02 % Rotamer: Outliers : 4.61 % Allowed : 22.95 % Favored : 72.43 % 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: -1.45 (0.15), residues: 3159 helix: 0.97 (0.20), residues: 690 sheet: -0.93 (0.20), residues: 681 loop : -1.82 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 633 HIS 0.003 0.001 HIS C1064 PHE 0.040 0.002 PHE C 135 TYR 0.026 0.002 TYR B1067 ARG 0.017 0.001 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 45) link_NAG-ASN : angle 3.73806 ( 135) link_BETA1-4 : bond 0.00432 ( 15) link_BETA1-4 : angle 3.41956 ( 45) hydrogen bonds : bond 0.04933 ( 913) hydrogen bonds : angle 6.27622 ( 2481) SS BOND : bond 0.00628 ( 39) SS BOND : angle 1.65049 ( 78) covalent geometry : bond 0.00550 (26349) covalent geometry : angle 0.74255 (35856) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 186 time to evaluate : 2.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.6758 (t70) REVERT: A 402 ILE cc_start: 0.8437 (tp) cc_final: 0.8143 (tp) REVERT: A 902 MET cc_start: 0.9231 (tpp) cc_final: 0.8981 (tpp) REVERT: B 127 PHE cc_start: 0.8249 (t80) cc_final: 0.7897 (m-80) REVERT: B 480 CYS cc_start: -0.0591 (OUTLIER) cc_final: -0.1715 (p) REVERT: B 508 TYR cc_start: 0.8244 (m-10) cc_final: 0.7939 (m-10) REVERT: B 900 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8272 (mtm) REVERT: B 926 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8259 (mp10) REVERT: C 101 ILE cc_start: 0.9364 (mm) cc_final: 0.8946 (tp) REVERT: C 191 GLU cc_start: 0.7991 (mp0) cc_final: 0.7778 (mp0) REVERT: C 303 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8280 (pp) REVERT: C 578 ASP cc_start: 0.9181 (OUTLIER) cc_final: 0.8892 (t0) REVERT: C 633 TRP cc_start: 0.7861 (p90) cc_final: 0.7581 (p90) REVERT: C 1002 GLN cc_start: 0.8532 (tt0) cc_final: 0.8099 (tt0) outliers start: 128 outliers final: 77 residues processed: 295 average time/residue: 0.2983 time to fit residues: 151.5844 Evaluate side-chains 247 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 164 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 25 optimal weight: 6.9990 chunk 310 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 223 optimal weight: 10.0000 chunk 275 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 293 optimal weight: 0.1980 chunk 298 optimal weight: 2.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 542 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.100005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.071099 restraints weight = 76098.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.073688 restraints weight = 41116.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.075362 restraints weight = 27942.175| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26448 Z= 0.164 Angle : 0.738 18.554 36114 Z= 0.351 Chirality : 0.051 0.617 4221 Planarity : 0.005 0.084 4554 Dihedral : 10.463 106.181 4664 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.96 % Favored : 92.94 % Rotamer: Outliers : 4.72 % Allowed : 23.14 % Favored : 72.14 % 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: -1.29 (0.15), residues: 3159 helix: 1.17 (0.20), residues: 693 sheet: -0.89 (0.20), residues: 687 loop : -1.73 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 633 HIS 0.003 0.001 HIS A1064 PHE 0.026 0.001 PHE C 220 TYR 0.019 0.001 TYR A1067 ARG 0.003 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00618 ( 45) link_NAG-ASN : angle 4.03186 ( 135) link_BETA1-4 : bond 0.00313 ( 15) link_BETA1-4 : angle 3.23218 ( 45) hydrogen bonds : bond 0.04286 ( 913) hydrogen bonds : angle 5.82309 ( 2481) SS BOND : bond 0.00583 ( 39) SS BOND : angle 1.56777 ( 78) covalent geometry : bond 0.00376 (26349) covalent geometry : angle 0.68426 (35856) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 188 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.6758 (mm-40) cc_final: 0.6549 (tm-30) REVERT: A 389 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.6744 (t70) REVERT: A 402 ILE cc_start: 0.8414 (tp) cc_final: 0.8000 (tp) REVERT: A 902 MET cc_start: 0.9184 (tpp) cc_final: 0.8952 (tpp) REVERT: B 127 PHE cc_start: 0.8315 (t80) cc_final: 0.8058 (m-80) REVERT: B 480 CYS cc_start: -0.0619 (OUTLIER) cc_final: -0.1684 (p) REVERT: B 508 TYR cc_start: 0.8472 (m-10) cc_final: 0.8130 (m-10) REVERT: B 926 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8238 (mp10) REVERT: B 1041 ASP cc_start: 0.6543 (t70) cc_final: 0.6316 (t0) REVERT: C 101 ILE cc_start: 0.9315 (mm) cc_final: 0.9059 (tp) REVERT: C 191 GLU cc_start: 0.8014 (mp0) cc_final: 0.7489 (mp0) REVERT: C 264 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.6728 (p0) REVERT: C 699 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7503 (mp) REVERT: C 779 GLN cc_start: 0.8831 (tp40) cc_final: 0.8469 (tm-30) REVERT: C 1002 GLN cc_start: 0.8490 (tt0) cc_final: 0.8054 (tt0) outliers start: 131 outliers final: 72 residues processed: 292 average time/residue: 0.3059 time to fit residues: 152.4964 Evaluate side-chains 244 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 167 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 1122 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 2 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 138 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 116 optimal weight: 0.0980 chunk 174 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 227 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN A1071 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.100683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.072026 restraints weight = 76611.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.074686 restraints weight = 40742.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.076448 restraints weight = 27352.195| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26448 Z= 0.127 Angle : 0.696 17.343 36114 Z= 0.332 Chirality : 0.049 0.588 4221 Planarity : 0.004 0.065 4554 Dihedral : 8.588 100.423 4659 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.19 % Favored : 92.72 % Rotamer: Outliers : 5.01 % Allowed : 22.85 % Favored : 72.14 % 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: -1.22 (0.15), residues: 3159 helix: 1.33 (0.20), residues: 693 sheet: -0.93 (0.19), residues: 693 loop : -1.69 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 633 HIS 0.002 0.000 HIS C 339 PHE 0.020 0.001 PHE C 220 TYR 0.017 0.001 TYR A1067 ARG 0.006 0.000 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00586 ( 45) link_NAG-ASN : angle 4.06846 ( 135) link_BETA1-4 : bond 0.00366 ( 15) link_BETA1-4 : angle 3.05719 ( 45) hydrogen bonds : bond 0.03894 ( 913) hydrogen bonds : angle 5.53686 ( 2481) SS BOND : bond 0.00609 ( 39) SS BOND : angle 1.66928 ( 78) covalent geometry : bond 0.00287 (26349) covalent geometry : angle 0.63848 (35856) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 186 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.6791 (mm-40) cc_final: 0.6575 (tm-30) REVERT: A 402 ILE cc_start: 0.8408 (tp) cc_final: 0.7922 (tp) REVERT: A 902 MET cc_start: 0.9181 (tpp) cc_final: 0.8941 (tpp) REVERT: B 127 PHE cc_start: 0.8318 (t80) cc_final: 0.8112 (m-80) REVERT: B 480 CYS cc_start: -0.0856 (OUTLIER) cc_final: -0.1787 (p) REVERT: B 508 TYR cc_start: 0.8508 (m-10) cc_final: 0.8213 (m-10) REVERT: B 922 LEU cc_start: 0.8811 (mt) cc_final: 0.8567 (mp) REVERT: B 926 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8238 (mt0) REVERT: C 191 GLU cc_start: 0.7845 (mp0) cc_final: 0.7465 (mp0) REVERT: C 264 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.6658 (p0) REVERT: C 578 ASP cc_start: 0.9068 (OUTLIER) cc_final: 0.8666 (t70) REVERT: C 699 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7471 (mp) REVERT: C 779 GLN cc_start: 0.8790 (tp40) cc_final: 0.8501 (tm-30) REVERT: C 1002 GLN cc_start: 0.8488 (tt0) cc_final: 0.7886 (tt0) outliers start: 139 outliers final: 83 residues processed: 296 average time/residue: 0.3370 time to fit residues: 169.9203 Evaluate side-chains 255 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 167 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 195 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 252 optimal weight: 20.0000 chunk 166 optimal weight: 0.0870 chunk 153 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 chunk 242 optimal weight: 0.5980 chunk 48 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 1.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.099725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.070930 restraints weight = 76672.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.073542 restraints weight = 41275.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.075280 restraints weight = 27988.226| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26448 Z= 0.144 Angle : 0.683 16.011 36114 Z= 0.328 Chirality : 0.048 0.584 4221 Planarity : 0.004 0.066 4554 Dihedral : 7.927 97.874 4659 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.90 % Favored : 93.00 % Rotamer: Outliers : 4.61 % Allowed : 23.28 % Favored : 72.11 % 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: -1.15 (0.15), residues: 3159 helix: 1.37 (0.20), residues: 696 sheet: -0.90 (0.20), residues: 693 loop : -1.64 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 633 HIS 0.002 0.000 HIS A1064 PHE 0.024 0.001 PHE A 220 TYR 0.018 0.001 TYR A1067 ARG 0.006 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00576 ( 45) link_NAG-ASN : angle 3.88018 ( 135) link_BETA1-4 : bond 0.00219 ( 15) link_BETA1-4 : angle 2.59721 ( 45) hydrogen bonds : bond 0.03886 ( 913) hydrogen bonds : angle 5.37848 ( 2481) SS BOND : bond 0.00524 ( 39) SS BOND : angle 1.52869 ( 78) covalent geometry : bond 0.00334 (26349) covalent geometry : angle 0.63185 (35856) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 180 time to evaluate : 2.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.6869 (p0) REVERT: A 402 ILE cc_start: 0.8527 (tp) cc_final: 0.7957 (tp) REVERT: A 508 TYR cc_start: 0.8452 (m-10) cc_final: 0.8244 (m-10) REVERT: A 699 LEU cc_start: 0.8391 (mt) cc_final: 0.8166 (mp) REVERT: A 902 MET cc_start: 0.9180 (tpp) cc_final: 0.8928 (tpp) REVERT: B 127 PHE cc_start: 0.8302 (t80) cc_final: 0.8095 (m-80) REVERT: B 480 CYS cc_start: -0.0714 (OUTLIER) cc_final: -0.1623 (p) REVERT: B 508 TYR cc_start: 0.8576 (m-10) cc_final: 0.8268 (m-10) REVERT: B 900 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8226 (mtm) REVERT: B 926 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8233 (mt0) REVERT: C 177 MET cc_start: 0.7350 (tpp) cc_final: 0.7117 (tpp) REVERT: C 191 GLU cc_start: 0.7847 (mp0) cc_final: 0.7307 (mp0) REVERT: C 264 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.6316 (p0) REVERT: C 699 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7494 (mp) REVERT: C 779 GLN cc_start: 0.8826 (tp40) cc_final: 0.8570 (tm-30) REVERT: C 1002 GLN cc_start: 0.8470 (tt0) cc_final: 0.7850 (tt0) outliers start: 128 outliers final: 87 residues processed: 286 average time/residue: 0.3189 time to fit residues: 155.4341 Evaluate side-chains 256 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 163 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 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 83 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 295 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN A 804 GLN A1011 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN C 628 GLN C 804 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.094627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.065797 restraints weight = 77462.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.068213 restraints weight = 42792.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.069810 restraints weight = 29566.636| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 26448 Z= 0.321 Angle : 0.808 15.085 36114 Z= 0.398 Chirality : 0.051 0.586 4221 Planarity : 0.005 0.061 4554 Dihedral : 8.130 98.487 4655 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.23 % Favored : 91.67 % Rotamer: Outliers : 6.09 % Allowed : 22.38 % Favored : 71.53 % 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: -1.46 (0.15), residues: 3159 helix: 0.99 (0.20), residues: 690 sheet: -1.06 (0.19), residues: 720 loop : -1.79 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 633 HIS 0.007 0.001 HIS C1064 PHE 0.030 0.002 PHE C 220 TYR 0.023 0.002 TYR A1067 ARG 0.013 0.001 ARG C 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00659 ( 45) link_NAG-ASN : angle 4.02559 ( 135) link_BETA1-4 : bond 0.00194 ( 15) link_BETA1-4 : angle 2.45908 ( 45) hydrogen bonds : bond 0.04770 ( 913) hydrogen bonds : angle 5.77308 ( 2481) SS BOND : bond 0.00624 ( 39) SS BOND : angle 1.91343 ( 78) covalent geometry : bond 0.00741 (26349) covalent geometry : angle 0.76189 (35856) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 170 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.9027 (mm) REVERT: A 264 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7312 (p0) REVERT: A 389 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.6809 (t70) REVERT: A 402 ILE cc_start: 0.8684 (tp) cc_final: 0.8377 (tp) REVERT: A 759 PHE cc_start: 0.7881 (m-80) cc_final: 0.7589 (m-10) REVERT: A 773 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7719 (tm-30) REVERT: A 784 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7769 (mp10) REVERT: B 101 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9051 (tp) REVERT: B 127 PHE cc_start: 0.8339 (t80) cc_final: 0.8023 (m-80) REVERT: B 306 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8804 (m-80) REVERT: B 389 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.6925 (t0) REVERT: B 480 CYS cc_start: -0.0838 (OUTLIER) cc_final: -0.1662 (p) REVERT: B 489 TYR cc_start: 0.7503 (m-80) cc_final: 0.7274 (m-10) REVERT: B 508 TYR cc_start: 0.8810 (m-10) cc_final: 0.8545 (m-10) REVERT: B 779 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8614 (tt0) REVERT: B 900 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8190 (mtm) REVERT: B 926 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8201 (mp10) REVERT: C 177 MET cc_start: 0.7598 (tpp) cc_final: 0.5854 (mmp) REVERT: C 191 GLU cc_start: 0.8252 (mp0) cc_final: 0.8044 (mp0) REVERT: C 264 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.6988 (p0) REVERT: C 306 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.8854 (m-80) REVERT: C 779 GLN cc_start: 0.8884 (tp40) cc_final: 0.8573 (tm-30) REVERT: C 869 MET cc_start: 0.8811 (mtp) cc_final: 0.8503 (ttm) REVERT: C 900 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8052 (mtm) outliers start: 169 outliers final: 112 residues processed: 315 average time/residue: 0.2995 time to fit residues: 160.0766 Evaluate side-chains 276 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 151 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 13 optimal weight: 10.0000 chunk 314 optimal weight: 6.9990 chunk 299 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 154 optimal weight: 8.9990 chunk 280 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 201 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 266 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.097588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.069015 restraints weight = 76868.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.071597 restraints weight = 41208.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.073271 restraints weight = 27951.122| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26448 Z= 0.126 Angle : 0.702 14.859 36114 Z= 0.336 Chirality : 0.049 0.579 4221 Planarity : 0.004 0.061 4554 Dihedral : 7.702 95.772 4655 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.09 % Favored : 92.81 % Rotamer: Outliers : 3.82 % Allowed : 25.01 % Favored : 71.17 % 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: -1.17 (0.15), residues: 3159 helix: 1.49 (0.20), residues: 681 sheet: -1.00 (0.19), residues: 681 loop : -1.65 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 633 HIS 0.002 0.000 HIS A 519 PHE 0.040 0.001 PHE B 592 TYR 0.018 0.001 TYR A 741 ARG 0.006 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00569 ( 45) link_NAG-ASN : angle 3.81764 ( 135) link_BETA1-4 : bond 0.00374 ( 15) link_BETA1-4 : angle 2.15545 ( 45) hydrogen bonds : bond 0.03987 ( 913) hydrogen bonds : angle 5.40206 ( 2481) SS BOND : bond 0.00467 ( 39) SS BOND : angle 1.45340 ( 78) covalent geometry : bond 0.00288 (26349) covalent geometry : angle 0.65633 (35856) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 170 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7162 (p0) REVERT: A 402 ILE cc_start: 0.8504 (tp) cc_final: 0.7901 (tp) REVERT: A 508 TYR cc_start: 0.8558 (m-10) cc_final: 0.8319 (m-10) REVERT: A 633 TRP cc_start: 0.7949 (p90) cc_final: 0.7518 (p90) REVERT: A 759 PHE cc_start: 0.7780 (m-80) cc_final: 0.6859 (m-10) REVERT: A 902 MET cc_start: 0.9192 (tpp) cc_final: 0.8908 (tpp) REVERT: B 127 PHE cc_start: 0.8321 (t80) cc_final: 0.8078 (m-80) REVERT: B 480 CYS cc_start: -0.0989 (OUTLIER) cc_final: -0.1752 (p) REVERT: B 489 TYR cc_start: 0.7515 (m-80) cc_final: 0.7288 (m-10) REVERT: B 508 TYR cc_start: 0.8784 (m-10) cc_final: 0.8494 (m-10) REVERT: B 779 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8571 (tt0) REVERT: B 926 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8155 (mt0) REVERT: C 191 GLU cc_start: 0.7933 (mp0) cc_final: 0.7401 (mp0) REVERT: C 264 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.6781 (p0) REVERT: C 386 LYS cc_start: 0.8350 (mtmm) cc_final: 0.7741 (ptpp) REVERT: C 508 TYR cc_start: 0.8751 (m-10) cc_final: 0.8293 (m-80) REVERT: C 779 GLN cc_start: 0.8732 (tp40) cc_final: 0.8524 (tm-30) REVERT: C 990 GLU cc_start: 0.7596 (pm20) cc_final: 0.7250 (pm20) REVERT: C 1002 GLN cc_start: 0.8458 (tt0) cc_final: 0.8163 (tt0) outliers start: 106 outliers final: 82 residues processed: 257 average time/residue: 0.2988 time to fit residues: 131.4579 Evaluate side-chains 241 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 155 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 180 optimal weight: 0.0570 chunk 199 optimal weight: 4.9990 chunk 267 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 311 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 308 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 278 optimal weight: 0.8980 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 965 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.096657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.068081 restraints weight = 76838.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.070645 restraints weight = 40807.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.072359 restraints weight = 27548.690| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26448 Z= 0.157 Angle : 0.699 14.584 36114 Z= 0.336 Chirality : 0.049 0.577 4221 Planarity : 0.004 0.058 4554 Dihedral : 7.592 95.580 4655 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.22 % Favored : 92.69 % Rotamer: Outliers : 3.96 % Allowed : 25.12 % Favored : 70.92 % 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: -1.12 (0.15), residues: 3159 helix: 1.43 (0.20), residues: 702 sheet: -0.99 (0.19), residues: 681 loop : -1.59 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 633 HIS 0.003 0.001 HIS A1064 PHE 0.028 0.001 PHE A 220 TYR 0.017 0.001 TYR A1067 ARG 0.003 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 45) link_NAG-ASN : angle 3.83027 ( 135) link_BETA1-4 : bond 0.00285 ( 15) link_BETA1-4 : angle 2.10463 ( 45) hydrogen bonds : bond 0.03983 ( 913) hydrogen bonds : angle 5.34379 ( 2481) SS BOND : bond 0.00471 ( 39) SS BOND : angle 1.57346 ( 78) covalent geometry : bond 0.00364 (26349) covalent geometry : angle 0.65212 (35856) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 164 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7181 (p0) REVERT: A 353 TRP cc_start: 0.7958 (p-90) cc_final: 0.7580 (p-90) REVERT: A 389 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.6809 (t0) REVERT: A 402 ILE cc_start: 0.8574 (tp) cc_final: 0.8028 (tp) REVERT: A 759 PHE cc_start: 0.7602 (m-80) cc_final: 0.7369 (m-10) REVERT: A 902 MET cc_start: 0.9210 (tpp) cc_final: 0.8901 (tpp) REVERT: B 306 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8614 (m-80) REVERT: B 480 CYS cc_start: -0.0921 (OUTLIER) cc_final: -0.1682 (p) REVERT: B 489 TYR cc_start: 0.7501 (m-80) cc_final: 0.7277 (m-10) REVERT: B 508 TYR cc_start: 0.8797 (m-10) cc_final: 0.8519 (m-10) REVERT: B 779 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8594 (tt0) REVERT: B 926 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8193 (mt0) REVERT: C 191 GLU cc_start: 0.7962 (mp0) cc_final: 0.7348 (mp0) REVERT: C 264 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.6765 (p0) REVERT: C 386 LYS cc_start: 0.8423 (mtmm) cc_final: 0.7797 (ptpp) REVERT: C 508 TYR cc_start: 0.8750 (m-10) cc_final: 0.8303 (m-80) REVERT: C 1002 GLN cc_start: 0.8504 (tt0) cc_final: 0.8034 (tt0) outliers start: 110 outliers final: 88 residues processed: 257 average time/residue: 0.3155 time to fit residues: 139.6396 Evaluate side-chains 249 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 155 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 89 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 249 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 195 optimal weight: 7.9990 chunk 146 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 174 optimal weight: 3.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1005 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.093723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.065086 restraints weight = 77887.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.067488 restraints weight = 42807.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.069094 restraints weight = 29530.060| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 26448 Z= 0.279 Angle : 0.786 13.857 36114 Z= 0.386 Chirality : 0.051 0.599 4221 Planarity : 0.005 0.061 4554 Dihedral : 7.989 98.112 4655 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.64 % Favored : 91.26 % Rotamer: Outliers : 4.14 % Allowed : 25.08 % Favored : 70.77 % 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: -1.35 (0.15), residues: 3159 helix: 1.12 (0.20), residues: 702 sheet: -1.18 (0.19), residues: 705 loop : -1.66 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 633 HIS 0.006 0.001 HIS C1064 PHE 0.042 0.002 PHE A 220 TYR 0.022 0.002 TYR A1067 ARG 0.004 0.001 ARG B1000 Details of bonding type rmsd link_NAG-ASN : bond 0.00641 ( 45) link_NAG-ASN : angle 3.95621 ( 135) link_BETA1-4 : bond 0.00231 ( 15) link_BETA1-4 : angle 2.22464 ( 45) hydrogen bonds : bond 0.04635 ( 913) hydrogen bonds : angle 5.66520 ( 2481) SS BOND : bond 0.00605 ( 39) SS BOND : angle 1.65157 ( 78) covalent geometry : bond 0.00643 (26349) covalent geometry : angle 0.74276 (35856) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 156 time to evaluate : 2.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7775 (ptmt) REVERT: A 264 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7321 (p0) REVERT: A 386 LYS cc_start: 0.8575 (mtmm) cc_final: 0.7846 (ptpt) REVERT: A 389 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.6892 (t0) REVERT: A 402 ILE cc_start: 0.8763 (tp) cc_final: 0.8299 (tp) REVERT: A 508 TYR cc_start: 0.8722 (m-10) cc_final: 0.8510 (m-80) REVERT: A 784 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7725 (mp10) REVERT: A 902 MET cc_start: 0.9253 (tpp) cc_final: 0.8957 (tpp) REVERT: B 101 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9170 (tp) REVERT: B 118 LEU cc_start: 0.8936 (tp) cc_final: 0.8724 (tp) REVERT: B 480 CYS cc_start: -0.0420 (OUTLIER) cc_final: -0.1029 (p) REVERT: B 489 TYR cc_start: 0.7514 (m-80) cc_final: 0.7275 (m-10) REVERT: B 508 TYR cc_start: 0.8890 (m-10) cc_final: 0.8651 (m-10) REVERT: B 900 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8209 (mtm) REVERT: B 926 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8038 (mt0) REVERT: C 191 GLU cc_start: 0.8232 (mp0) cc_final: 0.7708 (mp0) REVERT: C 264 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.6861 (p0) REVERT: C 386 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8068 (ptpt) REVERT: C 508 TYR cc_start: 0.8860 (m-10) cc_final: 0.8453 (m-80) REVERT: C 900 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8172 (mtm) REVERT: C 990 GLU cc_start: 0.7852 (pm20) cc_final: 0.7481 (pm20) REVERT: C 1002 GLN cc_start: 0.8582 (tt0) cc_final: 0.8112 (tt0) outliers start: 115 outliers final: 91 residues processed: 255 average time/residue: 0.3089 time to fit residues: 134.3481 Evaluate side-chains 246 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 145 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 81 optimal weight: 0.7980 chunk 276 optimal weight: 0.9990 chunk 153 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 316 optimal weight: 0.9990 chunk 233 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 255 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.096205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.067980 restraints weight = 76482.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.070525 restraints weight = 40934.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.072212 restraints weight = 27708.575| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26448 Z= 0.127 Angle : 0.702 13.648 36114 Z= 0.338 Chirality : 0.049 0.580 4221 Planarity : 0.004 0.059 4554 Dihedral : 7.615 96.113 4655 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.34 % Favored : 92.59 % Rotamer: Outliers : 3.39 % Allowed : 25.98 % Favored : 70.63 % 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: -1.15 (0.15), residues: 3159 helix: 1.42 (0.20), residues: 702 sheet: -1.08 (0.19), residues: 702 loop : -1.59 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 633 HIS 0.002 0.001 HIS A1064 PHE 0.031 0.001 PHE A 220 TYR 0.015 0.001 TYR C 904 ARG 0.003 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00557 ( 45) link_NAG-ASN : angle 3.78381 ( 135) link_BETA1-4 : bond 0.00401 ( 15) link_BETA1-4 : angle 1.99241 ( 45) hydrogen bonds : bond 0.03931 ( 913) hydrogen bonds : angle 5.34445 ( 2481) SS BOND : bond 0.00485 ( 39) SS BOND : angle 1.55571 ( 78) covalent geometry : bond 0.00289 (26349) covalent geometry : angle 0.65775 (35856) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 162 time to evaluate : 2.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 PHE cc_start: 0.8190 (m-10) cc_final: 0.7775 (m-10) REVERT: A 177 MET cc_start: 0.7487 (tpp) cc_final: 0.6140 (mmt) REVERT: A 264 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7482 (p0) REVERT: A 353 TRP cc_start: 0.8138 (p-90) cc_final: 0.7701 (p-90) REVERT: A 386 LYS cc_start: 0.8491 (mtmm) cc_final: 0.8012 (ptpt) REVERT: A 389 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.6877 (t0) REVERT: A 402 ILE cc_start: 0.8638 (tp) cc_final: 0.7920 (tp) REVERT: A 902 MET cc_start: 0.9207 (tpp) cc_final: 0.8885 (tpp) REVERT: B 480 CYS cc_start: -0.0481 (OUTLIER) cc_final: -0.1199 (p) REVERT: B 489 TYR cc_start: 0.7474 (m-80) cc_final: 0.7236 (m-10) REVERT: B 508 TYR cc_start: 0.8819 (m-10) cc_final: 0.8589 (m-10) REVERT: B 779 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8564 (tt0) REVERT: B 926 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8071 (mt0) REVERT: C 191 GLU cc_start: 0.7960 (mp0) cc_final: 0.7403 (mp0) REVERT: C 264 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.6905 (p0) REVERT: C 306 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8751 (m-80) REVERT: C 386 LYS cc_start: 0.8383 (mtmm) cc_final: 0.7896 (ptpt) REVERT: C 508 TYR cc_start: 0.8787 (m-10) cc_final: 0.8415 (m-80) REVERT: C 1002 GLN cc_start: 0.8500 (tt0) cc_final: 0.8084 (tt0) outliers start: 94 outliers final: 84 residues processed: 242 average time/residue: 0.3084 time to fit residues: 126.7426 Evaluate side-chains 242 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 152 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 29 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 217 optimal weight: 0.0770 chunk 21 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 290 optimal weight: 0.5980 chunk 174 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 212 optimal weight: 20.0000 chunk 125 optimal weight: 3.9990 overall best weight: 1.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** 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 = 0.3695 r_free = 0.3695 target = 0.095902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.067558 restraints weight = 77213.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.070078 restraints weight = 41614.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.071755 restraints weight = 28323.019| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26448 Z= 0.145 Angle : 0.698 13.481 36114 Z= 0.336 Chirality : 0.049 0.579 4221 Planarity : 0.004 0.060 4554 Dihedral : 7.534 95.711 4655 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.47 % Favored : 92.47 % Rotamer: Outliers : 3.57 % Allowed : 26.02 % Favored : 70.41 % 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: -1.13 (0.15), residues: 3159 helix: 1.44 (0.20), residues: 699 sheet: -1.22 (0.19), residues: 717 loop : -1.50 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 633 HIS 0.004 0.001 HIS A 505 PHE 0.019 0.001 PHE C 220 TYR 0.030 0.001 TYR A 508 ARG 0.005 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 45) link_NAG-ASN : angle 3.75904 ( 135) link_BETA1-4 : bond 0.00322 ( 15) link_BETA1-4 : angle 1.98276 ( 45) hydrogen bonds : bond 0.03908 ( 913) hydrogen bonds : angle 5.25497 ( 2481) SS BOND : bond 0.00490 ( 39) SS BOND : angle 1.57062 ( 78) covalent geometry : bond 0.00336 (26349) covalent geometry : angle 0.65325 (35856) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7280.59 seconds wall clock time: 129 minutes 17.76 seconds (7757.76 seconds total)