Starting phenix.real_space_refine on Tue Aug 26 23:35:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xuy_38686/08_2025/8xuy_38686.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xuy_38686/08_2025/8xuy_38686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xuy_38686/08_2025/8xuy_38686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xuy_38686/08_2025/8xuy_38686.map" model { file = "/net/cci-nas-00/data/ceres_data/8xuy_38686/08_2025/8xuy_38686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xuy_38686/08_2025/8xuy_38686.cif" } resolution = 3.14 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= -0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9794 atoms to isotropic. 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 166 5.16 5 C 22241 2.51 5 N 5666 2.21 5 O 6754 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 34827 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8056 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 55, 'TRANS': 972} Chain breaks: 6 Chain: "B" Number of atoms: 8017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8017 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 53, 'TRANS': 969} Chain breaks: 6 Chain: "C" Number of atoms: 8018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8018 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 54, 'TRANS': 968} Chain breaks: 6 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "O" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} 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 Time building chain proxies: 8.33, per 1000 atoms: 0.24 Number of scatterers: 34827 At special positions: 0 Unit cell: (135.675, 160.8, 235.17, 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 166 16.00 O 6754 8.00 N 5666 7.00 C 22241 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 300 " distance=2.03 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 431 " distance=2.03 Simple disulfide: pdb=" SG CYS A 390 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.03 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 647 " distance=2.03 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 300 " distance=2.03 Simple disulfide: pdb=" SG CYS B 335 " - pdb=" SG CYS B 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 431 " distance=2.03 Simple disulfide: pdb=" SG CYS B 390 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 300 " distance=2.03 Simple disulfide: pdb=" SG CYS C 335 " - pdb=" SG CYS C 360 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 431 " distance=2.03 Simple disulfide: pdb=" SG CYS C 390 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 479 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.03 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 647 " distance=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS O 133 " - pdb=" SG CYS O 141 " distance=2.03 Simple disulfide: pdb=" SG CYS O 344 " - pdb=" SG CYS O 361 " distance=2.03 Simple disulfide: pdb=" SG CYS O 530 " - pdb=" SG CYS O 542 " 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 ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " ALPHA1-6 " BMA Q 3 " - " MAN Q 5 " " BMA S 3 " - " MAN S 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 233 " " NAG A1305 " - " ASN A 281 " " NAG A1306 " - " ASN A 614 " " NAG A1307 " - " ASN A 655 " " NAG A1308 " - " ASN A 707 " " NAG A1309 " - " ASN A1072 " " NAG A1310 " - " ASN A1096 " " NAG A1311 " - " ASN A1132 " " NAG A1312 " - " ASN A 330 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 281 " " NAG B1304 " - " ASN B 614 " " NAG B1305 " - " ASN B 655 " " NAG B1306 " - " ASN B 707 " " NAG B1307 " - " ASN B1072 " " NAG B1308 " - " ASN B1096 " " NAG B1309 " - " ASN B 233 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 233 " " NAG C1304 " - " ASN C 281 " " NAG C1305 " - " ASN C 614 " " NAG C1306 " - " ASN C 655 " " NAG C1307 " - " ASN C 707 " " NAG C1308 " - " ASN C1072 " " NAG C1309 " - " ASN C1096 " " NAG C1310 " - " ASN C1132 " " NAG C1311 " - " ASN C 342 " " NAG C1312 " - " ASN C 353 " " NAG D 701 " - " ASN D 322 " " NAG D 702 " - " ASN D 432 " " NAG D 703 " - " ASN D 53 " " NAG E 1 " - " ASN A 715 " " NAG F 1 " - " ASN A 799 " " NAG G 1 " - " ASN B 715 " " NAG H 1 " - " ASN B 799 " " NAG I 1 " - " ASN C 165 " " NAG J 1 " - " ASN C 715 " " NAG K 1 " - " ASN C 799 " " NAG L 1 " - " ASN D 546 " " NAG M 1 " - " ASN O 53 " " NAG N 1 " - " ASN O 546 " " NAG O 701 " - " ASN O 322 " " NAG O 702 " - " ASN O 432 " " NAG P 1 " - " ASN D 90 " " NAG Q 1 " - " ASN D 103 " " NAG R 1 " - " ASN O 90 " " NAG S 1 " - " ASN O 103 " Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 1.2 microseconds 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8014 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 58 sheets defined 36.1% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 382 through 387 removed outlier: 4.479A pdb=" N ASN A 387 " --> pdb=" O PRO A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 438 through 442 removed outlier: 4.048A pdb=" N SER A 442 " --> pdb=" O LYS A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 624 removed outlier: 3.618A pdb=" N VAL A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 741 Processing helix chain 'A' and resid 744 through 752 removed outlier: 3.791A pdb=" N SER A 748 " --> pdb=" O SER A 744 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN A 749 " --> pdb=" O THR A 745 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 750 " --> pdb=" O GLU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 758 through 781 removed outlier: 3.811A pdb=" N ASP A 773 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 774 " --> pdb=" O VAL A 770 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR A 776 " --> pdb=" O GLN A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 825 removed outlier: 3.515A pdb=" N VAL A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR A 825 " --> pdb=" O PHE A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 879 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 911 through 916 removed outlier: 3.701A pdb=" N TYR A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 939 removed outlier: 3.646A pdb=" N ASN A 923 " --> pdb=" O LYS A 919 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 928 " --> pdb=" O GLN A 924 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLN A 933 " --> pdb=" O ILE A 929 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP A 934 " --> pdb=" O GLY A 930 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR A 939 " --> pdb=" O SER A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 942 No H-bonds generated for 'chain 'A' and resid 940 through 942' Processing helix chain 'A' and resid 943 through 962 removed outlier: 3.620A pdb=" N ASN A 953 " --> pdb=" O VAL A 949 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 956 " --> pdb=" O HIS A 952 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 962 " --> pdb=" O ASN A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 966 removed outlier: 3.723A pdb=" N SER A 966 " --> pdb=" O GLN A 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 963 through 966' Processing helix chain 'A' and resid 974 through 979 Processing helix chain 'A' and resid 983 through 1030 removed outlier: 5.341A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLN A 990 " --> pdb=" O GLU A 986 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A1022 " --> pdb=" O ALA A1018 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A1023 " --> pdb=" O SER A1019 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR A1025 " --> pdb=" O ASN A1021 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER A1028 " --> pdb=" O ALA A1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 removed outlier: 4.041A pdb=" N VAL B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 303 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.677A pdb=" N LEU B 389 " --> pdb=" O LEU B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 406 No H-bonds generated for 'chain 'B' and resid 404 through 406' Processing helix chain 'B' and resid 614 through 624 removed outlier: 3.558A pdb=" N VAL B 618 " --> pdb=" O ASN B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 741 Processing helix chain 'B' and resid 744 through 752 removed outlier: 3.666A pdb=" N SER B 748 " --> pdb=" O SER B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 758 through 775 removed outlier: 3.934A pdb=" N ASP B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS B 774 " --> pdb=" O VAL B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 780 removed outlier: 3.688A pdb=" N VAL B 779 " --> pdb=" O ASN B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 823 Processing helix chain 'B' and resid 864 through 879 removed outlier: 3.656A pdb=" N ALA B 869 " --> pdb=" O ASP B 865 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN B 870 " --> pdb=" O GLU B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 911 through 916 removed outlier: 3.720A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 938 removed outlier: 3.993A pdb=" N ALA B 928 " --> pdb=" O GLN B 924 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY B 930 " --> pdb=" O ASN B 926 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 933 " --> pdb=" O ILE B 929 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 934 " --> pdb=" O GLY B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 942 No H-bonds generated for 'chain 'B' and resid 940 through 942' Processing helix chain 'B' and resid 943 through 963 removed outlier: 3.536A pdb=" N VAL B 949 " --> pdb=" O LYS B 945 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN B 953 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 956 " --> pdb=" O HIS B 952 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 960 " --> pdb=" O ALA B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 980 Processing helix chain 'B' and resid 983 through 986 Processing helix chain 'B' and resid 987 through 1031 removed outlier: 3.883A pdb=" N ARG B 993 " --> pdb=" O VAL B 989 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 994 " --> pdb=" O GLN B 990 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B1022 " --> pdb=" O ALA B1018 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B1031 " --> pdb=" O MET B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1116 No H-bonds generated for 'chain 'B' and resid 1114 through 1116' Processing helix chain 'C' and resid 293 through 303 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.872A pdb=" N PHE C 370 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 366 through 371' Processing helix chain 'C' and resid 382 through 386 removed outlier: 3.762A pdb=" N LYS C 385 " --> pdb=" O SER C 382 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 386 " --> pdb=" O PRO C 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 382 through 386' Processing helix chain 'C' and resid 405 through 409 Processing helix chain 'C' and resid 415 through 421 Processing helix chain 'C' and resid 614 through 625 removed outlier: 3.534A pdb=" N VAL C 618 " --> pdb=" O ASN C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 741 Processing helix chain 'C' and resid 744 through 752 Processing helix chain 'C' and resid 756 through 780 removed outlier: 3.543A pdb=" N ASP C 773 " --> pdb=" O ALA C 769 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR C 776 " --> pdb=" O GLN C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 removed outlier: 3.718A pdb=" N VAL C 824 " --> pdb=" O LEU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 864 through 882 removed outlier: 3.754A pdb=" N GLN C 870 " --> pdb=" O GLU C 866 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR C 881 " --> pdb=" O ALA C 877 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 882 " --> pdb=" O GLY C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 895 through 906 removed outlier: 3.639A pdb=" N ALA C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR C 902 " --> pdb=" O MET C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 917 removed outlier: 3.712A pdb=" N TYR C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 939 removed outlier: 3.930A pdb=" N ILE C 932 " --> pdb=" O ALA C 928 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN C 933 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP C 934 " --> pdb=" O GLY C 930 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR C 939 " --> pdb=" O SER C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 963 removed outlier: 3.894A pdb=" N VAL C 949 " --> pdb=" O LYS C 945 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL C 950 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 980 Processing helix chain 'C' and resid 983 through 1030 removed outlier: 4.238A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 994 " --> pdb=" O GLN C 990 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR C1005 " --> pdb=" O SER C1001 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA C1014 " --> pdb=" O LEU C1010 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER C1019 " --> pdb=" O GLU C1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.757A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 92 through 105 removed outlier: 3.550A pdb=" N GLY D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER D 105 " --> pdb=" O GLN D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.648A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 220 through 249 removed outlier: 3.793A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 292 through 300 removed outlier: 4.093A pdb=" N ALA D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 331 Processing helix chain 'D' and resid 365 through 384 Processing helix chain 'D' and resid 397 through 414 removed outlier: 4.032A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR D 414 " --> pdb=" O LEU D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 447 Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.353A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 484 removed outlier: 4.530A pdb=" N MET D 474 " --> pdb=" O LYS D 470 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LYS D 475 " --> pdb=" O ASP D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 509 Processing helix chain 'D' and resid 513 through 532 removed outlier: 3.516A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.645A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 564 removed outlier: 4.142A pdb=" N GLU D 564 " --> pdb=" O GLY D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 4.003A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'O' and resid 20 through 53 removed outlier: 4.226A pdb=" N LYS O 31 " --> pdb=" O THR O 27 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE O 32 " --> pdb=" O PHE O 28 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS O 34 " --> pdb=" O ASP O 30 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE O 40 " --> pdb=" O ALA O 36 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 83 removed outlier: 3.747A pdb=" N LYS O 74 " --> pdb=" O SER O 70 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU O 75 " --> pdb=" O ALA O 71 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN O 76 " --> pdb=" O PHE O 72 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU O 79 " --> pdb=" O GLU O 75 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR O 83 " --> pdb=" O LEU O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 104 Processing helix chain 'O' and resid 109 through 130 Processing helix chain 'O' and resid 147 through 152 Processing helix chain 'O' and resid 157 through 194 removed outlier: 4.789A pdb=" N GLN O 175 " --> pdb=" O GLU O 171 " (cutoff:3.500A) Proline residue: O 178 - end of helix Processing helix chain 'O' and resid 198 through 205 Processing helix chain 'O' and resid 220 through 252 removed outlier: 3.974A pdb=" N GLU O 224 " --> pdb=" O GLY O 220 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL O 226 " --> pdb=" O LEU O 222 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU O 227 " --> pdb=" O ILE O 223 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS O 228 " --> pdb=" O GLU O 224 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR O 229 " --> pdb=" O ASP O 225 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU O 231 " --> pdb=" O GLU O 227 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU O 232 " --> pdb=" O HIS O 228 " (cutoff:3.500A) Proline residue: O 235 - end of helix removed outlier: 3.539A pdb=" N ARG O 245 " --> pdb=" O HIS O 241 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA O 246 " --> pdb=" O ALA O 242 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA O 251 " --> pdb=" O LYS O 247 " (cutoff:3.500A) Processing helix chain 'O' and resid 275 through 279 Processing helix chain 'O' and resid 293 through 300 removed outlier: 3.818A pdb=" N VAL O 298 " --> pdb=" O THR O 294 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP O 299 " --> pdb=" O ASP O 295 " (cutoff:3.500A) Processing helix chain 'O' and resid 303 through 319 removed outlier: 3.534A pdb=" N PHE O 315 " --> pdb=" O ALA O 311 " (cutoff:3.500A) Processing helix chain 'O' and resid 324 through 331 removed outlier: 3.583A pdb=" N ASN O 330 " --> pdb=" O GLY O 326 " (cutoff:3.500A) Processing helix chain 'O' and resid 365 through 386 removed outlier: 3.841A pdb=" N HIS O 378 " --> pdb=" O HIS O 374 " (cutoff:3.500A) Processing helix chain 'O' and resid 389 through 393 Processing helix chain 'O' and resid 397 through 412 removed outlier: 4.329A pdb=" N HIS O 401 " --> pdb=" O ASN O 397 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU O 402 " --> pdb=" O GLU O 398 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY O 405 " --> pdb=" O HIS O 401 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N MET O 408 " --> pdb=" O VAL O 404 " (cutoff:3.500A) Processing helix chain 'O' and resid 414 through 422 removed outlier: 3.676A pdb=" N GLY O 422 " --> pdb=" O LEU O 418 " (cutoff:3.500A) Processing helix chain 'O' and resid 431 through 434 removed outlier: 3.753A pdb=" N THR O 434 " --> pdb=" O ASP O 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 431 through 434' Processing helix chain 'O' and resid 435 through 447 Processing helix chain 'O' and resid 449 through 466 removed outlier: 3.847A pdb=" N GLU O 457 " --> pdb=" O THR O 453 " (cutoff:3.500A) Processing helix chain 'O' and resid 469 through 471 No H-bonds generated for 'chain 'O' and resid 469 through 471' Processing helix chain 'O' and resid 472 through 480 Processing helix chain 'O' and resid 498 through 502 Processing helix chain 'O' and resid 503 through 508 removed outlier: 3.500A pdb=" N ASN O 508 " --> pdb=" O PHE O 504 " (cutoff:3.500A) Processing helix chain 'O' and resid 512 through 533 removed outlier: 4.275A pdb=" N TYR O 516 " --> pdb=" O PHE O 512 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR O 517 " --> pdb=" O ILE O 513 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU O 520 " --> pdb=" O TYR O 516 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE O 523 " --> pdb=" O THR O 519 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN O 524 " --> pdb=" O LEU O 520 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA O 533 " --> pdb=" O LEU O 529 " (cutoff:3.500A) Processing helix chain 'O' and resid 548 through 559 removed outlier: 3.879A pdb=" N MET O 557 " --> pdb=" O LYS O 553 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG O 559 " --> pdb=" O PHE O 555 " (cutoff:3.500A) Processing helix chain 'O' and resid 565 through 575 removed outlier: 3.587A pdb=" N VAL O 573 " --> pdb=" O ALA O 569 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL O 574 " --> pdb=" O LEU O 570 " (cutoff:3.500A) Processing helix chain 'O' and resid 581 through 588 Processing helix chain 'O' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.994A pdb=" N VAL A 36 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 9.675A pdb=" N ALA A 221 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N HIS A 207 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE A 203 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.554A pdb=" N PHE A 43 " --> pdb=" O PHE B 563 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.961A pdb=" N ASP A 286 " --> pdb=" O LYS A 277 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 64 through 65 removed outlier: 4.237A pdb=" N TYR A 264 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.968A pdb=" N LEU A 84 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLY A 103 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA A 242 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE A 101 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.968A pdb=" N LEU A 84 " --> pdb=" O PHE A 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.500A pdb=" N VAL A 120 " --> pdb=" O PHE A 127 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.657A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 310 through 318 removed outlier: 6.942A pdb=" N VAL A 593 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ASN A 316 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY A 591 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.697A pdb=" N ASN A 393 " --> pdb=" O GLU A 514 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS A 431 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 451 through 453 Processing sheet with id=AB4, first strand: chain 'A' and resid 537 through 541 removed outlier: 3.883A pdb=" N GLY A 546 " --> pdb=" O PHE A 539 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 581 " --> pdb=" O ASP A 576 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 585 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.209A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 700 through 702 Processing sheet with id=AB7, first strand: chain 'A' and resid 709 through 711 removed outlier: 3.800A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 715 through 726 removed outlier: 3.717A pdb=" N SER A 719 " --> pdb=" O THR A1064 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.767A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 785 through 786 Processing sheet with id=AC2, first strand: chain 'A' and resid 1087 through 1088 Processing sheet with id=AC3, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.669A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.216A pdb=" N VAL B 36 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N SER B 205 " --> pdb=" O PRO B 224 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE B 92 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 50 through 55 Processing sheet with id=AC6, first strand: chain 'B' and resid 106 through 107 Processing sheet with id=AC7, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.566A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 126 through 127 removed outlier: 3.739A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 277 through 278 removed outlier: 7.225A pdb=" N LYS B 277 " --> pdb=" O THR B 285 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 310 through 318 removed outlier: 7.071A pdb=" N VAL B 593 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASN B 316 " --> pdb=" O GLY B 591 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY B 591 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 323 through 324 removed outlier: 6.451A pdb=" N GLU B 323 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY B 546 " --> pdb=" O PHE B 539 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B 551 " --> pdb=" O ASP B 584 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 360 through 361 removed outlier: 6.781A pdb=" N CYS B 360 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 377 through 378 Processing sheet with id=AD5, first strand: chain 'B' and resid 451 through 453 Processing sheet with id=AD6, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AD7, first strand: chain 'B' and resid 652 through 658 removed outlier: 5.298A pdb=" N THR B 694 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASN B 656 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 673 " --> pdb=" O SER B 689 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 709 through 726 removed outlier: 6.725A pdb=" N SER B 709 " --> pdb=" O THR B1074 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR B1074 " --> pdb=" O SER B 709 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA B 711 " --> pdb=" O ASN B1072 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN B1072 " --> pdb=" O ALA B 711 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 719 " --> pdb=" O THR B1064 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY B1057 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B1054 " --> pdb=" O GLY B1057 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.677A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 785 through 786 Processing sheet with id=AE2, first strand: chain 'B' and resid 1079 through 1080 Processing sheet with id=AE3, first strand: chain 'B' and resid 1087 through 1088 Processing sheet with id=AE4, first strand: chain 'B' and resid 1092 through 1095 Processing sheet with id=AE5, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.913A pdb=" N ASN C 61 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N TYR C 268 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 266 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 264 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 93 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE C 201 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASP C 227 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE C 203 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N HIS C 207 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N ALA C 221 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL C 36 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.655A pdb=" N VAL C 47 " --> pdb=" O TYR C 278 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP C 286 " --> pdb=" O LYS C 277 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 101 through 107 removed outlier: 4.067A pdb=" N LEU C 240 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N TRP C 104 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLN C 238 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N PHE C 106 " --> pdb=" O ARG C 236 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ARG C 236 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.858A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 310 through 318 removed outlier: 5.372A pdb=" N ILE C 311 " --> pdb=" O THR C 597 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR C 597 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLN C 313 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL C 595 " --> pdb=" O GLN C 313 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER C 315 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 355 through 357 removed outlier: 3.584A pdb=" N ALA C 396 " --> pdb=" O THR C 355 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 357 " --> pdb=" O VAL C 394 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL C 394 " --> pdb=" O ILE C 357 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 537 through 541 removed outlier: 3.573A pdb=" N GLY C 546 " --> pdb=" O PHE C 539 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 573 through 575 Processing sheet with id=AF4, first strand: chain 'C' and resid 652 through 658 removed outlier: 5.602A pdb=" N THR C 694 " --> pdb=" O VAL C 654 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN C 656 " --> pdb=" O THR C 694 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 709 through 711 removed outlier: 3.630A pdb=" N THR C1074 " --> pdb=" O SER C1095 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 715 through 726 removed outlier: 3.573A pdb=" N ALA C1054 " --> pdb=" O GLY C1057 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.635A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 733 " --> pdb=" O THR C 857 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1079 through 1080 Processing sheet with id=AF9, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AG1, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.664A pdb=" N LEU D 351 " --> pdb=" O ASP D 355 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 132 through 133 Processing sheet with id=AG3, first strand: chain 'O' and resid 262 through 263 removed outlier: 5.496A pdb=" N LEU O 262 " --> pdb=" O VAL O 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'O' and resid 347 through 348 removed outlier: 3.871A pdb=" N THR O 347 " --> pdb=" O LEU O 359 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU O 359 " --> pdb=" O THR O 347 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 1300 hydrogen bonds defined for protein. 3669 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: 6.55 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 10984 1.35 - 1.47: 9294 1.47 - 1.60: 15173 1.60 - 1.72: 0 1.72 - 1.85: 235 Bond restraints: 35686 Sorted by residual: bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C1 NAG C1306 " pdb=" O5 NAG C1306 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.84e+00 bond pdb=" C1 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.47e+00 ... (remaining 35681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 47314 1.72 - 3.44: 1066 3.44 - 5.17: 138 5.17 - 6.89: 19 6.89 - 8.61: 2 Bond angle restraints: 48539 Sorted by residual: angle pdb=" N ASN A 799 " pdb=" CA ASN A 799 " pdb=" CB ASN A 799 " ideal model delta sigma weight residual 110.36 116.58 -6.22 1.43e+00 4.89e-01 1.89e+01 angle pdb=" C PHE A 798 " pdb=" N ASN A 799 " pdb=" CA ASN A 799 " ideal model delta sigma weight residual 120.97 114.38 6.59 1.82e+00 3.02e-01 1.31e+01 angle pdb=" CA ARG B 453 " pdb=" CB ARG B 453 " pdb=" CG ARG B 453 " ideal model delta sigma weight residual 114.10 120.80 -6.70 2.00e+00 2.50e-01 1.12e+01 angle pdb=" N PRO C 984 " pdb=" CA PRO C 984 " pdb=" C PRO C 984 " ideal model delta sigma weight residual 110.70 114.24 -3.54 1.22e+00 6.72e-01 8.42e+00 angle pdb=" CB MET D 462 " pdb=" CG MET D 462 " pdb=" SD MET D 462 " ideal model delta sigma weight residual 112.70 121.31 -8.61 3.00e+00 1.11e-01 8.24e+00 ... (remaining 48534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.97: 20839 24.97 - 49.93: 1080 49.93 - 74.90: 133 74.90 - 99.86: 50 99.86 - 124.83: 25 Dihedral angle restraints: 22127 sinusoidal: 9673 harmonic: 12454 Sorted by residual: dihedral pdb=" CB CYS C 479 " pdb=" SG CYS C 479 " pdb=" SG CYS C 486 " pdb=" CB CYS C 486 " ideal model delta sinusoidal sigma weight residual 93.00 167.79 -74.79 1 1.00e+01 1.00e-02 7.08e+01 dihedral pdb=" CB CYS B 479 " pdb=" SG CYS B 479 " pdb=" SG CYS B 486 " pdb=" CB CYS B 486 " ideal model delta sinusoidal sigma weight residual 93.00 37.30 55.70 1 1.00e+01 1.00e-02 4.19e+01 dihedral pdb=" CB CYS B1080 " pdb=" SG CYS B1080 " pdb=" SG CYS B1124 " pdb=" CB CYS B1124 " ideal model delta sinusoidal sigma weight residual -86.00 -138.74 52.74 1 1.00e+01 1.00e-02 3.79e+01 ... (remaining 22124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.274: 5573 0.274 - 0.548: 10 0.548 - 0.823: 2 0.823 - 1.097: 0 1.097 - 1.371: 1 Chirality restraints: 5586 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 799 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.03 -1.37 2.00e-01 2.50e+01 4.70e+01 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B1072 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN O 103 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.95e+00 ... (remaining 5583 not shown) Planarity restraints: 6209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 799 " 0.050 2.00e-02 2.50e+03 4.79e-02 2.86e+01 pdb=" CG ASN A 799 " -0.067 2.00e-02 2.50e+03 pdb=" OD1 ASN A 799 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 799 " -0.046 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 799 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" CG ASN A 799 " -0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN A 799 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 799 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 558 " 0.037 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO A 559 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 559 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 559 " 0.031 5.00e-02 4.00e+02 ... (remaining 6206 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 460 2.63 - 3.20: 31952 3.20 - 3.77: 52455 3.77 - 4.33: 71951 4.33 - 4.90: 117960 Nonbonded interactions: 274778 Sorted by model distance: nonbonded pdb=" OG SER A 155 " pdb=" OE1 GLU A 156 " model vdw 2.063 3.040 nonbonded pdb=" O PHE B 328 " pdb=" NE2 GLN B 578 " model vdw 2.070 3.120 nonbonded pdb=" OE1 GLU A 405 " pdb=" OH TYR A 493 " model vdw 2.133 3.040 nonbonded pdb=" NH1 ARG D 460 " pdb=" O TYR D 510 " model vdw 2.135 3.120 nonbonded pdb=" NZ LYS B 809 " pdb=" OG SER B 811 " model vdw 2.137 3.120 ... (remaining 274773 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 66 or resid 86 through 177 or resid 188 through \ 673 or resid 687 through 825 or resid 853 through 1309)) selection = (chain 'B' and (resid 25 through 177 or resid 188 through 673 or resid 687 throu \ gh 1309)) selection = (chain 'C' and (resid 25 through 66 or resid 86 through 825 or resid 853 through \ 1309)) } ncs_group { reference = (chain 'D' and resid 19 through 702) selection = chain 'O' } ncs_group { reference = 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' } ncs_group { reference = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'Q' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 30.890 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 : 0.004 0.078 35805 Z= 0.196 Angle : 0.660 15.563 48851 Z= 0.321 Chirality : 0.053 1.371 5586 Planarity : 0.004 0.063 6157 Dihedral : 15.400 124.829 13978 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -1.39 (0.13), residues: 4220 helix: 0.44 (0.14), residues: 1405 sheet: -1.29 (0.21), residues: 605 loop : -1.75 (0.13), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 460 TYR 0.021 0.001 TYR O 385 PHE 0.031 0.001 PHE B 904 TRP 0.029 0.001 TRP D 478 HIS 0.004 0.001 HIS C 444 Details of bonding type rmsd covalent geometry : bond 0.00427 (35686) covalent geometry : angle 0.61274 (48539) SS BOND : bond 0.00276 ( 45) SS BOND : angle 1.25800 ( 90) hydrogen bonds : bond 0.22115 ( 1299) hydrogen bonds : angle 7.92164 ( 3669) link_ALPHA1-3 : bond 0.00421 ( 2) link_ALPHA1-3 : angle 1.67350 ( 6) link_ALPHA1-6 : bond 0.00455 ( 2) link_ALPHA1-6 : angle 1.52630 ( 6) link_BETA1-4 : bond 0.00410 ( 18) link_BETA1-4 : angle 1.63256 ( 54) link_NAG-ASN : bond 0.00696 ( 52) link_NAG-ASN : angle 4.19035 ( 156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7793 (mmm160) cc_final: 0.7013 (mmt180) REVERT: A 900 MET cc_start: 0.7815 (tpp) cc_final: 0.7534 (mmt) REVERT: B 493 TYR cc_start: 0.6740 (m-80) cc_final: 0.6154 (m-80) REVERT: C 129 LYS cc_start: 0.7442 (mmpt) cc_final: 0.6812 (mtmm) REVERT: C 133 PHE cc_start: 0.8020 (m-80) cc_final: 0.7788 (m-80) REVERT: C 135 PHE cc_start: 0.8200 (m-80) cc_final: 0.7870 (m-80) REVERT: C 136 CYS cc_start: 0.5782 (m) cc_final: 0.5109 (p) REVERT: C 170 TYR cc_start: 0.7627 (t80) cc_final: 0.7198 (t80) REVERT: C 241 LEU cc_start: 0.7698 (mt) cc_final: 0.7421 (tp) REVERT: C 364 TYR cc_start: 0.8481 (m-80) cc_final: 0.8224 (m-80) REVERT: C 488 PHE cc_start: 0.6842 (p90) cc_final: 0.6631 (p90) REVERT: C 509 VAL cc_start: 0.8579 (t) cc_final: 0.8340 (p) REVERT: D 114 LYS cc_start: 0.2897 (tptt) cc_final: 0.2688 (ptmt) REVERT: D 248 LEU cc_start: 0.4300 (mt) cc_final: 0.3941 (tp) REVERT: D 376 MET cc_start: -0.2140 (ttm) cc_final: -0.2352 (tpt) REVERT: D 408 MET cc_start: 0.2525 (mmm) cc_final: 0.2292 (mmt) REVERT: D 455 MET cc_start: 0.2487 (tmm) cc_final: 0.2264 (tmm) REVERT: D 557 MET cc_start: 0.2592 (tmm) cc_final: 0.1803 (ptm) REVERT: O 152 MET cc_start: 0.0447 (mmt) cc_final: 0.0097 (mmt) REVERT: O 190 MET cc_start: 0.4889 (tmm) cc_final: 0.4573 (ppp) REVERT: O 236 LEU cc_start: 0.4650 (tp) cc_final: 0.4334 (mp) REVERT: O 512 PHE cc_start: -0.1030 (t80) cc_final: -0.1261 (t80) REVERT: O 577 LYS cc_start: 0.3416 (mttp) cc_final: 0.3171 (tttm) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.2053 time to fit residues: 117.9276 Evaluate side-chains 190 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 0.0370 chunk 244 optimal weight: 0.0870 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 GLN A 485 ASN B 421 ASN B 639 ASN B1000 GLN B1104 GLN ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN D 338 ASN D 397 ASN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 ASN D 522 GLN D 578 ASN O 221 GLN O 374 HIS O 505 HIS O 578 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.158069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.101110 restraints weight = 92072.550| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 4.55 r_work: 0.3154 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35805 Z= 0.126 Angle : 0.628 15.050 48851 Z= 0.312 Chirality : 0.047 0.543 5586 Planarity : 0.004 0.071 6157 Dihedral : 10.608 116.496 6110 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.51 % Allowed : 5.66 % Favored : 93.83 % 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: -0.94 (0.13), residues: 4220 helix: 0.94 (0.14), residues: 1399 sheet: -0.85 (0.21), residues: 649 loop : -1.65 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 460 TYR 0.027 0.001 TYR D 252 PHE 0.030 0.001 PHE B 215 TRP 0.037 0.001 TRP D 461 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00263 (35686) covalent geometry : angle 0.58795 (48539) SS BOND : bond 0.00287 ( 45) SS BOND : angle 1.10194 ( 90) hydrogen bonds : bond 0.05198 ( 1299) hydrogen bonds : angle 5.59817 ( 3669) link_ALPHA1-3 : bond 0.01942 ( 2) link_ALPHA1-3 : angle 3.50470 ( 6) link_ALPHA1-6 : bond 0.00732 ( 2) link_ALPHA1-6 : angle 1.94291 ( 6) link_BETA1-4 : bond 0.00559 ( 18) link_BETA1-4 : angle 1.72642 ( 54) link_NAG-ASN : bond 0.00672 ( 52) link_NAG-ASN : angle 3.66208 ( 156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 229 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4420 (ppp) cc_final: 0.3638 (ppp) REVERT: B 129 LYS cc_start: 0.7602 (mmtm) cc_final: 0.7021 (tptt) REVERT: B 189 LEU cc_start: 0.7832 (tp) cc_final: 0.7495 (mt) REVERT: B 440 LEU cc_start: 0.8396 (mp) cc_final: 0.8059 (tp) REVERT: B 493 TYR cc_start: 0.6846 (m-80) cc_final: 0.6277 (m-80) REVERT: B 948 ASP cc_start: 0.8960 (m-30) cc_final: 0.8716 (m-30) REVERT: C 128 ILE cc_start: 0.8046 (mp) cc_final: 0.7646 (mp) REVERT: C 129 LYS cc_start: 0.7382 (mmpt) cc_final: 0.6836 (mtmm) REVERT: C 133 PHE cc_start: 0.8016 (m-80) cc_final: 0.7771 (m-80) REVERT: C 135 PHE cc_start: 0.8144 (m-80) cc_final: 0.7939 (m-80) REVERT: C 451 TRP cc_start: 0.8528 (m100) cc_final: 0.8073 (m100) REVERT: C 488 PHE cc_start: 0.6924 (p90) cc_final: 0.6627 (p90) REVERT: C 902 TYR cc_start: 0.7937 (m-80) cc_final: 0.7664 (m-80) REVERT: C 955 GLN cc_start: 0.8990 (tt0) cc_final: 0.8787 (tp40) REVERT: D 114 LYS cc_start: 0.3063 (tptt) cc_final: 0.2489 (ptmt) REVERT: D 323 MET cc_start: -0.1132 (mmp) cc_final: -0.1919 (mmm) REVERT: D 332 MET cc_start: 0.0840 (ppp) cc_final: 0.0297 (ppp) REVERT: D 376 MET cc_start: -0.1959 (ttm) cc_final: -0.2455 (tpt) REVERT: D 557 MET cc_start: 0.2273 (tmm) cc_final: 0.1817 (ptm) REVERT: O 270 MET cc_start: -0.0173 (tpt) cc_final: -0.0733 (tpt) REVERT: O 323 MET cc_start: -0.2901 (mpp) cc_final: -0.3160 (mpp) REVERT: O 577 LYS cc_start: 0.3352 (mttp) cc_final: 0.3047 (tttm) outliers start: 19 outliers final: 8 residues processed: 244 average time/residue: 0.2037 time to fit residues: 82.4065 Evaluate side-chains 196 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 188 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 285 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 106 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 74 optimal weight: 0.3980 chunk 184 optimal weight: 0.9990 chunk 231 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 321 optimal weight: 30.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 GLN B 207 HIS ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN B 753 GLN B 802 GLN C 99 ASN ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 GLN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 505 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.157970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.100998 restraints weight = 91378.258| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 4.37 r_work: 0.3131 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35805 Z= 0.129 Angle : 0.595 15.520 48851 Z= 0.292 Chirality : 0.046 0.487 5586 Planarity : 0.004 0.044 6157 Dihedral : 9.692 114.459 6110 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.67 % Allowed : 8.65 % Favored : 90.68 % 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: -0.78 (0.13), residues: 4220 helix: 1.21 (0.14), residues: 1378 sheet: -0.76 (0.21), residues: 663 loop : -1.63 (0.13), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 460 TYR 0.020 0.001 TYR O 385 PHE 0.032 0.001 PHE A 337 TRP 0.019 0.001 TRP D 461 HIS 0.012 0.001 HIS O 505 Details of bonding type rmsd covalent geometry : bond 0.00288 (35686) covalent geometry : angle 0.56001 (48539) SS BOND : bond 0.00241 ( 45) SS BOND : angle 1.00402 ( 90) hydrogen bonds : bond 0.04861 ( 1299) hydrogen bonds : angle 5.20750 ( 3669) link_ALPHA1-3 : bond 0.01083 ( 2) link_ALPHA1-3 : angle 2.07140 ( 6) link_ALPHA1-6 : bond 0.00936 ( 2) link_ALPHA1-6 : angle 2.00453 ( 6) link_BETA1-4 : bond 0.00405 ( 18) link_BETA1-4 : angle 1.71282 ( 54) link_NAG-ASN : bond 0.00579 ( 52) link_NAG-ASN : angle 3.38930 ( 156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 1.390 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 177 MET cc_start: 0.4482 (ppp) cc_final: 0.3530 (ppp) REVERT: A 399 PHE cc_start: 0.5437 (p90) cc_final: 0.5235 (p90) REVERT: B 440 LEU cc_start: 0.8410 (mp) cc_final: 0.8109 (tp) REVERT: B 493 TYR cc_start: 0.6921 (m-80) cc_final: 0.6389 (m-80) REVERT: C 129 LYS cc_start: 0.7384 (mmpt) cc_final: 0.6822 (mtmm) REVERT: C 133 PHE cc_start: 0.7979 (m-80) cc_final: 0.7754 (m-80) REVERT: C 451 TRP cc_start: 0.8519 (m100) cc_final: 0.8084 (m100) REVERT: C 488 PHE cc_start: 0.6829 (p90) cc_final: 0.6520 (p90) REVERT: C 955 GLN cc_start: 0.8952 (tt0) cc_final: 0.8658 (tp40) REVERT: D 82 MET cc_start: 0.3043 (ptt) cc_final: 0.2497 (tmm) REVERT: D 114 LYS cc_start: 0.2809 (tptt) cc_final: 0.2495 (ptmt) REVERT: D 332 MET cc_start: 0.1934 (ppp) cc_final: 0.1349 (ppp) REVERT: D 376 MET cc_start: -0.2085 (ttm) cc_final: -0.2424 (tpt) REVERT: D 557 MET cc_start: 0.2207 (tmm) cc_final: 0.1755 (ptm) REVERT: O 190 MET cc_start: 0.2412 (tmm) cc_final: 0.2207 (ppp) REVERT: O 270 MET cc_start: 0.1193 (tpt) cc_final: 0.0695 (tpt) REVERT: O 323 MET cc_start: -0.2370 (mpp) cc_final: -0.2667 (mpp) REVERT: O 577 LYS cc_start: 0.3326 (mttp) cc_final: 0.2715 (pttt) outliers start: 25 outliers final: 12 residues processed: 216 average time/residue: 0.2186 time to fit residues: 78.0664 Evaluate side-chains 192 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 197 GLU Chi-restraints excluded: chain O residue 297 MET Chi-restraints excluded: chain O residue 479 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 233 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 353 optimal weight: 20.0000 chunk 419 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 398 optimal weight: 30.0000 chunk 373 optimal weight: 20.0000 chunk 334 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 316 optimal weight: 40.0000 chunk 230 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 GLN ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.156083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.097877 restraints weight = 90638.273| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 4.23 r_work: 0.3069 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 35805 Z= 0.244 Angle : 0.676 15.352 48851 Z= 0.336 Chirality : 0.048 0.463 5586 Planarity : 0.004 0.049 6157 Dihedral : 9.400 116.101 6110 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.07 % Allowed : 10.57 % Favored : 88.36 % 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: -0.96 (0.13), residues: 4220 helix: 1.06 (0.14), residues: 1391 sheet: -0.80 (0.21), residues: 638 loop : -1.77 (0.13), residues: 2191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 44 TYR 0.029 0.002 TYR B 170 PHE 0.034 0.002 PHE B 904 TRP 0.015 0.001 TRP B 884 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00586 (35686) covalent geometry : angle 0.64204 (48539) SS BOND : bond 0.00339 ( 45) SS BOND : angle 1.27220 ( 90) hydrogen bonds : bond 0.05852 ( 1299) hydrogen bonds : angle 5.30445 ( 3669) link_ALPHA1-3 : bond 0.01233 ( 2) link_ALPHA1-3 : angle 1.86639 ( 6) link_ALPHA1-6 : bond 0.01101 ( 2) link_ALPHA1-6 : angle 2.13283 ( 6) link_BETA1-4 : bond 0.00424 ( 18) link_BETA1-4 : angle 1.72738 ( 54) link_NAG-ASN : bond 0.00573 ( 52) link_NAG-ASN : angle 3.56222 ( 156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4657 (ppp) cc_final: 0.3829 (ppp) REVERT: A 399 PHE cc_start: 0.5454 (p90) cc_final: 0.5233 (p90) REVERT: B 440 LEU cc_start: 0.8394 (mp) cc_final: 0.8152 (tp) REVERT: B 493 TYR cc_start: 0.6919 (m-80) cc_final: 0.6479 (m-80) REVERT: C 110 LEU cc_start: 0.8004 (mm) cc_final: 0.7301 (pp) REVERT: C 129 LYS cc_start: 0.7359 (mmpt) cc_final: 0.6664 (mtmm) REVERT: C 133 PHE cc_start: 0.7957 (m-80) cc_final: 0.7707 (m-80) REVERT: C 177 MET cc_start: 0.4894 (pmm) cc_final: 0.4625 (pmm) REVERT: C 488 PHE cc_start: 0.6950 (p90) cc_final: 0.6701 (p90) REVERT: D 114 LYS cc_start: 0.2941 (tptt) cc_final: 0.2592 (ptmt) REVERT: D 332 MET cc_start: 0.2010 (ppp) cc_final: 0.1456 (ppp) REVERT: D 376 MET cc_start: -0.2073 (ttm) cc_final: -0.2422 (tpt) REVERT: D 480 MET cc_start: 0.5831 (OUTLIER) cc_final: 0.5397 (ptm) REVERT: D 515 TYR cc_start: 0.0582 (m-10) cc_final: 0.0097 (m-80) REVERT: D 557 MET cc_start: 0.1984 (tmm) cc_final: 0.1631 (ptm) REVERT: O 95 LEU cc_start: 0.1205 (OUTLIER) cc_final: 0.0913 (tt) REVERT: O 270 MET cc_start: 0.0865 (tpt) cc_final: 0.0042 (tpp) REVERT: O 323 MET cc_start: -0.2155 (mpp) cc_final: -0.2535 (mpp) REVERT: O 577 LYS cc_start: 0.3390 (mttp) cc_final: 0.2766 (pttt) outliers start: 40 outliers final: 21 residues processed: 215 average time/residue: 0.2236 time to fit residues: 79.8789 Evaluate side-chains 199 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 197 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 179 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 263 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 353 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 406 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 GLN ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 ASN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.157718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.100831 restraints weight = 91344.848| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 4.68 r_work: 0.3109 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 35805 Z= 0.115 Angle : 0.580 15.702 48851 Z= 0.285 Chirality : 0.045 0.475 5586 Planarity : 0.004 0.050 6157 Dihedral : 8.711 114.933 6110 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.93 % Allowed : 11.67 % Favored : 87.40 % 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: -0.72 (0.13), residues: 4220 helix: 1.31 (0.14), residues: 1388 sheet: -0.72 (0.21), residues: 649 loop : -1.65 (0.13), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.021 0.001 TYR O 385 PHE 0.022 0.001 PHE A 337 TRP 0.012 0.001 TRP D 461 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00249 (35686) covalent geometry : angle 0.54621 (48539) SS BOND : bond 0.00259 ( 45) SS BOND : angle 1.06631 ( 90) hydrogen bonds : bond 0.04539 ( 1299) hydrogen bonds : angle 4.96964 ( 3669) link_ALPHA1-3 : bond 0.01201 ( 2) link_ALPHA1-3 : angle 2.18657 ( 6) link_ALPHA1-6 : bond 0.01057 ( 2) link_ALPHA1-6 : angle 1.94784 ( 6) link_BETA1-4 : bond 0.00408 ( 18) link_BETA1-4 : angle 1.52323 ( 54) link_NAG-ASN : bond 0.00554 ( 52) link_NAG-ASN : angle 3.27730 ( 156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 201 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 PHE cc_start: 0.5427 (p90) cc_final: 0.5163 (p90) REVERT: B 440 LEU cc_start: 0.8459 (mp) cc_final: 0.8186 (tp) REVERT: B 493 TYR cc_start: 0.6883 (m-80) cc_final: 0.6474 (m-80) REVERT: B 757 PHE cc_start: 0.8708 (m-80) cc_final: 0.8438 (m-80) REVERT: C 110 LEU cc_start: 0.7998 (mm) cc_final: 0.7450 (pp) REVERT: C 488 PHE cc_start: 0.6935 (p90) cc_final: 0.6667 (p90) REVERT: C 902 TYR cc_start: 0.7927 (m-80) cc_final: 0.7711 (m-80) REVERT: C 955 GLN cc_start: 0.8971 (tt0) cc_final: 0.8669 (tp40) REVERT: D 82 MET cc_start: 0.3062 (ptt) cc_final: 0.2585 (tmm) REVERT: D 114 LYS cc_start: 0.2913 (tptt) cc_final: 0.2617 (ptmt) REVERT: D 332 MET cc_start: 0.2263 (ppp) cc_final: 0.1663 (ppp) REVERT: D 376 MET cc_start: -0.2134 (ttm) cc_final: -0.2454 (tpt) REVERT: D 480 MET cc_start: 0.5685 (OUTLIER) cc_final: 0.5349 (ptm) REVERT: D 515 TYR cc_start: 0.0446 (m-10) cc_final: -0.0019 (m-80) REVERT: D 557 MET cc_start: 0.1680 (tmm) cc_final: 0.1299 (ptm) REVERT: O 95 LEU cc_start: 0.1267 (OUTLIER) cc_final: 0.1013 (tt) REVERT: O 270 MET cc_start: 0.1513 (tpt) cc_final: 0.0721 (tpp) REVERT: O 323 MET cc_start: -0.1823 (mpp) cc_final: -0.2274 (mpp) REVERT: O 577 LYS cc_start: 0.3448 (mttp) cc_final: 0.3235 (mtpp) outliers start: 35 outliers final: 18 residues processed: 223 average time/residue: 0.2257 time to fit residues: 83.4801 Evaluate side-chains 202 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 197 GLU Chi-restraints excluded: chain O residue 285 PHE Chi-restraints excluded: chain O residue 297 MET Chi-restraints excluded: chain O residue 360 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 233 optimal weight: 7.9990 chunk 327 optimal weight: 10.0000 chunk 336 optimal weight: 8.9990 chunk 278 optimal weight: 2.9990 chunk 75 optimal weight: 0.0980 chunk 347 optimal weight: 20.0000 chunk 344 optimal weight: 40.0000 chunk 264 optimal weight: 0.9980 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 GLN ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.156585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.099414 restraints weight = 91423.180| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 4.56 r_work: 0.3118 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 35805 Z= 0.199 Angle : 0.633 15.611 48851 Z= 0.311 Chirality : 0.047 0.469 5586 Planarity : 0.004 0.046 6157 Dihedral : 8.542 115.753 6110 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.07 % Allowed : 12.42 % Favored : 86.52 % 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: -0.81 (0.13), residues: 4220 helix: 1.23 (0.14), residues: 1393 sheet: -0.80 (0.20), residues: 654 loop : -1.69 (0.13), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.021 0.001 TYR O 385 PHE 0.023 0.002 PHE C 127 TRP 0.023 0.001 TRP O 566 HIS 0.004 0.001 HIS C1062 Details of bonding type rmsd covalent geometry : bond 0.00474 (35686) covalent geometry : angle 0.59989 (48539) SS BOND : bond 0.00274 ( 45) SS BOND : angle 1.26620 ( 90) hydrogen bonds : bond 0.05212 ( 1299) hydrogen bonds : angle 5.04872 ( 3669) link_ALPHA1-3 : bond 0.01259 ( 2) link_ALPHA1-3 : angle 1.96002 ( 6) link_ALPHA1-6 : bond 0.01051 ( 2) link_ALPHA1-6 : angle 1.93000 ( 6) link_BETA1-4 : bond 0.00394 ( 18) link_BETA1-4 : angle 1.58319 ( 54) link_NAG-ASN : bond 0.00542 ( 52) link_NAG-ASN : angle 3.37376 ( 156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 THR cc_start: 0.4555 (OUTLIER) cc_final: 0.4104 (m) REVERT: A 399 PHE cc_start: 0.5468 (p90) cc_final: 0.5176 (p90) REVERT: B 389 LEU cc_start: 0.5581 (mt) cc_final: 0.5327 (mt) REVERT: B 440 LEU cc_start: 0.8460 (mp) cc_final: 0.8203 (tp) REVERT: B 493 TYR cc_start: 0.6849 (m-80) cc_final: 0.6437 (m-80) REVERT: B 757 PHE cc_start: 0.8725 (m-80) cc_final: 0.8479 (m-80) REVERT: C 110 LEU cc_start: 0.7987 (mm) cc_final: 0.7468 (pp) REVERT: C 352 TRP cc_start: 0.7783 (OUTLIER) cc_final: 0.7520 (p90) REVERT: C 373 PHE cc_start: 0.7726 (m-80) cc_final: 0.7382 (m-80) REVERT: C 488 PHE cc_start: 0.6954 (p90) cc_final: 0.6707 (p90) REVERT: C 738 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.8935 (tpp) REVERT: C 955 GLN cc_start: 0.8979 (tt0) cc_final: 0.8671 (tp40) REVERT: D 114 LYS cc_start: 0.3040 (tptt) cc_final: 0.2552 (ptmt) REVERT: D 332 MET cc_start: 0.1419 (ppp) cc_final: 0.1009 (ppp) REVERT: D 376 MET cc_start: -0.2005 (ttm) cc_final: -0.2473 (tpt) REVERT: D 480 MET cc_start: 0.5601 (OUTLIER) cc_final: 0.5268 (ttp) REVERT: D 515 TYR cc_start: 0.0375 (m-10) cc_final: -0.0114 (m-80) REVERT: D 557 MET cc_start: 0.1844 (tmm) cc_final: 0.1545 (ptm) REVERT: O 95 LEU cc_start: 0.1198 (OUTLIER) cc_final: 0.0870 (tt) REVERT: O 270 MET cc_start: -0.0217 (tpt) cc_final: -0.0969 (tpp) REVERT: O 323 MET cc_start: -0.2280 (mpp) cc_final: -0.2639 (mpp) REVERT: O 557 MET cc_start: 0.6905 (tpt) cc_final: 0.6669 (ptp) REVERT: O 577 LYS cc_start: 0.3271 (mttp) cc_final: 0.2980 (mtpp) outliers start: 40 outliers final: 30 residues processed: 210 average time/residue: 0.2215 time to fit residues: 77.6792 Evaluate side-chains 213 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 352 TRP Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 197 GLU Chi-restraints excluded: chain O residue 226 VAL Chi-restraints excluded: chain O residue 297 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 86 optimal weight: 0.0570 chunk 162 optimal weight: 6.9990 chunk 385 optimal weight: 20.0000 chunk 414 optimal weight: 30.0000 chunk 32 optimal weight: 5.9990 chunk 293 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 264 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 chunk 399 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 overall best weight: 1.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 GLN ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.157365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.100713 restraints weight = 91281.251| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 4.68 r_work: 0.3135 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35805 Z= 0.138 Angle : 0.590 15.895 48851 Z= 0.288 Chirality : 0.045 0.477 5586 Planarity : 0.004 0.050 6157 Dihedral : 8.038 115.293 6110 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.17 % Allowed : 12.74 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.69 (0.13), residues: 4220 helix: 1.36 (0.14), residues: 1387 sheet: -0.73 (0.21), residues: 654 loop : -1.63 (0.13), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.020 0.001 TYR O 385 PHE 0.017 0.001 PHE C 175 TRP 0.011 0.001 TRP O 566 HIS 0.003 0.001 HIS O 540 Details of bonding type rmsd covalent geometry : bond 0.00317 (35686) covalent geometry : angle 0.55737 (48539) SS BOND : bond 0.00324 ( 45) SS BOND : angle 1.13559 ( 90) hydrogen bonds : bond 0.04542 ( 1299) hydrogen bonds : angle 4.87999 ( 3669) link_ALPHA1-3 : bond 0.01298 ( 2) link_ALPHA1-3 : angle 2.22064 ( 6) link_ALPHA1-6 : bond 0.01034 ( 2) link_ALPHA1-6 : angle 1.60258 ( 6) link_BETA1-4 : bond 0.00429 ( 18) link_BETA1-4 : angle 1.51467 ( 54) link_NAG-ASN : bond 0.00532 ( 52) link_NAG-ASN : angle 3.26420 ( 156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 1.389 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 51 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8558 (p) REVERT: A 167 THR cc_start: 0.4567 (OUTLIER) cc_final: 0.4110 (m) REVERT: A 399 PHE cc_start: 0.5472 (p90) cc_final: 0.5158 (p90) REVERT: B 440 LEU cc_start: 0.8481 (mp) cc_final: 0.8206 (tp) REVERT: B 493 TYR cc_start: 0.6826 (m-80) cc_final: 0.6447 (m-80) REVERT: C 110 LEU cc_start: 0.7945 (mm) cc_final: 0.7468 (pp) REVERT: C 118 LEU cc_start: 0.8192 (tt) cc_final: 0.7739 (mp) REVERT: C 373 PHE cc_start: 0.7752 (m-80) cc_final: 0.7425 (m-80) REVERT: C 488 PHE cc_start: 0.6932 (p90) cc_final: 0.6679 (p90) REVERT: C 738 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.8929 (tpp) REVERT: C 955 GLN cc_start: 0.8951 (tt0) cc_final: 0.8685 (tp40) REVERT: D 114 LYS cc_start: 0.3047 (tptt) cc_final: 0.2557 (ptmt) REVERT: D 332 MET cc_start: 0.1337 (ppp) cc_final: 0.0938 (ppp) REVERT: D 376 MET cc_start: -0.1998 (ttm) cc_final: -0.2469 (tpt) REVERT: D 480 MET cc_start: 0.5863 (OUTLIER) cc_final: 0.5500 (ttp) REVERT: D 515 TYR cc_start: 0.0179 (m-10) cc_final: -0.0258 (m-80) REVERT: D 557 MET cc_start: 0.1822 (tmm) cc_final: 0.1530 (ptm) REVERT: O 95 LEU cc_start: 0.1253 (OUTLIER) cc_final: 0.0950 (tt) REVERT: O 270 MET cc_start: -0.0243 (tpt) cc_final: -0.0999 (tpp) REVERT: O 323 MET cc_start: -0.2231 (mpp) cc_final: -0.2588 (mpp) REVERT: O 557 MET cc_start: 0.6994 (tpt) cc_final: 0.6751 (ptp) REVERT: O 577 LYS cc_start: 0.3247 (mttp) cc_final: 0.3000 (mtpp) outliers start: 44 outliers final: 27 residues processed: 217 average time/residue: 0.2285 time to fit residues: 82.1073 Evaluate side-chains 213 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 197 GLU Chi-restraints excluded: chain O residue 285 PHE Chi-restraints excluded: chain O residue 297 MET Chi-restraints excluded: chain O residue 360 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 284 optimal weight: 0.9980 chunk 211 optimal weight: 6.9990 chunk 294 optimal weight: 4.9990 chunk 388 optimal weight: 20.0000 chunk 184 optimal weight: 0.2980 chunk 255 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 361 optimal weight: 7.9990 chunk 213 optimal weight: 9.9990 chunk 289 optimal weight: 1.9990 chunk 323 optimal weight: 20.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN B1104 GLN ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 505 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.156284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.097347 restraints weight = 91035.705| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 4.13 r_work: 0.3084 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 35805 Z= 0.200 Angle : 0.641 16.032 48851 Z= 0.314 Chirality : 0.047 0.496 5586 Planarity : 0.004 0.050 6157 Dihedral : 7.910 116.503 6110 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 1.26 % Allowed : 13.30 % Favored : 85.45 % 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: -0.79 (0.13), residues: 4220 helix: 1.26 (0.14), residues: 1399 sheet: -0.79 (0.20), residues: 672 loop : -1.70 (0.13), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 44 TYR 0.020 0.001 TYR O 385 PHE 0.020 0.002 PHE C 175 TRP 0.025 0.001 TRP O 566 HIS 0.004 0.001 HIS C1062 Details of bonding type rmsd covalent geometry : bond 0.00474 (35686) covalent geometry : angle 0.60744 (48539) SS BOND : bond 0.00310 ( 45) SS BOND : angle 1.26823 ( 90) hydrogen bonds : bond 0.05204 ( 1299) hydrogen bonds : angle 5.00196 ( 3669) link_ALPHA1-3 : bond 0.01395 ( 2) link_ALPHA1-3 : angle 2.06052 ( 6) link_ALPHA1-6 : bond 0.01237 ( 2) link_ALPHA1-6 : angle 1.27517 ( 6) link_BETA1-4 : bond 0.00416 ( 18) link_BETA1-4 : angle 1.59601 ( 54) link_NAG-ASN : bond 0.00546 ( 52) link_NAG-ASN : angle 3.41951 ( 156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8536 (p) REVERT: A 399 PHE cc_start: 0.5405 (p90) cc_final: 0.5148 (p90) REVERT: B 440 LEU cc_start: 0.8445 (mp) cc_final: 0.8185 (tp) REVERT: B 578 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7352 (mp10) REVERT: C 110 LEU cc_start: 0.8013 (mm) cc_final: 0.7555 (pp) REVERT: C 118 LEU cc_start: 0.8004 (tt) cc_final: 0.7577 (mp) REVERT: C 352 TRP cc_start: 0.7669 (OUTLIER) cc_final: 0.7362 (p90) REVERT: C 373 PHE cc_start: 0.7761 (m-80) cc_final: 0.7468 (m-80) REVERT: C 488 PHE cc_start: 0.6932 (p90) cc_final: 0.6666 (p90) REVERT: C 738 MET cc_start: 0.9310 (OUTLIER) cc_final: 0.8959 (tpp) REVERT: C 955 GLN cc_start: 0.8945 (tt0) cc_final: 0.8630 (tp40) REVERT: D 114 LYS cc_start: 0.2933 (tptt) cc_final: 0.2580 (ptmt) REVERT: D 332 MET cc_start: 0.2166 (ppp) cc_final: 0.1680 (ppp) REVERT: D 376 MET cc_start: -0.2097 (ttm) cc_final: -0.2422 (tpt) REVERT: D 480 MET cc_start: 0.5955 (OUTLIER) cc_final: 0.5428 (ttp) REVERT: D 515 TYR cc_start: 0.0247 (m-10) cc_final: -0.0187 (m-80) REVERT: O 95 LEU cc_start: 0.0659 (OUTLIER) cc_final: 0.0445 (tt) REVERT: O 270 MET cc_start: 0.0829 (tpt) cc_final: 0.0029 (tpp) REVERT: O 323 MET cc_start: -0.1540 (mpp) cc_final: -0.2094 (mpp) REVERT: O 577 LYS cc_start: 0.3231 (mttp) cc_final: 0.3024 (mtpp) outliers start: 47 outliers final: 33 residues processed: 215 average time/residue: 0.2118 time to fit residues: 76.3637 Evaluate side-chains 214 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 578 GLN Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 352 TRP Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 197 GLU Chi-restraints excluded: chain O residue 297 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 88 optimal weight: 1.9990 chunk 306 optimal weight: 8.9990 chunk 233 optimal weight: 5.9990 chunk 33 optimal weight: 30.0000 chunk 291 optimal weight: 1.9990 chunk 268 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 290 optimal weight: 3.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 GLN ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.157188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.098160 restraints weight = 91323.157| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.98 r_work: 0.3136 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35805 Z= 0.140 Angle : 0.602 16.273 48851 Z= 0.294 Chirality : 0.045 0.490 5586 Planarity : 0.004 0.051 6157 Dihedral : 7.568 115.917 6110 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.12 % Allowed : 13.72 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.68 (0.13), residues: 4220 helix: 1.34 (0.14), residues: 1396 sheet: -0.65 (0.20), residues: 657 loop : -1.65 (0.13), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 993 TYR 0.020 0.001 TYR O 385 PHE 0.034 0.001 PHE B 215 TRP 0.020 0.001 TRP B 451 HIS 0.005 0.001 HIS O 505 Details of bonding type rmsd covalent geometry : bond 0.00323 (35686) covalent geometry : angle 0.56874 (48539) SS BOND : bond 0.00273 ( 45) SS BOND : angle 1.08903 ( 90) hydrogen bonds : bond 0.04576 ( 1299) hydrogen bonds : angle 4.87245 ( 3669) link_ALPHA1-3 : bond 0.01155 ( 2) link_ALPHA1-3 : angle 2.02623 ( 6) link_ALPHA1-6 : bond 0.01127 ( 2) link_ALPHA1-6 : angle 1.18417 ( 6) link_BETA1-4 : bond 0.00434 ( 18) link_BETA1-4 : angle 1.52134 ( 54) link_NAG-ASN : bond 0.00535 ( 52) link_NAG-ASN : angle 3.33030 ( 156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8567 (p) REVERT: A 399 PHE cc_start: 0.5394 (p90) cc_final: 0.5128 (p90) REVERT: B 376 PHE cc_start: 0.7171 (t80) cc_final: 0.6755 (p90) REVERT: B 440 LEU cc_start: 0.8486 (mp) cc_final: 0.8219 (tp) REVERT: B 493 TYR cc_start: 0.6953 (m-80) cc_final: 0.6265 (m-80) REVERT: B 578 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7383 (mp10) REVERT: C 110 LEU cc_start: 0.7971 (mm) cc_final: 0.7511 (pp) REVERT: C 118 LEU cc_start: 0.8051 (tt) cc_final: 0.7628 (mp) REVERT: C 352 TRP cc_start: 0.7714 (OUTLIER) cc_final: 0.7465 (p90) REVERT: C 373 PHE cc_start: 0.7781 (m-80) cc_final: 0.7554 (m-80) REVERT: C 488 PHE cc_start: 0.6901 (p90) cc_final: 0.6623 (p90) REVERT: C 955 GLN cc_start: 0.8930 (tt0) cc_final: 0.8668 (tp40) REVERT: D 114 LYS cc_start: 0.2992 (tptt) cc_final: 0.2501 (ptmt) REVERT: D 332 MET cc_start: 0.1565 (ppp) cc_final: 0.1187 (ppp) REVERT: D 360 MET cc_start: -0.1957 (ptt) cc_final: -0.2308 (ptt) REVERT: D 376 MET cc_start: -0.2056 (ttm) cc_final: -0.2500 (tpt) REVERT: D 480 MET cc_start: 0.5899 (OUTLIER) cc_final: 0.5474 (ttp) REVERT: D 557 MET cc_start: 0.0441 (ptm) cc_final: 0.0098 (ptm) REVERT: O 95 LEU cc_start: 0.0703 (OUTLIER) cc_final: 0.0495 (tt) REVERT: O 270 MET cc_start: -0.0043 (tpt) cc_final: -0.0812 (tpp) REVERT: O 323 MET cc_start: -0.1853 (mpp) cc_final: -0.2395 (mpp) REVERT: O 577 LYS cc_start: 0.3327 (mttp) cc_final: 0.3081 (mtpp) outliers start: 42 outliers final: 30 residues processed: 216 average time/residue: 0.1760 time to fit residues: 65.4961 Evaluate side-chains 210 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 578 GLN Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 352 TRP Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 197 GLU Chi-restraints excluded: chain O residue 285 PHE Chi-restraints excluded: chain O residue 297 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 124 optimal weight: 0.7980 chunk 258 optimal weight: 5.9990 chunk 259 optimal weight: 7.9990 chunk 321 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 205 optimal weight: 5.9990 chunk 283 optimal weight: 0.7980 chunk 338 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 GLN ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.157382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.099291 restraints weight = 91008.193| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 4.51 r_work: 0.3119 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35805 Z= 0.140 Angle : 0.605 16.406 48851 Z= 0.296 Chirality : 0.045 0.500 5586 Planarity : 0.004 0.049 6157 Dihedral : 7.364 115.706 6110 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.99 % Allowed : 13.81 % Favored : 85.21 % 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: -0.65 (0.13), residues: 4220 helix: 1.37 (0.14), residues: 1397 sheet: -0.60 (0.20), residues: 654 loop : -1.64 (0.13), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.018 0.001 TYR C 634 PHE 0.029 0.001 PHE B 215 TRP 0.015 0.001 TRP O 566 HIS 0.006 0.001 HIS O 505 Details of bonding type rmsd covalent geometry : bond 0.00323 (35686) covalent geometry : angle 0.57268 (48539) SS BOND : bond 0.00329 ( 45) SS BOND : angle 1.14534 ( 90) hydrogen bonds : bond 0.04544 ( 1299) hydrogen bonds : angle 4.85132 ( 3669) link_ALPHA1-3 : bond 0.01116 ( 2) link_ALPHA1-3 : angle 1.90885 ( 6) link_ALPHA1-6 : bond 0.01295 ( 2) link_ALPHA1-6 : angle 1.44067 ( 6) link_BETA1-4 : bond 0.00441 ( 18) link_BETA1-4 : angle 1.52598 ( 54) link_NAG-ASN : bond 0.00536 ( 52) link_NAG-ASN : angle 3.29420 ( 156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8579 (p) REVERT: A 399 PHE cc_start: 0.5393 (p90) cc_final: 0.5118 (p90) REVERT: B 377 LYS cc_start: 0.6217 (mmtt) cc_final: 0.4937 (tptm) REVERT: B 440 LEU cc_start: 0.8483 (mp) cc_final: 0.8217 (tp) REVERT: B 493 TYR cc_start: 0.7035 (m-80) cc_final: 0.6505 (m-80) REVERT: B 578 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7404 (mp10) REVERT: C 110 LEU cc_start: 0.8008 (mm) cc_final: 0.7555 (pp) REVERT: C 118 LEU cc_start: 0.8020 (tt) cc_final: 0.7642 (mp) REVERT: C 352 TRP cc_start: 0.7696 (OUTLIER) cc_final: 0.7451 (p90) REVERT: C 488 PHE cc_start: 0.6886 (p90) cc_final: 0.6626 (p90) REVERT: C 955 GLN cc_start: 0.8958 (tt0) cc_final: 0.8685 (tp40) REVERT: D 67 ASP cc_start: 0.7450 (m-30) cc_final: 0.7108 (t0) REVERT: D 114 LYS cc_start: 0.2972 (tptt) cc_final: 0.2505 (ptmt) REVERT: D 332 MET cc_start: 0.1542 (ppp) cc_final: 0.1165 (ppp) REVERT: D 360 MET cc_start: -0.1952 (ptt) cc_final: -0.2302 (ptt) REVERT: D 376 MET cc_start: -0.2063 (ttm) cc_final: -0.2509 (tpt) REVERT: D 480 MET cc_start: 0.5913 (OUTLIER) cc_final: 0.5540 (ttp) REVERT: D 515 TYR cc_start: -0.0102 (m-10) cc_final: -0.0539 (m-80) REVERT: D 557 MET cc_start: 0.0448 (ptm) cc_final: 0.0082 (ptm) REVERT: O 95 LEU cc_start: 0.0693 (OUTLIER) cc_final: 0.0483 (tt) REVERT: O 123 MET cc_start: -0.0124 (ptt) cc_final: -0.0389 (ptt) REVERT: O 270 MET cc_start: -0.0016 (tpt) cc_final: -0.0730 (tpp) REVERT: O 323 MET cc_start: -0.1813 (mpp) cc_final: -0.2418 (mpp) REVERT: O 577 LYS cc_start: 0.3505 (mttp) cc_final: 0.3220 (mtpp) outliers start: 37 outliers final: 29 residues processed: 204 average time/residue: 0.1810 time to fit residues: 62.4822 Evaluate side-chains 211 residues out of total 3745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 578 GLN Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 352 TRP Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 197 GLU Chi-restraints excluded: chain O residue 285 PHE Chi-restraints excluded: chain O residue 297 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 206 optimal weight: 0.9990 chunk 395 optimal weight: 5.9990 chunk 270 optimal weight: 4.9990 chunk 359 optimal weight: 20.0000 chunk 283 optimal weight: 0.9990 chunk 242 optimal weight: 0.0030 chunk 291 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 31 optimal weight: 0.0980 chunk 154 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN C 99 ASN ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.158882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.101395 restraints weight = 91578.909| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 4.07 r_work: 0.3183 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 35805 Z= 0.101 Angle : 0.573 16.716 48851 Z= 0.279 Chirality : 0.044 0.484 5586 Planarity : 0.004 0.049 6157 Dihedral : 6.954 113.858 6110 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.75 % Allowed : 14.15 % Favored : 85.10 % 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: -0.42 (0.13), residues: 4220 helix: 1.58 (0.14), residues: 1385 sheet: -0.39 (0.21), residues: 658 loop : -1.55 (0.13), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 993 TYR 0.021 0.001 TYR O 385 PHE 0.030 0.001 PHE B 215 TRP 0.013 0.001 TRP A 631 HIS 0.007 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00212 (35686) covalent geometry : angle 0.54203 (48539) SS BOND : bond 0.00235 ( 45) SS BOND : angle 0.95120 ( 90) hydrogen bonds : bond 0.03678 ( 1299) hydrogen bonds : angle 4.62408 ( 3669) link_ALPHA1-3 : bond 0.00815 ( 2) link_ALPHA1-3 : angle 1.88267 ( 6) link_ALPHA1-6 : bond 0.01066 ( 2) link_ALPHA1-6 : angle 1.50186 ( 6) link_BETA1-4 : bond 0.00464 ( 18) link_BETA1-4 : angle 1.47280 ( 54) link_NAG-ASN : bond 0.00566 ( 52) link_NAG-ASN : angle 3.12924 ( 156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13116.54 seconds wall clock time: 224 minutes 0.98 seconds (13440.98 seconds total)