Starting phenix.real_space_refine on Sat May 24 23:23:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x4h_38049/05_2025/8x4h_38049.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x4h_38049/05_2025/8x4h_38049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x4h_38049/05_2025/8x4h_38049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x4h_38049/05_2025/8x4h_38049.map" model { file = "/net/cci-nas-00/data/ceres_data/8x4h_38049/05_2025/8x4h_38049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x4h_38049/05_2025/8x4h_38049.cif" } resolution = 3.65 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= 0.001 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16458 2.51 5 N 4200 2.21 5 O 5052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25824 Number of models: 1 Model: "" Number of chains: 24 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': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 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': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 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': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 15.29, per 1000 atoms: 0.59 Number of scatterers: 25824 At special positions: 0 Unit cell: (134, 148, 171, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 5052 8.00 N 4200 7.00 C 16458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " BMA D 2 " " NAG E 1 " - " BMA E 2 " " NAG F 1 " - " BMA F 2 " " NAG G 1 " - " BMA G 2 " " NAG H 1 " - " BMA H 2 " " NAG I 1 " - " BMA I 2 " " NAG J 1 " - " BMA J 2 " " NAG K 1 " - " BMA K 2 " " NAG L 1 " - " BMA L 2 " " NAG M 1 " - " BMA M 2 " " NAG N 1 " - " BMA N 2 " " NAG O 1 " - " BMA O 2 " " NAG P 1 " - " BMA P 2 " " NAG Q 1 " - " BMA Q 2 " " NAG R 1 " - " BMA R 2 " " NAG S 1 " - " BMA S 2 " " NAG T 1 " - " BMA T 2 " " NAG U 1 " - " BMA U 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 61 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 234 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 234 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG D 1 " - " ASN A 354 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN B 354 " " NAG K 1 " - " ASN B 282 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN C 354 " " NAG Q 1 " - " ASN C 282 " " NAG R 1 " - " ASN C1134 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C1098 " Time building additional restraints: 6.73 Conformation dependent library (CDL) restraints added in 3.4 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: 69 helices and 52 sheets defined 25.2% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.51 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: 3.667A 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 409 removed outlier: 4.218A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.567A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.504A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 844 removed outlier: 4.161A pdb=" N ILE A 844 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.521A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.599A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (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: 4.294A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.753A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.504A 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 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.855A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.843A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.822A 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 505 Processing helix chain 'B' and resid 616 through 626 removed outlier: 3.632A 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 755 removed outlier: 3.594A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.610A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 869 through 884 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: 4.234A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.557A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 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: 5.332A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) 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: 3.791A 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: 3.826A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.504A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 616 through 626 removed outlier: 3.608A 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 758 through 783 removed outlier: 3.775A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.624A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 844 removed outlier: 4.068A pdb=" N ILE C 844 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 868 through 884 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: 4.237A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.590A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.986A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 6.955A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ASP A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N THR A 95 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.422A 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: 3.726A 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: 3.865A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 7.122A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.625A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.846A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.999A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 552 through 553 removed outlier: 3.874A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A 586 " --> pdb=" O THR A 553 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.810A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.990A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 713 through 715 removed outlier: 3.840A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.219A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.106A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.187A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR B 95 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC3, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.808A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.900A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.007A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.543A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.924A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.015A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 713 through 715 removed outlier: 3.694A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.566A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.182A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.584A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.761A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 50 through 55 Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.122A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 116 through 118 removed outlier: 4.833A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.022A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.837A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.017A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.879A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.107A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 713 through 715 removed outlier: 3.840A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.243A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.109A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'C' and resid 1094 through 1097 906 hydrogen bonds defined for protein. 2475 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.15 Time building geometry restraints manager: 7.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7768 1.34 - 1.46: 6688 1.46 - 1.59: 11826 1.59 - 1.71: 1 1.71 - 1.84: 141 Bond restraints: 26424 Sorted by residual: bond pdb=" N VAL C 308 " pdb=" CA VAL C 308 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.10e-02 8.26e+03 9.75e+00 bond pdb=" N VAL B 193 " pdb=" CA VAL B 193 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.19e-02 7.06e+03 9.53e+00 bond pdb=" N ILE A 410 " pdb=" CA ILE A 410 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.23e+00 bond pdb=" N VAL C 159 " pdb=" CA VAL C 159 " ideal model delta sigma weight residual 1.462 1.494 -0.031 1.06e-02 8.90e+03 8.69e+00 bond pdb=" N GLN A 414 " pdb=" CA GLN A 414 " ideal model delta sigma weight residual 1.453 1.489 -0.035 1.22e-02 6.72e+03 8.37e+00 ... (remaining 26419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 35136 2.53 - 5.07: 713 5.07 - 7.60: 102 7.60 - 10.13: 6 10.13 - 12.67: 1 Bond angle restraints: 35958 Sorted by residual: angle pdb=" C ASN A1074 " pdb=" N PHE A1075 " pdb=" CA PHE A1075 " ideal model delta sigma weight residual 121.90 114.32 7.58 1.26e+00 6.30e-01 3.62e+01 angle pdb=" N CYS C 136 " pdb=" CA CYS C 136 " pdb=" C CYS C 136 " ideal model delta sigma weight residual 114.62 108.48 6.14 1.14e+00 7.69e-01 2.90e+01 angle pdb=" N CYS A 136 " pdb=" CA CYS A 136 " pdb=" C CYS A 136 " ideal model delta sigma weight residual 114.75 108.33 6.42 1.26e+00 6.30e-01 2.60e+01 angle pdb=" CA ASP B 198 " pdb=" CB ASP B 198 " pdb=" CG ASP B 198 " ideal model delta sigma weight residual 112.60 117.33 -4.73 1.00e+00 1.00e+00 2.23e+01 angle pdb=" CA GLY B 89 " pdb=" C GLY B 89 " pdb=" O GLY B 89 " ideal model delta sigma weight residual 122.24 118.18 4.06 8.70e-01 1.32e+00 2.18e+01 ... (remaining 35953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.97: 14775 22.97 - 45.95: 1372 45.95 - 68.92: 165 68.92 - 91.90: 133 91.90 - 114.87: 121 Dihedral angle restraints: 16566 sinusoidal: 7290 harmonic: 9276 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 145.16 -52.16 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 42.68 50.32 1 1.00e+01 1.00e-02 3.47e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 142.14 -49.14 1 1.00e+01 1.00e-02 3.32e+01 ... (remaining 16563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.182: 4200 0.182 - 0.364: 48 0.364 - 0.546: 0 0.546 - 0.728: 0 0.728 - 0.909: 3 Chirality restraints: 4251 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.49 -0.91 2.00e-01 2.50e+01 2.07e+01 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.93e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.56 -0.84 2.00e-01 2.50e+01 1.75e+01 ... (remaining 4248 not shown) Planarity restraints: 4605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1303 " 0.069 2.00e-02 2.50e+03 5.71e-02 4.07e+01 pdb=" C7 NAG C1303 " -0.021 2.00e-02 2.50e+03 pdb=" C8 NAG C1303 " 0.053 2.00e-02 2.50e+03 pdb=" N2 NAG C1303 " -0.090 2.00e-02 2.50e+03 pdb=" O7 NAG C1303 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 592 " 0.028 2.00e-02 2.50e+03 3.18e-02 1.77e+01 pdb=" CG PHE B 592 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE B 592 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE B 592 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 592 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 592 " 0.025 2.00e-02 2.50e+03 pdb=" CZ PHE B 592 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 371 " -0.034 2.00e-02 2.50e+03 3.11e-02 1.70e+01 pdb=" CG PHE C 371 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE C 371 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE C 371 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE C 371 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE C 371 " -0.033 2.00e-02 2.50e+03 pdb=" CZ PHE C 371 " 0.000 2.00e-02 2.50e+03 ... (remaining 4602 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 554 2.64 - 3.21: 24741 3.21 - 3.77: 40149 3.77 - 4.34: 55575 4.34 - 4.90: 90859 Nonbonded interactions: 211878 Sorted by model distance: nonbonded pdb=" O CYS A 590 " pdb=" OH TYR C 837 " model vdw 2.078 3.040 nonbonded pdb=" OH TYR B 837 " pdb=" O CYS C 590 " model vdw 2.111 3.040 nonbonded pdb=" OG1 THR B 912 " pdb=" OD1 ASN B 914 " model vdw 2.132 3.040 nonbonded pdb=" OH TYR A 837 " pdb=" O PRO B 589 " model vdw 2.142 3.040 nonbonded pdb=" NE2 GLN A 804 " pdb=" OE1 GLN A 935 " model vdw 2.147 3.120 ... (remaining 211873 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.020 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 59.550 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.150 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 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 : 0.006 0.093 26529 Z= 0.330 Angle : 0.886 14.832 36234 Z= 0.477 Chirality : 0.060 0.909 4251 Planarity : 0.005 0.072 4557 Dihedral : 20.987 114.871 10491 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.67 % Favored : 91.23 % Rotamer: Outliers : 0.68 % Allowed : 23.87 % Favored : 75.45 % 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: -1.87 (0.15), residues: 3159 helix: 0.56 (0.21), residues: 690 sheet: -1.27 (0.21), residues: 582 loop : -2.01 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 633 HIS 0.005 0.001 HIS B 66 PHE 0.068 0.002 PHE B 592 TYR 0.024 0.002 TYR C 873 ARG 0.014 0.001 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00696 ( 48) link_NAG-ASN : angle 3.66097 ( 144) link_BETA1-4 : bond 0.00478 ( 18) link_BETA1-4 : angle 2.28803 ( 54) hydrogen bonds : bond 0.18951 ( 906) hydrogen bonds : angle 8.41402 ( 2475) SS BOND : bond 0.00417 ( 39) SS BOND : angle 1.53934 ( 78) covalent geometry : bond 0.00604 (26424) covalent geometry : angle 0.85137 (35958) *********************** 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 167 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 3.001 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: B 201 PHE cc_start: 0.8199 (t80) cc_final: 0.7977 (t80) REVERT: C 214 ARG cc_start: -0.0039 (OUTLIER) cc_final: -0.1926 (ptt-90) outliers start: 19 outliers final: 11 residues processed: 160 average time/residue: 0.3503 time to fit residues: 93.3536 Evaluate side-chains 134 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 973 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 7.9990 chunk 241 optimal weight: 8.9990 chunk 133 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 249 optimal weight: 8.9990 chunk 96 optimal weight: 0.9980 chunk 151 optimal weight: 0.3980 chunk 185 optimal weight: 3.9990 chunk 288 optimal weight: 20.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 804 GLN B1106 GLN C 30 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.091247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.071422 restraints weight = 88066.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.073767 restraints weight = 42727.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.075280 restraints weight = 26887.988| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26529 Z= 0.144 Angle : 0.732 15.665 36234 Z= 0.351 Chirality : 0.051 0.609 4251 Planarity : 0.004 0.042 4557 Dihedral : 14.696 112.277 4796 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.35 % Allowed : 21.17 % Favored : 75.49 % 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: -1.65 (0.15), residues: 3159 helix: 0.95 (0.20), residues: 699 sheet: -1.32 (0.19), residues: 678 loop : -1.91 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 633 HIS 0.003 0.001 HIS A 339 PHE 0.032 0.001 PHE C 592 TYR 0.020 0.001 TYR C1067 ARG 0.008 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00698 ( 48) link_NAG-ASN : angle 3.75387 ( 144) link_BETA1-4 : bond 0.00604 ( 18) link_BETA1-4 : angle 3.16459 ( 54) hydrogen bonds : bond 0.04417 ( 906) hydrogen bonds : angle 6.24541 ( 2475) SS BOND : bond 0.00353 ( 39) SS BOND : angle 1.17277 ( 78) covalent geometry : bond 0.00318 (26424) covalent geometry : angle 0.68245 (35958) *********************** 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 239 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 146 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.8652 (t80) cc_final: 0.8290 (t80) REVERT: A 869 MET cc_start: 0.9082 (ptp) cc_final: 0.8823 (ptp) REVERT: B 421 TYR cc_start: 0.7476 (m-10) cc_final: 0.7066 (m-10) REVERT: B 591 SER cc_start: 0.7498 (OUTLIER) cc_final: 0.7076 (m) REVERT: B 740 MET cc_start: 0.8434 (ttm) cc_final: 0.8163 (ttm) REVERT: B 773 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7838 (tm-30) REVERT: C 133 PHE cc_start: 0.6746 (OUTLIER) cc_final: 0.5733 (m-80) REVERT: C 214 ARG cc_start: 0.1183 (OUTLIER) cc_final: 0.0708 (mmm-85) REVERT: C 495 TYR cc_start: 0.4289 (OUTLIER) cc_final: 0.4077 (m-10) REVERT: C 592 PHE cc_start: 0.6795 (t80) cc_final: 0.6403 (t80) REVERT: C 882 ILE cc_start: 0.9343 (pt) cc_final: 0.8867 (mt) outliers start: 93 outliers final: 35 residues processed: 231 average time/residue: 0.3171 time to fit residues: 123.3941 Evaluate side-chains 158 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 78 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 170 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 228 optimal weight: 0.1980 chunk 286 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 251 optimal weight: 0.5980 chunk 30 optimal weight: 0.0770 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A1011 GLN B 185 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.092258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.071991 restraints weight = 88205.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.074425 restraints weight = 42999.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.076008 restraints weight = 27252.881| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26529 Z= 0.120 Angle : 0.691 15.188 36234 Z= 0.331 Chirality : 0.050 0.622 4251 Planarity : 0.004 0.046 4557 Dihedral : 9.983 106.741 4783 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.95 % Allowed : 22.43 % Favored : 74.62 % 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: -1.53 (0.15), residues: 3159 helix: 1.14 (0.20), residues: 693 sheet: -1.22 (0.20), residues: 639 loop : -1.88 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 104 HIS 0.003 0.000 HIS C1048 PHE 0.020 0.001 PHE C 592 TYR 0.019 0.001 TYR B 369 ARG 0.004 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00733 ( 48) link_NAG-ASN : angle 3.63372 ( 144) link_BETA1-4 : bond 0.00543 ( 18) link_BETA1-4 : angle 2.98099 ( 54) hydrogen bonds : bond 0.03955 ( 906) hydrogen bonds : angle 5.78510 ( 2475) SS BOND : bond 0.00343 ( 39) SS BOND : angle 1.26902 ( 78) covalent geometry : bond 0.00260 (26424) covalent geometry : angle 0.64118 (35958) *********************** 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 228 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 146 time to evaluate : 2.891 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 759 PHE cc_start: 0.8562 (t80) cc_final: 0.8201 (t80) REVERT: A 869 MET cc_start: 0.9146 (ptp) cc_final: 0.8862 (ptp) REVERT: B 194 PHE cc_start: 0.7246 (m-80) cc_final: 0.6751 (m-80) REVERT: B 421 TYR cc_start: 0.7490 (m-10) cc_final: 0.7098 (m-10) REVERT: B 773 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7856 (tm-30) REVERT: C 133 PHE cc_start: 0.6786 (OUTLIER) cc_final: 0.5806 (m-80) REVERT: C 241 LEU cc_start: 0.5665 (mm) cc_final: 0.5455 (mm) REVERT: C 882 ILE cc_start: 0.9264 (pt) cc_final: 0.8922 (mt) REVERT: C 1050 MET cc_start: 0.8927 (ptp) cc_final: 0.8721 (ptt) outliers start: 82 outliers final: 29 residues processed: 219 average time/residue: 0.3168 time to fit residues: 118.7254 Evaluate side-chains 155 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1037 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 270 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 184 optimal weight: 0.7980 chunk 153 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 239 optimal weight: 5.9990 chunk 296 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 265 optimal weight: 0.0570 chunk 214 optimal weight: 8.9990 chunk 251 optimal weight: 10.0000 overall best weight: 3.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A 955 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 487 ASN B 914 ASN B1005 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.088267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.068202 restraints weight = 88949.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.070405 restraints weight = 45636.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.071840 restraints weight = 29770.655| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 26529 Z= 0.240 Angle : 0.726 15.730 36234 Z= 0.355 Chirality : 0.050 0.623 4251 Planarity : 0.004 0.048 4557 Dihedral : 8.371 100.397 4775 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 4.00 % Allowed : 21.85 % Favored : 74.15 % 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: -1.64 (0.15), residues: 3159 helix: 0.90 (0.20), residues: 705 sheet: -1.30 (0.20), residues: 630 loop : -1.89 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 104 HIS 0.003 0.001 HIS C1064 PHE 0.027 0.002 PHE C 592 TYR 0.019 0.002 TYR C 837 ARG 0.004 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 48) link_NAG-ASN : angle 3.72157 ( 144) link_BETA1-4 : bond 0.00449 ( 18) link_BETA1-4 : angle 2.66512 ( 54) hydrogen bonds : bond 0.04159 ( 906) hydrogen bonds : angle 5.74432 ( 2475) SS BOND : bond 0.00380 ( 39) SS BOND : angle 1.45220 ( 78) covalent geometry : bond 0.00538 (26424) covalent geometry : angle 0.67900 (35958) *********************** 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 229 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 118 time to evaluate : 2.852 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 492 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7527 (pp) REVERT: A 740 MET cc_start: 0.7662 (ttt) cc_final: 0.6483 (ttt) REVERT: A 759 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8363 (t80) REVERT: B 104 TRP cc_start: 0.7447 (m-10) cc_final: 0.6971 (m-10) REVERT: B 421 TYR cc_start: 0.7431 (m-10) cc_final: 0.6900 (m-10) REVERT: B 588 THR cc_start: 0.9392 (OUTLIER) cc_final: 0.9132 (p) REVERT: C 46 SER cc_start: 0.8432 (m) cc_final: 0.7966 (p) REVERT: C 129 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7490 (tttt) REVERT: C 133 PHE cc_start: 0.6995 (OUTLIER) cc_final: 0.6291 (m-80) REVERT: C 176 LEU cc_start: 0.5373 (OUTLIER) cc_final: 0.4863 (mp) REVERT: C 592 PHE cc_start: 0.6769 (t80) cc_final: 0.6519 (t80) REVERT: C 850 ILE cc_start: 0.5377 (mp) cc_final: 0.5082 (mt) REVERT: C 1039 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8448 (ptm160) outliers start: 111 outliers final: 63 residues processed: 213 average time/residue: 0.3165 time to fit residues: 115.6048 Evaluate side-chains 180 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 110 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 83 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 301 optimal weight: 0.1980 chunk 179 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 157 optimal weight: 0.0470 overall best weight: 0.8482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 317 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 = 0.3809 r_free = 0.3809 target = 0.089834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.069873 restraints weight = 87978.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.072206 restraints weight = 43384.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.073688 restraints weight = 27666.132| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 26529 Z= 0.125 Angle : 0.657 15.123 36234 Z= 0.321 Chirality : 0.048 0.620 4251 Planarity : 0.004 0.054 4557 Dihedral : 7.831 97.424 4775 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.06 % Favored : 92.91 % Rotamer: Outliers : 2.95 % Allowed : 22.68 % Favored : 74.37 % 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: -1.44 (0.15), residues: 3159 helix: 1.14 (0.20), residues: 687 sheet: -1.21 (0.20), residues: 651 loop : -1.75 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 104 HIS 0.003 0.000 HIS C1048 PHE 0.036 0.001 PHE A 592 TYR 0.020 0.001 TYR A 380 ARG 0.007 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 48) link_NAG-ASN : angle 3.52731 ( 144) link_BETA1-4 : bond 0.00444 ( 18) link_BETA1-4 : angle 2.28814 ( 54) hydrogen bonds : bond 0.03768 ( 906) hydrogen bonds : angle 5.59101 ( 2475) SS BOND : bond 0.00286 ( 39) SS BOND : angle 1.66253 ( 78) covalent geometry : bond 0.00285 (26424) covalent geometry : angle 0.60960 (35958) *********************** 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 212 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 130 time to evaluate : 2.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7333 (pt) REVERT: A 759 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8409 (t80) REVERT: B 369 TYR cc_start: 0.7607 (OUTLIER) cc_final: 0.6328 (m-80) REVERT: B 421 TYR cc_start: 0.7569 (m-10) cc_final: 0.7153 (m-10) REVERT: B 588 THR cc_start: 0.9344 (OUTLIER) cc_final: 0.9090 (p) REVERT: B 869 MET cc_start: 0.8571 (pmm) cc_final: 0.8289 (pmm) REVERT: C 46 SER cc_start: 0.8484 (m) cc_final: 0.7992 (p) REVERT: C 129 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7488 (tttt) REVERT: C 133 PHE cc_start: 0.6960 (OUTLIER) cc_final: 0.6258 (m-80) REVERT: C 176 LEU cc_start: 0.5346 (OUTLIER) cc_final: 0.4870 (mp) REVERT: C 873 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.8797 (m-80) REVERT: C 882 ILE cc_start: 0.9291 (pt) cc_final: 0.9010 (mt) REVERT: C 900 MET cc_start: 0.8458 (mtp) cc_final: 0.8257 (mtt) outliers start: 82 outliers final: 45 residues processed: 201 average time/residue: 0.3049 time to fit residues: 106.6370 Evaluate side-chains 170 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 117 time to evaluate : 2.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 252 optimal weight: 1.9990 chunk 218 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 160 optimal weight: 0.2980 chunk 124 optimal weight: 10.0000 chunk 205 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 41 optimal weight: 30.0000 chunk 61 optimal weight: 0.8980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 317 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 = 0.3775 r_free = 0.3775 target = 0.087970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.068136 restraints weight = 88073.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.070361 restraints weight = 45207.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.071805 restraints weight = 29439.669| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 26529 Z= 0.203 Angle : 0.695 15.374 36234 Z= 0.339 Chirality : 0.049 0.610 4251 Planarity : 0.004 0.060 4557 Dihedral : 7.612 94.370 4775 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.57 % Favored : 92.40 % Rotamer: Outliers : 3.78 % Allowed : 22.64 % Favored : 73.58 % 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: -1.60 (0.15), residues: 3159 helix: 0.98 (0.20), residues: 714 sheet: -1.44 (0.20), residues: 633 loop : -1.83 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 104 HIS 0.003 0.001 HIS B 207 PHE 0.033 0.001 PHE C 592 TYR 0.023 0.001 TYR A 380 ARG 0.006 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 48) link_NAG-ASN : angle 3.57476 ( 144) link_BETA1-4 : bond 0.00425 ( 18) link_BETA1-4 : angle 2.12360 ( 54) hydrogen bonds : bond 0.03909 ( 906) hydrogen bonds : angle 5.58902 ( 2475) SS BOND : bond 0.00331 ( 39) SS BOND : angle 1.79463 ( 78) covalent geometry : bond 0.00463 (26424) covalent geometry : angle 0.64932 (35958) *********************** 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 227 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 122 time to evaluate : 2.765 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 492 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7443 (pt) REVERT: A 565 PHE cc_start: 0.7418 (m-10) cc_final: 0.7204 (m-10) REVERT: A 759 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8454 (t80) REVERT: B 421 TYR cc_start: 0.7654 (m-10) cc_final: 0.7056 (m-10) REVERT: B 588 THR cc_start: 0.9375 (OUTLIER) cc_final: 0.9128 (p) REVERT: B 869 MET cc_start: 0.8605 (pmm) cc_final: 0.8263 (pmm) REVERT: B 902 MET cc_start: 0.9021 (tpp) cc_final: 0.8152 (tpt) REVERT: B 1050 MET cc_start: 0.7770 (mtm) cc_final: 0.7407 (mtm) REVERT: C 46 SER cc_start: 0.8534 (m) cc_final: 0.8151 (p) REVERT: C 129 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7492 (tttt) REVERT: C 133 PHE cc_start: 0.7188 (OUTLIER) cc_final: 0.6474 (m-80) REVERT: C 176 LEU cc_start: 0.5251 (OUTLIER) cc_final: 0.4738 (mp) REVERT: C 592 PHE cc_start: 0.6634 (t80) cc_final: 0.6401 (t80) REVERT: C 873 TYR cc_start: 0.9153 (OUTLIER) cc_final: 0.8843 (m-80) REVERT: C 878 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8942 (tt) REVERT: C 1039 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8438 (ptm160) outliers start: 105 outliers final: 66 residues processed: 215 average time/residue: 0.3260 time to fit residues: 120.2860 Evaluate side-chains 190 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 115 time to evaluate : 2.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 35 optimal weight: 5.9990 chunk 294 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 288 optimal weight: 20.0000 chunk 126 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 254 optimal weight: 10.0000 chunk 258 optimal weight: 0.0980 chunk 279 optimal weight: 3.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 955 ASN ** C 317 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 = 0.3811 r_free = 0.3811 target = 0.089822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.070410 restraints weight = 88007.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.072705 restraints weight = 42574.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.074218 restraints weight = 26793.798| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26529 Z= 0.120 Angle : 0.651 14.993 36234 Z= 0.317 Chirality : 0.048 0.624 4251 Planarity : 0.004 0.080 4557 Dihedral : 7.310 92.640 4775 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.19 % Favored : 92.78 % Rotamer: Outliers : 3.13 % Allowed : 23.04 % Favored : 73.83 % 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: -1.49 (0.15), residues: 3159 helix: 1.18 (0.20), residues: 696 sheet: -1.36 (0.19), residues: 681 loop : -1.78 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 104 HIS 0.003 0.000 HIS C1048 PHE 0.025 0.001 PHE C 592 TYR 0.027 0.001 TYR A 380 ARG 0.005 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 48) link_NAG-ASN : angle 3.62490 ( 144) link_BETA1-4 : bond 0.00498 ( 18) link_BETA1-4 : angle 1.98433 ( 54) hydrogen bonds : bond 0.03672 ( 906) hydrogen bonds : angle 5.46059 ( 2475) SS BOND : bond 0.00352 ( 39) SS BOND : angle 1.32325 ( 78) covalent geometry : bond 0.00274 (26424) covalent geometry : angle 0.60354 (35958) *********************** 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 217 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 130 time to evaluate : 3.024 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 492 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7420 (pt) REVERT: A 565 PHE cc_start: 0.7286 (m-10) cc_final: 0.7048 (m-10) REVERT: A 759 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8405 (t80) REVERT: A 902 MET cc_start: 0.9010 (mmm) cc_final: 0.8655 (tpt) REVERT: B 414 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8572 (mm-40) REVERT: B 421 TYR cc_start: 0.7659 (m-10) cc_final: 0.7207 (m-10) REVERT: B 588 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.9067 (p) REVERT: B 869 MET cc_start: 0.8574 (pmm) cc_final: 0.8266 (pmm) REVERT: B 902 MET cc_start: 0.8996 (tpp) cc_final: 0.8437 (tpt) REVERT: C 46 SER cc_start: 0.8552 (m) cc_final: 0.8102 (p) REVERT: C 129 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7560 (tttt) REVERT: C 133 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6392 (m-80) REVERT: C 176 LEU cc_start: 0.5148 (OUTLIER) cc_final: 0.4678 (mp) REVERT: C 241 LEU cc_start: 0.7384 (mm) cc_final: 0.7175 (mm) REVERT: C 873 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.8787 (m-80) outliers start: 87 outliers final: 53 residues processed: 205 average time/residue: 0.3121 time to fit residues: 109.7279 Evaluate side-chains 181 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 121 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 267 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 chunk 62 optimal weight: 0.3980 chunk 188 optimal weight: 0.8980 chunk 297 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 chunk 219 optimal weight: 3.9990 chunk 292 optimal weight: 0.9990 chunk 233 optimal weight: 7.9990 chunk 161 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A 907 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1005 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.088967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.069560 restraints weight = 87280.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.071867 restraints weight = 42480.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.073379 restraints weight = 26824.636| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26529 Z= 0.141 Angle : 0.651 15.145 36234 Z= 0.316 Chirality : 0.048 0.621 4251 Planarity : 0.004 0.092 4557 Dihedral : 7.187 90.783 4775 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 3.10 % Allowed : 23.07 % Favored : 73.83 % 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: -1.52 (0.15), residues: 3159 helix: 1.18 (0.20), residues: 696 sheet: -1.48 (0.19), residues: 708 loop : -1.76 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 104 HIS 0.002 0.000 HIS C1048 PHE 0.025 0.001 PHE C 592 TYR 0.015 0.001 TYR A 380 ARG 0.004 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 48) link_NAG-ASN : angle 3.54050 ( 144) link_BETA1-4 : bond 0.00467 ( 18) link_BETA1-4 : angle 1.95342 ( 54) hydrogen bonds : bond 0.03652 ( 906) hydrogen bonds : angle 5.40832 ( 2475) SS BOND : bond 0.00307 ( 39) SS BOND : angle 1.32450 ( 78) covalent geometry : bond 0.00324 (26424) covalent geometry : angle 0.60659 (35958) *********************** 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 211 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 125 time to evaluate : 2.792 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 492 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7483 (pt) REVERT: A 565 PHE cc_start: 0.7332 (m-10) cc_final: 0.7122 (m-10) REVERT: A 759 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8454 (t80) REVERT: B 421 TYR cc_start: 0.7656 (m-10) cc_final: 0.7068 (m-10) REVERT: B 869 MET cc_start: 0.8612 (pmm) cc_final: 0.8209 (pmm) REVERT: B 873 TYR cc_start: 0.9417 (OUTLIER) cc_final: 0.9118 (m-10) REVERT: C 46 SER cc_start: 0.8516 (m) cc_final: 0.8121 (p) REVERT: C 129 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7601 (tttt) REVERT: C 133 PHE cc_start: 0.7159 (OUTLIER) cc_final: 0.6383 (m-80) REVERT: C 176 LEU cc_start: 0.5085 (OUTLIER) cc_final: 0.4464 (mp) REVERT: C 241 LEU cc_start: 0.7587 (mm) cc_final: 0.7312 (mm) REVERT: C 873 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.8818 (m-80) REVERT: C 1039 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8016 (mtp180) outliers start: 86 outliers final: 58 residues processed: 202 average time/residue: 0.3158 time to fit residues: 111.3955 Evaluate side-chains 181 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 115 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 80 optimal weight: 0.9990 chunk 315 optimal weight: 3.9990 chunk 220 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 238 optimal weight: 4.9990 chunk 299 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 86 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A 907 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 317 ASN C 448 ASN C 804 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.088709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.068633 restraints weight = 88498.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.070963 restraints weight = 43550.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.072503 restraints weight = 27768.448| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26529 Z= 0.161 Angle : 0.667 15.183 36234 Z= 0.324 Chirality : 0.048 0.615 4251 Planarity : 0.004 0.056 4557 Dihedral : 7.151 89.939 4775 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.99 % Allowed : 23.33 % Favored : 73.69 % 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: -1.47 (0.15), residues: 3159 helix: 1.19 (0.20), residues: 693 sheet: -1.29 (0.20), residues: 666 loop : -1.78 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP B 104 HIS 0.002 0.001 HIS C1048 PHE 0.029 0.001 PHE C 592 TYR 0.021 0.001 TYR A 380 ARG 0.004 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 48) link_NAG-ASN : angle 3.52284 ( 144) link_BETA1-4 : bond 0.00461 ( 18) link_BETA1-4 : angle 1.93228 ( 54) hydrogen bonds : bond 0.03702 ( 906) hydrogen bonds : angle 5.42177 ( 2475) SS BOND : bond 0.00307 ( 39) SS BOND : angle 1.34664 ( 78) covalent geometry : bond 0.00370 (26424) covalent geometry : angle 0.62361 (35958) *********************** 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 204 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 121 time to evaluate : 2.880 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 492 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7469 (pt) REVERT: A 565 PHE cc_start: 0.7397 (m-10) cc_final: 0.7191 (m-10) REVERT: A 759 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.8468 (t80) REVERT: B 421 TYR cc_start: 0.7685 (m-10) cc_final: 0.7070 (m-10) REVERT: B 869 MET cc_start: 0.8662 (pmm) cc_final: 0.8263 (pmm) REVERT: B 873 TYR cc_start: 0.9422 (OUTLIER) cc_final: 0.9114 (m-10) REVERT: C 46 SER cc_start: 0.8593 (m) cc_final: 0.8197 (p) REVERT: C 129 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7505 (tttt) REVERT: C 133 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.6395 (m-80) REVERT: C 176 LEU cc_start: 0.5053 (OUTLIER) cc_final: 0.4336 (mp) REVERT: C 873 TYR cc_start: 0.9118 (OUTLIER) cc_final: 0.8784 (m-80) outliers start: 83 outliers final: 63 residues processed: 194 average time/residue: 0.3045 time to fit residues: 102.6258 Evaluate side-chains 183 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 113 time to evaluate : 3.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 191 optimal weight: 0.8980 chunk 179 optimal weight: 0.3980 chunk 263 optimal weight: 2.9990 chunk 306 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A 907 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 321 GLN C 448 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.090333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.070096 restraints weight = 88581.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.072428 restraints weight = 43790.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.073972 restraints weight = 27976.862| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26529 Z= 0.115 Angle : 0.648 14.930 36234 Z= 0.314 Chirality : 0.048 0.625 4251 Planarity : 0.004 0.056 4557 Dihedral : 6.964 87.778 4775 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.38 % Allowed : 23.94 % Favored : 73.69 % 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: -1.45 (0.15), residues: 3159 helix: 1.20 (0.20), residues: 696 sheet: -1.42 (0.19), residues: 705 loop : -1.70 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 104 HIS 0.002 0.000 HIS C1048 PHE 0.031 0.001 PHE C 592 TYR 0.019 0.001 TYR A 380 ARG 0.006 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 48) link_NAG-ASN : angle 3.45592 ( 144) link_BETA1-4 : bond 0.00498 ( 18) link_BETA1-4 : angle 1.89335 ( 54) hydrogen bonds : bond 0.03565 ( 906) hydrogen bonds : angle 5.34540 ( 2475) SS BOND : bond 0.00259 ( 39) SS BOND : angle 1.19192 ( 78) covalent geometry : bond 0.00260 (26424) covalent geometry : angle 0.60606 (35958) ********************** 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 197 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 131 time to evaluate : 2.961 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 492 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7528 (pt) REVERT: A 565 PHE cc_start: 0.7314 (m-10) cc_final: 0.7099 (m-10) REVERT: A 759 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.8381 (t80) REVERT: B 421 TYR cc_start: 0.7691 (m-10) cc_final: 0.7041 (m-10) REVERT: B 869 MET cc_start: 0.8615 (pmm) cc_final: 0.8239 (pmm) REVERT: B 873 TYR cc_start: 0.9402 (OUTLIER) cc_final: 0.9112 (m-10) REVERT: C 46 SER cc_start: 0.8611 (m) cc_final: 0.8207 (p) REVERT: C 129 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7517 (tttt) REVERT: C 133 PHE cc_start: 0.7144 (OUTLIER) cc_final: 0.6309 (m-80) REVERT: C 176 LEU cc_start: 0.5171 (OUTLIER) cc_final: 0.4464 (mp) REVERT: C 241 LEU cc_start: 0.7674 (mm) cc_final: 0.7351 (mm) REVERT: C 586 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7777 (m-30) REVERT: C 873 TYR cc_start: 0.9072 (OUTLIER) cc_final: 0.8745 (m-80) REVERT: C 973 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8978 (pt) outliers start: 66 outliers final: 53 residues processed: 190 average time/residue: 0.3184 time to fit residues: 104.8759 Evaluate side-chains 174 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 112 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 7 optimal weight: 7.9990 chunk 299 optimal weight: 0.8980 chunk 279 optimal weight: 5.9990 chunk 252 optimal weight: 5.9990 chunk 229 optimal weight: 0.6980 chunk 226 optimal weight: 0.9980 chunk 217 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 245 optimal weight: 7.9990 chunk 240 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A 907 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 188 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.089617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.070100 restraints weight = 87721.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.072449 restraints weight = 43135.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.073954 restraints weight = 27316.528| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 26529 Z= 0.126 Angle : 0.660 14.982 36234 Z= 0.317 Chirality : 0.048 0.622 4251 Planarity : 0.004 0.055 4557 Dihedral : 6.886 86.270 4775 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.56 % Allowed : 24.01 % Favored : 73.43 % 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: -1.44 (0.15), residues: 3159 helix: 1.27 (0.20), residues: 687 sheet: -1.39 (0.19), residues: 705 loop : -1.73 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 104 HIS 0.003 0.000 HIS C1048 PHE 0.030 0.001 PHE C 592 TYR 0.037 0.001 TYR A 636 ARG 0.005 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 48) link_NAG-ASN : angle 3.43718 ( 144) link_BETA1-4 : bond 0.00515 ( 18) link_BETA1-4 : angle 1.90312 ( 54) hydrogen bonds : bond 0.03564 ( 906) hydrogen bonds : angle 5.31604 ( 2475) SS BOND : bond 0.00308 ( 39) SS BOND : angle 1.42776 ( 78) covalent geometry : bond 0.00291 (26424) covalent geometry : angle 0.61759 (35958) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6915.99 seconds wall clock time: 123 minutes 13.99 seconds (7393.99 seconds total)