Starting phenix.real_space_refine on Mon Aug 25 07:01:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x4h_38049/08_2025/8x4h_38049.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x4h_38049/08_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_38049/08_2025/8x4h_38049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x4h_38049/08_2025/8x4h_38049.map" model { file = "/net/cci-nas-00/data/ceres_data/8x4h_38049/08_2025/8x4h_38049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x4h_38049/08_2025/8x4h_38049.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.63, per 1000 atoms: 0.22 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: 2.13 Conformation dependent library (CDL) restraints added in 793.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 1.09 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: 4.52 Time building geometry restraints manager: 2.65 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: 0.03 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 21.520 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.800 ------------------------------------------------------------------------------- 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 : 16.10 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.014 0.001 ARG C1107 TYR 0.024 0.002 TYR C 873 PHE 0.068 0.002 PHE B 592 TRP 0.045 0.002 TRP C 633 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00604 (26424) covalent geometry : angle 0.85137 (35958) SS BOND : bond 0.00417 ( 39) SS BOND : angle 1.53934 ( 78) hydrogen bonds : bond 0.18951 ( 906) hydrogen bonds : angle 8.41402 ( 2475) link_BETA1-4 : bond 0.00478 ( 18) link_BETA1-4 : angle 2.28803 ( 54) link_NAG-ASN : bond 0.00696 ( 48) link_NAG-ASN : angle 3.66097 ( 144) *********************** 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 : 0.741 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: 0.7976 (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: 0.1454 time to fit residues: 38.8516 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 : 0.613 ------------------------------------------------------------------------------- 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 197 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 394 ASN B 487 ASN B 804 GLN B1106 GLN C 30 ASN C 607 GLN C 804 GLN C 957 GLN C1036 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.086817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.066661 restraints weight = 88674.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.068822 restraints weight = 45713.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.070249 restraints weight = 29935.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.071141 restraints weight = 22679.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.071707 restraints weight = 18974.876| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 26529 Z= 0.308 Angle : 0.859 16.374 36234 Z= 0.414 Chirality : 0.055 0.664 4251 Planarity : 0.005 0.049 4557 Dihedral : 13.218 113.782 4796 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 5.69 % Allowed : 21.09 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.14), residues: 3159 helix: 0.75 (0.20), residues: 696 sheet: -1.49 (0.20), residues: 630 loop : -2.08 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 214 TYR 0.025 0.002 TYR C1067 PHE 0.044 0.002 PHE C 59 TRP 0.028 0.002 TRP C 633 HIS 0.005 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00690 (26424) covalent geometry : angle 0.80835 (35958) SS BOND : bond 0.00471 ( 39) SS BOND : angle 1.50726 ( 78) hydrogen bonds : bond 0.04734 ( 906) hydrogen bonds : angle 6.25828 ( 2475) link_BETA1-4 : bond 0.00742 ( 18) link_BETA1-4 : angle 3.67597 ( 54) link_NAG-ASN : bond 0.00787 ( 48) link_NAG-ASN : angle 4.04824 ( 144) *********************** 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 286 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 128 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7430 (tp) REVERT: A 366 SER cc_start: 0.8651 (m) cc_final: 0.8367 (p) REVERT: A 740 MET cc_start: 0.7925 (ttt) cc_final: 0.6598 (ttt) REVERT: A 759 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8423 (t80) REVERT: A 1039 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8732 (ptm160) REVERT: B 104 TRP cc_start: 0.7509 (m-90) cc_final: 0.7073 (m-90) REVERT: B 269 TYR cc_start: 0.7785 (m-80) cc_final: 0.7535 (m-80) REVERT: B 421 TYR cc_start: 0.7441 (m-10) cc_final: 0.7050 (m-10) REVERT: B 902 MET cc_start: 0.9353 (mmm) cc_final: 0.9045 (tpt) REVERT: C 129 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7445 (tttt) REVERT: C 133 PHE cc_start: 0.7174 (OUTLIER) cc_final: 0.6338 (m-80) REVERT: C 176 LEU cc_start: 0.5296 (OUTLIER) cc_final: 0.4791 (mp) REVERT: C 214 ARG cc_start: 0.0981 (OUTLIER) cc_final: 0.0139 (mmm160) REVERT: C 414 GLN cc_start: 0.6329 (mm-40) cc_final: 0.5970 (mm-40) REVERT: C 850 ILE cc_start: 0.5277 (mp) cc_final: 0.5021 (mt) REVERT: C 878 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8932 (tt) REVERT: C 1039 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8518 (ptm160) outliers start: 158 outliers final: 76 residues processed: 269 average time/residue: 0.1250 time to fit residues: 56.8921 Evaluate side-chains 193 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 108 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 117 LEU 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 425 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 53 ASP 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 189 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 553 THR 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 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 781 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 135 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 214 ARG Chi-restraints excluded: chain C residue 229 LEU 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 551 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 642 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 760 CYS Chi-restraints excluded: chain C residue 866 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 77 optimal weight: 0.6980 chunk 209 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 218 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 267 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 296 optimal weight: 0.9980 chunk 225 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 253 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 B1005 GLN C1036 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.089521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.069535 restraints weight = 88429.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.071889 restraints weight = 43475.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.073407 restraints weight = 27588.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.074373 restraints weight = 20540.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.074947 restraints weight = 16949.285| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1796 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= 0.131 Angle : 0.711 15.479 36234 Z= 0.343 Chirality : 0.051 0.629 4251 Planarity : 0.004 0.063 4557 Dihedral : 9.930 106.314 4781 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.12 % Favored : 92.85 % Rotamer: Outliers : 3.46 % Allowed : 22.43 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.15), residues: 3159 helix: 0.99 (0.20), residues: 693 sheet: -1.43 (0.21), residues: 591 loop : -1.92 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 319 TYR 0.023 0.001 TYR B 369 PHE 0.031 0.001 PHE C 592 TRP 0.018 0.001 TRP C 633 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00292 (26424) covalent geometry : angle 0.65933 (35958) SS BOND : bond 0.00393 ( 39) SS BOND : angle 1.69231 ( 78) hydrogen bonds : bond 0.04074 ( 906) hydrogen bonds : angle 5.90456 ( 2475) link_BETA1-4 : bond 0.00531 ( 18) link_BETA1-4 : angle 3.00946 ( 54) link_NAG-ASN : bond 0.00664 ( 48) link_NAG-ASN : angle 3.69203 ( 144) *********************** 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 232 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 136 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7455 (pp) REVERT: A 759 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8373 (t80) REVERT: A 869 MET cc_start: 0.9133 (ptp) cc_final: 0.8882 (ptp) REVERT: B 104 TRP cc_start: 0.7302 (m-90) cc_final: 0.6944 (m-90) REVERT: B 269 TYR cc_start: 0.7742 (m-80) cc_final: 0.7420 (m-80) REVERT: B 421 TYR cc_start: 0.7557 (m-10) cc_final: 0.7195 (m-10) REVERT: B 591 SER cc_start: 0.7556 (OUTLIER) cc_final: 0.7134 (m) REVERT: B 869 MET cc_start: 0.8517 (pmm) cc_final: 0.8284 (pmm) REVERT: C 133 PHE cc_start: 0.6714 (OUTLIER) cc_final: 0.5806 (m-80) REVERT: C 214 ARG cc_start: 0.1158 (OUTLIER) cc_final: 0.0638 (mmm160) REVERT: C 878 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8877 (tt) REVERT: C 882 ILE cc_start: 0.9353 (pt) cc_final: 0.8934 (mt) outliers start: 96 outliers final: 37 residues processed: 221 average time/residue: 0.1339 time to fit residues: 50.9587 Evaluate side-chains 157 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 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 410 ILE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 907 ASN 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 179 LEU Chi-restraints excluded: chain B residue 189 LEU 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 998 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER 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 635 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 973 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 295 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 229 optimal weight: 0.0770 chunk 70 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 258 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 233 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B1005 GLN C 317 ASN C1036 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.088472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.068663 restraints weight = 88019.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.070893 restraints weight = 44861.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.072342 restraints weight = 29097.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.073232 restraints weight = 21955.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.073732 restraints weight = 18372.346| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 26529 Z= 0.172 Angle : 0.694 15.575 36234 Z= 0.336 Chirality : 0.049 0.637 4251 Planarity : 0.004 0.049 4557 Dihedral : 8.383 100.415 4781 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.50 % Favored : 92.47 % Rotamer: Outliers : 4.10 % Allowed : 22.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.15), residues: 3159 helix: 1.06 (0.20), residues: 693 sheet: -1.37 (0.20), residues: 636 loop : -1.91 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.016 0.001 TYR C 837 PHE 0.025 0.001 PHE C 592 TRP 0.021 0.002 TRP B 633 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00391 (26424) covalent geometry : angle 0.64657 (35958) SS BOND : bond 0.00578 ( 39) SS BOND : angle 1.46167 ( 78) hydrogen bonds : bond 0.03879 ( 906) hydrogen bonds : angle 5.72395 ( 2475) link_BETA1-4 : bond 0.00430 ( 18) link_BETA1-4 : angle 2.63952 ( 54) link_NAG-ASN : bond 0.00560 ( 48) link_NAG-ASN : angle 3.59004 ( 144) *********************** 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 236 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 122 time to evaluate : 0.981 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 371 PHE cc_start: 0.4091 (m-10) cc_final: 0.3867 (m-10) REVERT: A 492 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7477 (pt) REVERT: A 759 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8408 (t80) REVERT: A 981 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8410 (mm) REVERT: A 1039 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8676 (ptm160) REVERT: B 104 TRP cc_start: 0.7303 (m-90) cc_final: 0.7065 (m-90) REVERT: B 269 TYR cc_start: 0.7780 (m-80) cc_final: 0.7496 (m-80) REVERT: B 421 TYR cc_start: 0.7571 (m-10) cc_final: 0.7168 (m-10) REVERT: B 588 THR cc_start: 0.9366 (OUTLIER) cc_final: 0.9110 (p) REVERT: B 591 SER cc_start: 0.7654 (OUTLIER) cc_final: 0.7337 (m) REVERT: B 592 PHE cc_start: 0.6072 (t80) cc_final: 0.5741 (t80) REVERT: B 633 TRP cc_start: 0.6981 (p90) cc_final: 0.6557 (p90) REVERT: B 699 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8750 (mt) REVERT: B 869 MET cc_start: 0.8548 (pmm) cc_final: 0.8140 (pmm) REVERT: B 873 TYR cc_start: 0.9406 (OUTLIER) cc_final: 0.9123 (m-10) REVERT: B 993 ILE cc_start: 0.9028 (mm) cc_final: 0.8722 (mt) REVERT: C 133 PHE cc_start: 0.7075 (OUTLIER) cc_final: 0.6178 (m-80) REVERT: C 176 LEU cc_start: 0.5234 (OUTLIER) cc_final: 0.4697 (mp) REVERT: C 214 ARG cc_start: 0.1086 (OUTLIER) cc_final: 0.0614 (mmm160) REVERT: C 878 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8955 (tt) REVERT: C 1050 MET cc_start: 0.8906 (ptp) cc_final: 0.8687 (ptt) outliers start: 114 outliers final: 60 residues processed: 223 average time/residue: 0.1383 time to fit residues: 51.7495 Evaluate side-chains 184 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 112 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 339 HIS Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 410 ILE 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 495 TYR 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 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 785 VAL 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 981 LEU Chi-restraints excluded: chain A residue 1039 ARG 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 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 366 SER 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 590 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 631 PRO Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 699 LEU 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 B residue 1073 LYS 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 176 LEU 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 503 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET 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 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 4 optimal weight: 0.0870 chunk 222 optimal weight: 0.0770 chunk 15 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 159 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 169 optimal weight: 3.9990 chunk 184 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.090133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.070432 restraints weight = 87300.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.072802 restraints weight = 42937.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.074320 restraints weight = 27197.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.075278 restraints weight = 20195.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.075847 restraints weight = 16655.803| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2345 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= 0.112 Angle : 0.657 15.109 36234 Z= 0.317 Chirality : 0.048 0.650 4251 Planarity : 0.004 0.054 4557 Dihedral : 7.735 97.297 4781 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.42 % Allowed : 22.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.15), residues: 3159 helix: 1.15 (0.20), residues: 696 sheet: -1.20 (0.20), residues: 645 loop : -1.84 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 246 TYR 0.016 0.001 TYR B 501 PHE 0.015 0.001 PHE C 592 TRP 0.013 0.001 TRP B 633 HIS 0.003 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00251 (26424) covalent geometry : angle 0.60704 (35958) SS BOND : bond 0.00264 ( 39) SS BOND : angle 1.74233 ( 78) hydrogen bonds : bond 0.03654 ( 906) hydrogen bonds : angle 5.54677 ( 2475) link_BETA1-4 : bond 0.00436 ( 18) link_BETA1-4 : angle 2.21033 ( 54) link_NAG-ASN : bond 0.00578 ( 48) link_NAG-ASN : angle 3.60307 ( 144) *********************** 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 236 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 141 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7437 (pt) REVERT: A 759 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8389 (t80) REVERT: A 981 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8464 (mm) REVERT: B 269 TYR cc_start: 0.7774 (m-80) cc_final: 0.7468 (m-80) REVERT: B 421 TYR cc_start: 0.7573 (m-10) cc_final: 0.7171 (m-10) REVERT: B 588 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.9085 (p) REVERT: B 591 SER cc_start: 0.7468 (OUTLIER) cc_final: 0.7229 (m) REVERT: B 592 PHE cc_start: 0.6004 (t80) cc_final: 0.5493 (t80) REVERT: B 869 MET cc_start: 0.8456 (pmm) cc_final: 0.8131 (pmm) REVERT: B 873 TYR cc_start: 0.9372 (OUTLIER) cc_final: 0.9068 (m-10) REVERT: C 129 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7527 (tttt) REVERT: C 133 PHE cc_start: 0.6971 (OUTLIER) cc_final: 0.6283 (m-80) REVERT: C 214 ARG cc_start: 0.0932 (OUTLIER) cc_final: 0.0696 (mmm160) REVERT: C 241 LEU cc_start: 0.7572 (mm) cc_final: 0.7284 (mm) REVERT: C 873 TYR cc_start: 0.9100 (OUTLIER) cc_final: 0.8685 (m-80) REVERT: C 882 ILE cc_start: 0.9304 (pt) cc_final: 0.8920 (mt) REVERT: C 1050 MET cc_start: 0.8868 (ptp) cc_final: 0.8624 (ptt) outliers start: 95 outliers final: 48 residues processed: 226 average time/residue: 0.1343 time to fit residues: 52.2235 Evaluate side-chains 173 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 115 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 90 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 410 ILE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 595 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 786 LYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 981 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 350 VAL Chi-restraints excluded: chain B residue 523 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 591 SER 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 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1097 SER 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 200 TYR Chi-restraints excluded: chain C residue 205 SER 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 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 873 TYR Chi-restraints excluded: chain C residue 973 ILE 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 239 optimal weight: 8.9990 chunk 222 optimal weight: 0.1980 chunk 72 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 147 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 137 optimal weight: 6.9990 chunk 271 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 199 optimal weight: 3.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN B 955 ASN C 448 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.087850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.068117 restraints weight = 88333.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.070322 restraints weight = 45214.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.071765 restraints weight = 29413.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.072659 restraints weight = 22174.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.073168 restraints weight = 18499.982| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 26529 Z= 0.205 Angle : 0.697 15.519 36234 Z= 0.338 Chirality : 0.049 0.629 4251 Planarity : 0.004 0.059 4557 Dihedral : 7.665 95.091 4781 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.63 % Favored : 92.34 % Rotamer: Outliers : 3.64 % Allowed : 23.04 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.15), residues: 3159 helix: 1.12 (0.20), residues: 696 sheet: -1.32 (0.20), residues: 663 loop : -1.83 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.016 0.001 TYR A 837 PHE 0.021 0.001 PHE C 592 TRP 0.021 0.002 TRP B 633 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00470 (26424) covalent geometry : angle 0.65099 (35958) SS BOND : bond 0.00414 ( 39) SS BOND : angle 1.67551 ( 78) hydrogen bonds : bond 0.03876 ( 906) hydrogen bonds : angle 5.60264 ( 2475) link_BETA1-4 : bond 0.00411 ( 18) link_BETA1-4 : angle 2.12094 ( 54) link_NAG-ASN : bond 0.00556 ( 48) link_NAG-ASN : angle 3.62425 ( 144) *********************** 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 220 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 119 time to evaluate : 0.990 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 759 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8504 (t80) REVERT: B 269 TYR cc_start: 0.7800 (m-80) cc_final: 0.7534 (m-80) REVERT: B 421 TYR cc_start: 0.7660 (m-10) cc_final: 0.7077 (m-10) REVERT: B 588 THR cc_start: 0.9334 (OUTLIER) cc_final: 0.9123 (p) REVERT: B 591 SER cc_start: 0.7634 (OUTLIER) cc_final: 0.7370 (m) REVERT: B 592 PHE cc_start: 0.6256 (t80) cc_final: 0.5987 (t80) REVERT: B 869 MET cc_start: 0.8558 (pmm) cc_final: 0.8324 (pmm) REVERT: B 993 ILE cc_start: 0.9037 (mm) cc_final: 0.8755 (mt) REVERT: C 129 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7514 (tttt) REVERT: C 133 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.6420 (m-80) REVERT: C 176 LEU cc_start: 0.5209 (OUTLIER) cc_final: 0.4473 (mp) REVERT: C 214 ARG cc_start: 0.0964 (OUTLIER) cc_final: 0.0669 (mmm160) REVERT: C 873 TYR cc_start: 0.9141 (OUTLIER) cc_final: 0.8827 (m-80) REVERT: C 882 ILE cc_start: 0.9287 (pt) cc_final: 0.9019 (mt) outliers start: 101 outliers final: 65 residues processed: 208 average time/residue: 0.1309 time to fit residues: 46.8842 Evaluate side-chains 184 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 111 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 343 ASN Chi-restraints excluded: chain A residue 410 ILE 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 495 TYR 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 642 VAL 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 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 977 LEU Chi-restraints excluded: chain A residue 1039 ARG 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 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 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 591 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 1073 LYS 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 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 368 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 791 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 1076 THR 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 250 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 149 optimal weight: 0.5980 chunk 167 optimal weight: 7.9990 chunk 182 optimal weight: 20.0000 chunk 59 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 311 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.088486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.068916 restraints weight = 87981.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.071143 restraints weight = 44663.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.072560 restraints weight = 28910.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.073499 restraints weight = 21909.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.074121 restraints weight = 18105.261| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26529 Z= 0.150 Angle : 0.666 15.286 36234 Z= 0.323 Chirality : 0.048 0.630 4251 Planarity : 0.004 0.064 4557 Dihedral : 7.466 93.168 4781 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.35 % Allowed : 23.00 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.15), residues: 3159 helix: 1.18 (0.20), residues: 693 sheet: -1.25 (0.20), residues: 657 loop : -1.80 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 44 TYR 0.017 0.001 TYR A 380 PHE 0.033 0.001 PHE A 592 TRP 0.017 0.001 TRP B 633 HIS 0.003 0.000 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00343 (26424) covalent geometry : angle 0.62201 (35958) SS BOND : bond 0.00334 ( 39) SS BOND : angle 1.43185 ( 78) hydrogen bonds : bond 0.03703 ( 906) hydrogen bonds : angle 5.52441 ( 2475) link_BETA1-4 : bond 0.00454 ( 18) link_BETA1-4 : angle 2.00746 ( 54) link_NAG-ASN : bond 0.00536 ( 48) link_NAG-ASN : angle 3.53952 ( 144) *********************** 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 209 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 116 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7552 (pt) REVERT: A 759 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8506 (t80) REVERT: A 858 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8500 (mp) REVERT: B 269 TYR cc_start: 0.7804 (m-80) cc_final: 0.7506 (m-80) REVERT: B 421 TYR cc_start: 0.7664 (m-10) cc_final: 0.7075 (m-10) REVERT: B 588 THR cc_start: 0.9289 (OUTLIER) cc_final: 0.9043 (p) REVERT: B 591 SER cc_start: 0.7633 (OUTLIER) cc_final: 0.7365 (m) REVERT: B 869 MET cc_start: 0.8515 (pmm) cc_final: 0.8303 (pmm) REVERT: B 873 TYR cc_start: 0.9416 (OUTLIER) cc_final: 0.9139 (m-10) REVERT: B 993 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8717 (mt) REVERT: C 129 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7500 (tttt) REVERT: C 133 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.6293 (m-80) REVERT: C 176 LEU cc_start: 0.5109 (OUTLIER) cc_final: 0.4327 (mp) REVERT: C 241 LEU cc_start: 0.7537 (mm) cc_final: 0.7262 (mm) REVERT: C 873 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.8825 (m-80) REVERT: C 882 ILE cc_start: 0.9268 (pt) cc_final: 0.8990 (mt) outliers start: 93 outliers final: 58 residues processed: 203 average time/residue: 0.1284 time to fit residues: 45.1672 Evaluate side-chains 179 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 110 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 410 ILE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 TYR 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 858 LEU 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 1039 ARG 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 179 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 523 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 591 SER 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 873 TYR Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1097 SER 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 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU 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 1076 THR 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 299 optimal weight: 8.9990 chunk 165 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 195 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 184 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 315 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1005 GLN C 66 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.088866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.069489 restraints weight = 87503.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.071701 restraints weight = 44719.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.073091 restraints weight = 28923.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.074001 restraints weight = 22004.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.074565 restraints weight = 18210.089| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26529 Z= 0.131 Angle : 0.662 15.195 36234 Z= 0.320 Chirality : 0.048 0.634 4251 Planarity : 0.004 0.071 4557 Dihedral : 7.254 90.919 4777 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.24 % Allowed : 23.29 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.15), residues: 3159 helix: 1.20 (0.20), residues: 690 sheet: -1.24 (0.20), residues: 657 loop : -1.75 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1039 TYR 0.025 0.001 TYR B 369 PHE 0.021 0.001 PHE A 592 TRP 0.033 0.001 TRP B 633 HIS 0.002 0.000 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00299 (26424) covalent geometry : angle 0.61734 (35958) SS BOND : bond 0.00315 ( 39) SS BOND : angle 1.28147 ( 78) hydrogen bonds : bond 0.03651 ( 906) hydrogen bonds : angle 5.46717 ( 2475) link_BETA1-4 : bond 0.00460 ( 18) link_BETA1-4 : angle 1.96200 ( 54) link_NAG-ASN : bond 0.00530 ( 48) link_NAG-ASN : angle 3.59333 ( 144) *********************** 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 212 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 122 time to evaluate : 0.722 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: 0.8049 (OUTLIER) cc_final: 0.7640 (pt) REVERT: B 269 TYR cc_start: 0.7800 (m-80) cc_final: 0.7518 (m-80) REVERT: B 421 TYR cc_start: 0.7608 (m-10) cc_final: 0.6998 (m-10) REVERT: B 592 PHE cc_start: 0.5939 (t80) cc_final: 0.5635 (t80) REVERT: B 869 MET cc_start: 0.8520 (pmm) cc_final: 0.8277 (pmm) REVERT: B 873 TYR cc_start: 0.9410 (OUTLIER) cc_final: 0.9131 (m-10) REVERT: C 129 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7578 (tttt) REVERT: C 133 PHE cc_start: 0.7003 (OUTLIER) cc_final: 0.6219 (m-80) REVERT: C 176 LEU cc_start: 0.5116 (OUTLIER) cc_final: 0.4357 (mp) REVERT: C 873 TYR cc_start: 0.9098 (OUTLIER) cc_final: 0.8813 (m-80) REVERT: C 882 ILE cc_start: 0.9248 (pt) cc_final: 0.8953 (mt) outliers start: 90 outliers final: 60 residues processed: 205 average time/residue: 0.1294 time to fit residues: 45.6717 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 : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 410 ILE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 TYR 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 699 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 785 VAL 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 1039 ARG 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 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 523 THR 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 697 MET 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 B residue 1076 THR Chi-restraints excluded: chain C residue 113 LYS 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 468 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 858 LEU 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 1076 THR 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 20 optimal weight: 0.0870 chunk 142 optimal weight: 7.9990 chunk 137 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 264 optimal weight: 4.9990 chunk 159 optimal weight: 0.0670 chunk 11 optimal weight: 30.0000 chunk 244 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.088596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.069052 restraints weight = 87784.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.071271 restraints weight = 44641.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.072724 restraints weight = 28948.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.073643 restraints weight = 21804.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.074194 restraints weight = 18111.964| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26529 Z= 0.147 Angle : 0.666 15.235 36234 Z= 0.321 Chirality : 0.048 0.629 4251 Planarity : 0.004 0.058 4557 Dihedral : 7.147 88.615 4777 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.88 % Allowed : 23.61 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.15), residues: 3159 helix: 1.18 (0.20), residues: 696 sheet: -1.24 (0.20), residues: 657 loop : -1.74 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 983 TYR 0.018 0.001 TYR A 636 PHE 0.020 0.001 PHE C 238 TRP 0.028 0.001 TRP B 633 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00336 (26424) covalent geometry : angle 0.62239 (35958) SS BOND : bond 0.00307 ( 39) SS BOND : angle 1.31180 ( 78) hydrogen bonds : bond 0.03650 ( 906) hydrogen bonds : angle 5.43294 ( 2475) link_BETA1-4 : bond 0.00450 ( 18) link_BETA1-4 : angle 1.93994 ( 54) link_NAG-ASN : bond 0.00512 ( 48) link_NAG-ASN : angle 3.53306 ( 144) *********************** 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 199 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 119 time to evaluate : 0.815 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: 0.8068 (OUTLIER) cc_final: 0.7668 (pt) REVERT: B 421 TYR cc_start: 0.7647 (m-10) cc_final: 0.7005 (m-10) REVERT: B 830 ASP cc_start: 0.4582 (t0) cc_final: 0.4276 (m-30) REVERT: B 869 MET cc_start: 0.8572 (pmm) cc_final: 0.8304 (pmm) REVERT: B 873 TYR cc_start: 0.9427 (OUTLIER) cc_final: 0.9130 (m-10) REVERT: B 993 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8695 (mt) REVERT: B 1050 MET cc_start: 0.7841 (mtm) cc_final: 0.7403 (mtt) REVERT: C 129 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7513 (tttt) REVERT: C 133 PHE cc_start: 0.6956 (OUTLIER) cc_final: 0.6110 (m-80) REVERT: C 176 LEU cc_start: 0.5242 (OUTLIER) cc_final: 0.4439 (mp) REVERT: C 241 LEU cc_start: 0.7485 (mm) cc_final: 0.7207 (mm) REVERT: C 873 TYR cc_start: 0.9088 (OUTLIER) cc_final: 0.8827 (m-80) REVERT: C 882 ILE cc_start: 0.9264 (pt) cc_final: 0.8960 (mt) outliers start: 80 outliers final: 62 residues processed: 193 average time/residue: 0.1331 time to fit residues: 43.9534 Evaluate side-chains 183 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 114 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 410 ILE 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 495 TYR 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 699 LEU 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 785 VAL 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 1039 ARG 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 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 523 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 113 LYS 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 468 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU 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 1076 THR 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 121 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 168 optimal weight: 0.4980 chunk 68 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 259 optimal weight: 3.9990 chunk 296 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 256 optimal weight: 0.3980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.088764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.068875 restraints weight = 87541.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.071162 restraints weight = 43405.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.072661 restraints weight = 27780.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.073591 restraints weight = 20728.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.074187 restraints weight = 17144.268| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26529 Z= 0.135 Angle : 0.662 15.175 36234 Z= 0.318 Chirality : 0.048 0.629 4251 Planarity : 0.004 0.062 4557 Dihedral : 7.040 86.812 4777 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.59 % Allowed : 23.94 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.15), residues: 3159 helix: 1.23 (0.20), residues: 693 sheet: -1.10 (0.20), residues: 627 loop : -1.75 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 319 TYR 0.025 0.001 TYR B 369 PHE 0.040 0.001 PHE B 592 TRP 0.024 0.001 TRP B 633 HIS 0.002 0.000 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00310 (26424) covalent geometry : angle 0.61901 (35958) SS BOND : bond 0.00306 ( 39) SS BOND : angle 1.27145 ( 78) hydrogen bonds : bond 0.03595 ( 906) hydrogen bonds : angle 5.39980 ( 2475) link_BETA1-4 : bond 0.00474 ( 18) link_BETA1-4 : angle 1.93065 ( 54) link_NAG-ASN : bond 0.00510 ( 48) link_NAG-ASN : angle 3.48837 ( 144) ********************** 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 191 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 119 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7693 (pt) REVERT: B 421 TYR cc_start: 0.7603 (m-10) cc_final: 0.6958 (m-10) REVERT: B 873 TYR cc_start: 0.9421 (OUTLIER) cc_final: 0.9197 (m-10) REVERT: B 993 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8669 (mt) REVERT: C 133 PHE cc_start: 0.6968 (OUTLIER) cc_final: 0.6166 (m-80) REVERT: C 873 TYR cc_start: 0.9066 (OUTLIER) cc_final: 0.8778 (m-80) REVERT: C 882 ILE cc_start: 0.9256 (pt) cc_final: 0.8943 (mt) outliers start: 72 outliers final: 59 residues processed: 187 average time/residue: 0.1293 time to fit residues: 41.2188 Evaluate side-chains 176 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 112 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 133 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 410 ILE 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 495 TYR 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 699 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 785 VAL 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 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 523 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 113 LYS 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 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 468 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU 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 1076 THR 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 115 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 223 optimal weight: 20.0000 chunk 143 optimal weight: 30.0000 chunk 48 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 118 optimal weight: 0.2980 chunk 155 optimal weight: 4.9990 chunk 262 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.087914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.067951 restraints weight = 87704.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.070189 restraints weight = 44435.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.071644 restraints weight = 28775.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.072562 restraints weight = 21654.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.073074 restraints weight = 18064.598| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 26529 Z= 0.175 Angle : 0.681 15.254 36234 Z= 0.329 Chirality : 0.048 0.625 4251 Planarity : 0.004 0.060 4557 Dihedral : 7.070 86.142 4777 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.70 % Allowed : 24.05 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.15), residues: 3159 helix: 1.21 (0.20), residues: 693 sheet: -1.26 (0.20), residues: 657 loop : -1.72 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1039 TYR 0.045 0.001 TYR B 904 PHE 0.017 0.001 PHE B 135 TRP 0.022 0.001 TRP B 633 HIS 0.002 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00399 (26424) covalent geometry : angle 0.63900 (35958) SS BOND : bond 0.00314 ( 39) SS BOND : angle 1.35736 ( 78) hydrogen bonds : bond 0.03708 ( 906) hydrogen bonds : angle 5.44199 ( 2475) link_BETA1-4 : bond 0.00458 ( 18) link_BETA1-4 : angle 1.92909 ( 54) link_NAG-ASN : bond 0.00511 ( 48) link_NAG-ASN : angle 3.50183 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3336.78 seconds wall clock time: 59 minutes 3.03 seconds (3543.03 seconds total)