Starting phenix.real_space_refine on Sun Feb 18 12:24:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9j_25759/02_2024/7t9j_25759.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9j_25759/02_2024/7t9j_25759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9j_25759/02_2024/7t9j_25759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9j_25759/02_2024/7t9j_25759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9j_25759/02_2024/7t9j_25759.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9j_25759/02_2024/7t9j_25759.pdb" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 95 5.16 5 C 13995 2.51 5 N 3573 2.21 5 O 4297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21960 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6519 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 45, 'TRANS': 789} Chain breaks: 9 Chain: "B" Number of atoms: 6528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6528 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 45, 'TRANS': 790} Chain breaks: 9 Chain: "C" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "D" 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: "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: "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 Chain: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 10.86, per 1000 atoms: 0.49 Number of scatterers: 21960 At special positions: 0 Unit cell: (134, 143, 172, 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 95 16.00 O 4297 8.00 N 3573 7.00 C 13995 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " 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 O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 17 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 17 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 8.17 Conformation dependent library (CDL) restraints added in 4.1 seconds 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5082 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 39 sheets defined 26.0% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.063A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.553A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.918A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.973A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.540A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.041A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.526A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.961A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.081A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.585A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.951A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.883A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.599A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.856A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.521A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.969A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.126A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.937A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.801A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.962A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.650A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.253A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.341A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.446A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.769A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.604A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.858A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.711A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.459A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.459A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.265A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.716A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB5, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.194A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.104A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.788A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.691A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 9.885A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU B 156 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 85 removed outlier: 13.172A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.293A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.704A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.691A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 9.885A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU B 156 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.760A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.548A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.812A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.608A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.476A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.476A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.319A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AC8, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.098A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.051A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.918A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 133 through 141 removed outlier: 6.470A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS C 136 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 12.143A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.885A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.169A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.972A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.972A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.617A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.869A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.450A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.450A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.322A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1120 through 1122 1002 hydrogen bonds defined for protein. 2808 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.02 Time building geometry restraints manager: 8.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6756 1.34 - 1.46: 5578 1.46 - 1.59: 9979 1.59 - 1.71: 0 1.71 - 1.83: 122 Bond restraints: 22435 Sorted by residual: bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.84e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.17e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.93e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.92e+00 ... (remaining 22430 not shown) Histogram of bond angle deviations from ideal: 95.78 - 103.44: 287 103.44 - 111.09: 8724 111.09 - 118.74: 9147 118.74 - 126.39: 12091 126.39 - 134.05: 261 Bond angle restraints: 30510 Sorted by residual: angle pdb=" N ALA C 372 " pdb=" CA ALA C 372 " pdb=" C ALA C 372 " ideal model delta sigma weight residual 109.81 122.00 -12.19 2.21e+00 2.05e-01 3.04e+01 angle pdb=" CA PRO C 373 " pdb=" N PRO C 373 " pdb=" CD PRO C 373 " ideal model delta sigma weight residual 112.00 104.51 7.49 1.40e+00 5.10e-01 2.86e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.17 -5.47 1.22e+00 6.72e-01 2.01e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.06 -5.36 1.22e+00 6.72e-01 1.93e+01 angle pdb=" CB ARG A 995 " pdb=" CG ARG A 995 " pdb=" CD ARG A 995 " ideal model delta sigma weight residual 111.30 120.53 -9.23 2.30e+00 1.89e-01 1.61e+01 ... (remaining 30505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 13048 17.81 - 35.62: 875 35.62 - 53.43: 167 53.43 - 71.24: 59 71.24 - 89.05: 27 Dihedral angle restraints: 14176 sinusoidal: 6312 harmonic: 7864 Sorted by residual: dihedral pdb=" CA CYS A 590 " pdb=" C CYS A 590 " pdb=" N SER A 591 " pdb=" CA SER A 591 " ideal model delta harmonic sigma weight residual -180.00 -161.64 -18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 162.56 17.44 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ASP B 578 " pdb=" CB ASP B 578 " pdb=" CG ASP B 578 " pdb=" OD1 ASP B 578 " ideal model delta sinusoidal sigma weight residual -30.00 -88.47 58.47 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 14173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2944 0.073 - 0.147: 659 0.147 - 0.220: 50 0.220 - 0.294: 3 0.294 - 0.367: 3 Chirality restraints: 3659 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 3656 not shown) Planarity restraints: 3897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 372 " -0.059 5.00e-02 4.00e+02 8.54e-02 1.17e+01 pdb=" N PRO C 373 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO C 373 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 373 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 954 " 0.018 2.00e-02 2.50e+03 2.52e-02 9.51e+00 pdb=" CG HIS A 954 " -0.053 2.00e-02 2.50e+03 pdb=" ND1 HIS A 954 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 HIS A 954 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 HIS A 954 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS A 954 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 954 " -0.016 2.00e-02 2.50e+03 2.30e-02 7.91e+00 pdb=" CG HIS B 954 " 0.048 2.00e-02 2.50e+03 pdb=" ND1 HIS B 954 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS B 954 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 HIS B 954 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 954 " 0.001 2.00e-02 2.50e+03 ... (remaining 3894 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2919 2.76 - 3.29: 19848 3.29 - 3.83: 37805 3.83 - 4.36: 44066 4.36 - 4.90: 76249 Nonbonded interactions: 180887 Sorted by model distance: nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.225 2.440 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.248 2.440 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.274 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.279 2.440 nonbonded pdb=" OE1 GLN B 115 " pdb=" OG1 THR B 167 " model vdw 2.300 2.440 ... (remaining 180882 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 528 or resid 530 through 1147 or resid 1301 thr \ ough 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.240 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 59.320 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.250 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:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 22435 Z= 0.375 Angle : 0.860 12.187 30510 Z= 0.471 Chirality : 0.059 0.367 3659 Planarity : 0.007 0.085 3857 Dihedral : 13.015 89.053 8992 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.74 % Favored : 98.22 % Rotamer: Outliers : 0.17 % Allowed : 3.53 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 2645 helix: 1.29 (0.18), residues: 618 sheet: 0.93 (0.20), residues: 596 loop : -0.74 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP C 886 HIS 0.033 0.003 HIS A 954 PHE 0.044 0.003 PHE B 981 TYR 0.032 0.003 TYR A1067 ARG 0.014 0.001 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 441 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6949 (m90) cc_final: 0.6748 (m-70) REVERT: A 83 VAL cc_start: 0.7014 (t) cc_final: 0.6776 (p) REVERT: A 223 LEU cc_start: 0.6521 (mp) cc_final: 0.6096 (mp) REVERT: A 589 PRO cc_start: 0.5576 (Cg_exo) cc_final: 0.5232 (Cg_endo) REVERT: B 656 VAL cc_start: 0.7365 (OUTLIER) cc_final: 0.7089 (m) REVERT: B 731 MET cc_start: 0.7406 (mtm) cc_final: 0.7181 (mtm) REVERT: B 859 THR cc_start: 0.6875 (p) cc_final: 0.6670 (m) REVERT: B 988 GLU cc_start: 0.7539 (mp0) cc_final: 0.7273 (mp0) REVERT: C 85 PRO cc_start: 0.9162 (Cg_exo) cc_final: 0.8901 (Cg_endo) REVERT: C 271 GLN cc_start: 0.8162 (mp10) cc_final: 0.7865 (mp10) REVERT: C 353 TRP cc_start: 0.8248 (p-90) cc_final: 0.7595 (p-90) REVERT: C 913 GLN cc_start: 0.6588 (OUTLIER) cc_final: 0.6342 (pt0) outliers start: 4 outliers final: 2 residues processed: 445 average time/residue: 0.9586 time to fit residues: 507.8601 Evaluate side-chains 208 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 204 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 PRO Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain C residue 913 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 227 optimal weight: 0.5980 chunk 203 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 210 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 156 optimal weight: 0.7980 chunk 244 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 317 ASN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1054 GLN B 125 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 954 HIS B 955 ASN B1005 GLN C 314 GLN C 580 GLN C 913 GLN C 926 GLN C 965 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 22435 Z= 0.247 Angle : 0.639 10.113 30510 Z= 0.326 Chirality : 0.046 0.248 3659 Planarity : 0.005 0.063 3857 Dihedral : 6.548 59.387 4098 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.15 % Allowed : 10.89 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 2645 helix: 1.78 (0.20), residues: 629 sheet: 0.63 (0.22), residues: 513 loop : -0.55 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 886 HIS 0.009 0.001 HIS A 954 PHE 0.033 0.002 PHE C 220 TYR 0.024 0.002 TYR B1067 ARG 0.012 0.001 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 247 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7448 (t) cc_final: 0.7226 (p) REVERT: A 97 LYS cc_start: 0.5565 (OUTLIER) cc_final: 0.5110 (mmmm) REVERT: A 102 ARG cc_start: 0.6973 (mmp80) cc_final: 0.6401 (mmp80) REVERT: A 697 MET cc_start: 0.7356 (ptt) cc_final: 0.7027 (ptt) REVERT: B 55 PHE cc_start: 0.6966 (m-80) cc_final: 0.6599 (m-80) REVERT: B 984 LEU cc_start: 0.8505 (tp) cc_final: 0.8286 (tp) REVERT: B 988 GLU cc_start: 0.7632 (mp0) cc_final: 0.7237 (mp0) REVERT: C 200 TYR cc_start: 0.5810 (OUTLIER) cc_final: 0.5521 (t80) REVERT: C 353 TRP cc_start: 0.8451 (p-90) cc_final: 0.7724 (p-90) REVERT: C 434 ILE cc_start: 0.6014 (OUTLIER) cc_final: 0.5548 (pt) REVERT: C 516 GLU cc_start: 0.7394 (pp20) cc_final: 0.7116 (pp20) REVERT: C 957 GLN cc_start: 0.7625 (tm-30) cc_final: 0.7267 (tm-30) REVERT: C 983 ARG cc_start: 0.7450 (ttm-80) cc_final: 0.6720 (tpm170) REVERT: C 985 ASP cc_start: 0.7874 (p0) cc_final: 0.7590 (p0) REVERT: C 1142 GLN cc_start: 0.8697 (tp40) cc_final: 0.8072 (tm-30) outliers start: 75 outliers final: 19 residues processed: 293 average time/residue: 0.9672 time to fit residues: 341.8335 Evaluate side-chains 200 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 178 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 135 optimal weight: 0.1980 chunk 75 optimal weight: 1.9990 chunk 203 optimal weight: 10.0000 chunk 166 optimal weight: 40.0000 chunk 67 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 264 optimal weight: 0.8980 chunk 217 optimal weight: 4.9990 chunk 242 optimal weight: 0.6980 chunk 83 optimal weight: 40.0000 chunk 196 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 824 ASN A 872 GLN A 907 ASN A 955 ASN B 125 ASN B 901 GLN B 907 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 314 GLN C 450 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN C 926 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 22435 Z= 0.266 Angle : 0.613 12.154 30510 Z= 0.315 Chirality : 0.046 0.290 3659 Planarity : 0.004 0.053 3857 Dihedral : 5.689 57.400 4089 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.49 % Allowed : 12.36 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.16), residues: 2645 helix: 1.82 (0.21), residues: 626 sheet: 0.56 (0.21), residues: 572 loop : -0.54 (0.15), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 886 HIS 0.008 0.001 HIS A 954 PHE 0.026 0.002 PHE C 168 TYR 0.028 0.002 TYR C 741 ARG 0.005 0.001 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 213 time to evaluate : 2.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7884 (tm-30) REVERT: A 83 VAL cc_start: 0.7659 (t) cc_final: 0.6994 (p) REVERT: A 97 LYS cc_start: 0.5901 (OUTLIER) cc_final: 0.5035 (mptp) REVERT: A 239 GLN cc_start: 0.6925 (mm110) cc_final: 0.6719 (mm-40) REVERT: A 269 TYR cc_start: 0.7009 (m-80) cc_final: 0.6675 (m-80) REVERT: A 314 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7992 (tp-100) REVERT: A 585 LEU cc_start: 0.7615 (mt) cc_final: 0.7397 (tp) REVERT: A 900 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8591 (mtp) REVERT: A 964 LYS cc_start: 0.8505 (tppp) cc_final: 0.8242 (mttt) REVERT: A 1005 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8126 (mm-40) REVERT: B 238 PHE cc_start: 0.7148 (p90) cc_final: 0.6735 (p90) REVERT: B 740 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8021 (tpp) REVERT: B 988 GLU cc_start: 0.7695 (mp0) cc_final: 0.7229 (mp0) REVERT: B 1050 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8585 (ptm) REVERT: C 100 ILE cc_start: 0.8357 (mm) cc_final: 0.8149 (mm) REVERT: C 200 TYR cc_start: 0.5975 (OUTLIER) cc_final: 0.5675 (t80) REVERT: C 302 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8830 (p) REVERT: C 353 TRP cc_start: 0.8374 (p-90) cc_final: 0.7876 (p-90) REVERT: C 434 ILE cc_start: 0.6063 (OUTLIER) cc_final: 0.5655 (pt) REVERT: C 934 ILE cc_start: 0.7111 (OUTLIER) cc_final: 0.6896 (mp) REVERT: C 947 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8571 (mtpt) REVERT: C 954 HIS cc_start: 0.8205 (m90) cc_final: 0.7972 (m-70) REVERT: C 983 ARG cc_start: 0.7747 (ttm-80) cc_final: 0.6702 (tpm170) REVERT: C 1142 GLN cc_start: 0.8667 (tp40) cc_final: 0.8162 (tm-30) outliers start: 83 outliers final: 25 residues processed: 269 average time/residue: 0.8972 time to fit residues: 292.7269 Evaluate side-chains 201 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 167 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 241 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 245 optimal weight: 0.7980 chunk 260 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 232 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 121 ASN A 762 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1011 GLN C 314 GLN C 450 ASN C 580 GLN C 965 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 22435 Z= 0.237 Angle : 0.572 9.842 30510 Z= 0.289 Chirality : 0.045 0.263 3659 Planarity : 0.004 0.081 3857 Dihedral : 5.390 53.908 4089 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.90 % Allowed : 13.46 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.16), residues: 2645 helix: 1.92 (0.20), residues: 633 sheet: 0.42 (0.20), residues: 601 loop : -0.58 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 104 HIS 0.006 0.001 HIS A 954 PHE 0.017 0.002 PHE A 92 TYR 0.020 0.001 TYR A1067 ARG 0.004 0.000 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 196 time to evaluate : 2.605 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 52 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7941 (tm-30) REVERT: A 83 VAL cc_start: 0.7864 (t) cc_final: 0.7292 (p) REVERT: A 97 LYS cc_start: 0.5537 (OUTLIER) cc_final: 0.4799 (mptp) REVERT: A 200 TYR cc_start: 0.6524 (OUTLIER) cc_final: 0.5565 (m-80) REVERT: A 269 TYR cc_start: 0.7090 (m-80) cc_final: 0.6706 (m-80) REVERT: A 314 GLN cc_start: 0.8322 (tm-30) cc_final: 0.8003 (tp-100) REVERT: A 585 LEU cc_start: 0.7651 (mt) cc_final: 0.7415 (tp) REVERT: A 950 ASP cc_start: 0.8000 (t0) cc_final: 0.7730 (t0) REVERT: A 964 LYS cc_start: 0.8611 (tppp) cc_final: 0.8312 (mttt) REVERT: B 55 PHE cc_start: 0.7059 (m-80) cc_final: 0.6685 (m-80) REVERT: B 140 PHE cc_start: 0.6839 (p90) cc_final: 0.6448 (p90) REVERT: B 237 ARG cc_start: 0.8713 (mtp180) cc_final: 0.8445 (mtm110) REVERT: B 238 PHE cc_start: 0.7188 (p90) cc_final: 0.6815 (p90) REVERT: B 740 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7907 (tpp) REVERT: B 988 GLU cc_start: 0.7684 (mp0) cc_final: 0.7308 (mp0) REVERT: B 1050 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8699 (ptm) REVERT: C 100 ILE cc_start: 0.8430 (mm) cc_final: 0.8227 (mm) REVERT: C 200 TYR cc_start: 0.6140 (OUTLIER) cc_final: 0.5888 (t80) REVERT: C 353 TRP cc_start: 0.8283 (p-90) cc_final: 0.7754 (p-90) REVERT: C 423 TYR cc_start: 0.7715 (t80) cc_final: 0.7422 (t80) REVERT: C 586 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7561 (m-30) REVERT: C 859 THR cc_start: 0.9079 (m) cc_final: 0.8836 (p) REVERT: C 983 ARG cc_start: 0.7605 (ttm-80) cc_final: 0.6811 (tpm170) REVERT: C 1013 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.9070 (mt) REVERT: C 1031 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7936 (mt-10) REVERT: C 1050 MET cc_start: 0.8917 (ptm) cc_final: 0.8663 (ptm) REVERT: C 1142 GLN cc_start: 0.8706 (tp40) cc_final: 0.8229 (tm-30) outliers start: 69 outliers final: 26 residues processed: 243 average time/residue: 0.9463 time to fit residues: 277.0816 Evaluate side-chains 207 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 173 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 216 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 3 optimal weight: 0.0570 chunk 193 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 221 optimal weight: 0.0770 chunk 179 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 233 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 121 ASN A 762 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 824 ASN C 314 GLN C 965 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22435 Z= 0.197 Angle : 0.544 10.823 30510 Z= 0.276 Chirality : 0.045 0.277 3659 Planarity : 0.004 0.056 3857 Dihedral : 5.072 53.199 4089 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.86 % Allowed : 13.84 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.16), residues: 2645 helix: 2.02 (0.21), residues: 640 sheet: 0.41 (0.20), residues: 605 loop : -0.50 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 104 HIS 0.005 0.001 HIS A 954 PHE 0.030 0.001 PHE C 592 TYR 0.019 0.001 TYR B1067 ARG 0.007 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 188 time to evaluate : 2.226 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 52 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7994 (tm-30) REVERT: A 83 VAL cc_start: 0.7570 (t) cc_final: 0.7338 (p) REVERT: A 97 LYS cc_start: 0.5750 (OUTLIER) cc_final: 0.4888 (mptp) REVERT: A 200 TYR cc_start: 0.6496 (OUTLIER) cc_final: 0.5568 (m-80) REVERT: A 269 TYR cc_start: 0.7111 (m-80) cc_final: 0.6728 (m-80) REVERT: A 314 GLN cc_start: 0.8328 (tm-30) cc_final: 0.8101 (tp-100) REVERT: A 585 LEU cc_start: 0.7660 (mt) cc_final: 0.7436 (tp) REVERT: A 950 ASP cc_start: 0.7937 (t0) cc_final: 0.7673 (t0) REVERT: A 964 LYS cc_start: 0.8622 (tppp) cc_final: 0.8395 (mttt) REVERT: A 979 ASP cc_start: 0.7964 (t0) cc_final: 0.7662 (t0) REVERT: A 985 ASP cc_start: 0.7619 (p0) cc_final: 0.7299 (p0) REVERT: A 988 GLU cc_start: 0.8254 (mp0) cc_final: 0.7991 (mp0) REVERT: B 55 PHE cc_start: 0.7193 (m-80) cc_final: 0.6829 (m-80) REVERT: B 140 PHE cc_start: 0.6777 (p90) cc_final: 0.6334 (p90) REVERT: B 237 ARG cc_start: 0.8721 (mtp180) cc_final: 0.8450 (mtm110) REVERT: B 238 PHE cc_start: 0.7240 (p90) cc_final: 0.6935 (p90) REVERT: B 740 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7851 (tpp) REVERT: B 1050 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8686 (ptm) REVERT: C 200 TYR cc_start: 0.6240 (OUTLIER) cc_final: 0.5996 (t80) REVERT: C 302 THR cc_start: 0.9325 (OUTLIER) cc_final: 0.9046 (p) REVERT: C 353 TRP cc_start: 0.8316 (p-90) cc_final: 0.7892 (p-90) REVERT: C 516 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6945 (pp20) REVERT: C 983 ARG cc_start: 0.7654 (ttm-80) cc_final: 0.6849 (tpm170) REVERT: C 1013 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9056 (mt) REVERT: C 1031 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7941 (mt-10) REVERT: C 1142 GLN cc_start: 0.8692 (tp40) cc_final: 0.8297 (tm-30) outliers start: 68 outliers final: 30 residues processed: 235 average time/residue: 0.9624 time to fit residues: 270.5552 Evaluate side-chains 207 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 168 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 87 optimal weight: 6.9990 chunk 234 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 152 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 216 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 136 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 66 HIS B 125 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 314 GLN C 388 ASN C 926 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.6202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22435 Z= 0.252 Angle : 0.563 9.666 30510 Z= 0.284 Chirality : 0.045 0.278 3659 Planarity : 0.004 0.049 3857 Dihedral : 4.900 52.520 4089 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.73 % Allowed : 14.80 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.16), residues: 2645 helix: 1.99 (0.21), residues: 641 sheet: 0.40 (0.20), residues: 610 loop : -0.48 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 104 HIS 0.005 0.001 HIS A 954 PHE 0.027 0.002 PHE A 981 TYR 0.020 0.001 TYR B1067 ARG 0.006 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 173 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8135 (tm-30) REVERT: A 54 LEU cc_start: 0.8361 (mt) cc_final: 0.8119 (mm) REVERT: A 97 LYS cc_start: 0.5844 (OUTLIER) cc_final: 0.4931 (mptp) REVERT: A 102 ARG cc_start: 0.7085 (mmp80) cc_final: 0.6787 (tpp-160) REVERT: A 200 TYR cc_start: 0.6476 (OUTLIER) cc_final: 0.5515 (m-80) REVERT: A 269 TYR cc_start: 0.7224 (m-80) cc_final: 0.6835 (m-80) REVERT: A 314 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8098 (tp-100) REVERT: A 585 LEU cc_start: 0.7603 (mt) cc_final: 0.7300 (tp) REVERT: A 964 LYS cc_start: 0.8635 (tppp) cc_final: 0.8317 (mttt) REVERT: A 979 ASP cc_start: 0.7873 (t0) cc_final: 0.7576 (t0) REVERT: A 988 GLU cc_start: 0.8255 (mp0) cc_final: 0.8007 (mp0) REVERT: B 55 PHE cc_start: 0.7191 (m-80) cc_final: 0.6933 (m-80) REVERT: B 237 ARG cc_start: 0.8749 (mtp180) cc_final: 0.8462 (mtm110) REVERT: B 238 PHE cc_start: 0.7255 (p90) cc_final: 0.6916 (p90) REVERT: B 740 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7805 (tpp) REVERT: C 54 LEU cc_start: 0.8637 (mp) cc_final: 0.8252 (mp) REVERT: C 200 TYR cc_start: 0.6344 (OUTLIER) cc_final: 0.6069 (t80) REVERT: C 353 TRP cc_start: 0.8402 (p-90) cc_final: 0.7899 (p-90) REVERT: C 516 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6929 (tm-30) REVERT: C 960 ASN cc_start: 0.8623 (m-40) cc_final: 0.8409 (t0) REVERT: C 983 ARG cc_start: 0.7684 (ttm-80) cc_final: 0.6857 (tpm170) REVERT: C 1031 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.7993 (mt-10) REVERT: C 1142 GLN cc_start: 0.8710 (tp40) cc_final: 0.8319 (tm-30) outliers start: 65 outliers final: 38 residues processed: 219 average time/residue: 0.9743 time to fit residues: 255.4097 Evaluate side-chains 202 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 158 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 250 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 219 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 259 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 762 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 755 GLN C 926 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.6559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 22435 Z= 0.303 Angle : 0.570 9.931 30510 Z= 0.291 Chirality : 0.046 0.278 3659 Planarity : 0.004 0.046 3857 Dihedral : 4.912 52.066 4089 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.69 % Allowed : 15.05 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.16), residues: 2645 helix: 1.92 (0.20), residues: 641 sheet: 0.34 (0.20), residues: 634 loop : -0.47 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 104 HIS 0.005 0.001 HIS A 954 PHE 0.027 0.002 PHE A 133 TYR 0.021 0.001 TYR B1067 ARG 0.005 0.000 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 165 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8146 (tm-30) REVERT: A 97 LYS cc_start: 0.5961 (OUTLIER) cc_final: 0.4993 (mptp) REVERT: A 102 ARG cc_start: 0.7096 (mmp80) cc_final: 0.6379 (tpp-160) REVERT: A 153 MET cc_start: 0.4221 (ppp) cc_final: 0.3990 (pmm) REVERT: A 200 TYR cc_start: 0.6439 (OUTLIER) cc_final: 0.5501 (m-80) REVERT: A 201 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6167 (t80) REVERT: A 314 GLN cc_start: 0.8353 (tm-30) cc_final: 0.8142 (tp-100) REVERT: A 964 LYS cc_start: 0.8680 (tppp) cc_final: 0.8399 (mttt) REVERT: A 979 ASP cc_start: 0.7972 (t0) cc_final: 0.7677 (t0) REVERT: A 985 ASP cc_start: 0.7668 (p0) cc_final: 0.7227 (p0) REVERT: A 988 GLU cc_start: 0.8258 (mp0) cc_final: 0.7978 (mp0) REVERT: B 55 PHE cc_start: 0.7531 (m-80) cc_final: 0.7145 (m-80) REVERT: B 237 ARG cc_start: 0.8745 (mtp180) cc_final: 0.8462 (mtm110) REVERT: B 238 PHE cc_start: 0.7268 (p90) cc_final: 0.6950 (p90) REVERT: B 740 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7750 (tpp) REVERT: B 1050 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8761 (ptm) REVERT: C 134 GLN cc_start: 0.8827 (tp40) cc_final: 0.8229 (mm110) REVERT: C 200 TYR cc_start: 0.6488 (OUTLIER) cc_final: 0.6230 (t80) REVERT: C 302 THR cc_start: 0.9381 (OUTLIER) cc_final: 0.9123 (p) REVERT: C 353 TRP cc_start: 0.8440 (p-90) cc_final: 0.7929 (p-90) REVERT: C 516 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6902 (tm-30) REVERT: C 983 ARG cc_start: 0.7623 (ttm-80) cc_final: 0.6845 (tpm170) REVERT: C 1001 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8728 (mm) REVERT: C 1031 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: C 1142 GLN cc_start: 0.8763 (tp40) cc_final: 0.8366 (tm-30) outliers start: 64 outliers final: 40 residues processed: 210 average time/residue: 0.9379 time to fit residues: 236.9334 Evaluate side-chains 202 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 152 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 160 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 154 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 164 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 chunk 235 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 87 ASN A 762 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 314 GLN C 606 ASN C 926 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.6745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22435 Z= 0.214 Angle : 0.548 10.295 30510 Z= 0.276 Chirality : 0.045 0.278 3659 Planarity : 0.004 0.042 3857 Dihedral : 4.781 52.943 4089 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.48 % Allowed : 15.43 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.16), residues: 2645 helix: 2.05 (0.21), residues: 641 sheet: 0.35 (0.20), residues: 615 loop : -0.42 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 104 HIS 0.004 0.001 HIS A 954 PHE 0.025 0.001 PHE C 135 TYR 0.020 0.001 TYR B1067 ARG 0.004 0.000 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 157 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8446 (tm-30) cc_final: 0.8156 (tm-30) REVERT: A 97 LYS cc_start: 0.5872 (OUTLIER) cc_final: 0.4814 (mptp) REVERT: A 102 ARG cc_start: 0.7090 (mmp80) cc_final: 0.6520 (tpp-160) REVERT: A 200 TYR cc_start: 0.6253 (OUTLIER) cc_final: 0.5426 (m-80) REVERT: A 964 LYS cc_start: 0.8661 (tppp) cc_final: 0.8449 (mttt) REVERT: A 979 ASP cc_start: 0.7890 (t0) cc_final: 0.7596 (t0) REVERT: A 985 ASP cc_start: 0.7694 (p0) cc_final: 0.7217 (p0) REVERT: A 988 GLU cc_start: 0.8269 (mp0) cc_final: 0.8034 (mp0) REVERT: B 55 PHE cc_start: 0.7520 (m-80) cc_final: 0.7194 (m-80) REVERT: B 237 ARG cc_start: 0.8750 (mtp180) cc_final: 0.8454 (mtm110) REVERT: B 238 PHE cc_start: 0.7280 (p90) cc_final: 0.6957 (p90) REVERT: B 740 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7720 (tpp) REVERT: C 302 THR cc_start: 0.9382 (OUTLIER) cc_final: 0.9123 (p) REVERT: C 353 TRP cc_start: 0.8376 (p-90) cc_final: 0.7931 (p-90) REVERT: C 516 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6797 (tm-30) REVERT: C 983 ARG cc_start: 0.7702 (ttm-80) cc_final: 0.6851 (tpm170) REVERT: C 1001 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8635 (mm) REVERT: C 1031 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: C 1142 GLN cc_start: 0.8767 (tp40) cc_final: 0.8377 (tm-30) outliers start: 59 outliers final: 36 residues processed: 201 average time/residue: 1.0168 time to fit residues: 245.4870 Evaluate side-chains 192 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 149 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 248 optimal weight: 1.9990 chunk 226 optimal weight: 0.6980 chunk 241 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 218 optimal weight: 0.7980 chunk 228 optimal weight: 0.7980 chunk 240 optimal weight: 0.9980 chunk 158 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 762 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN C 314 GLN C 926 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.6883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22435 Z= 0.201 Angle : 0.554 11.527 30510 Z= 0.279 Chirality : 0.045 0.280 3659 Planarity : 0.004 0.053 3857 Dihedral : 4.713 52.628 4089 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.19 % Allowed : 15.85 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.16), residues: 2645 helix: 2.08 (0.21), residues: 641 sheet: 0.41 (0.20), residues: 614 loop : -0.37 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 104 HIS 0.004 0.001 HIS A 954 PHE 0.033 0.001 PHE C 592 TYR 0.020 0.001 TYR B1067 ARG 0.004 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 156 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8214 (tm-30) REVERT: A 97 LYS cc_start: 0.5888 (OUTLIER) cc_final: 0.4773 (mptp) REVERT: A 102 ARG cc_start: 0.7086 (mmp80) cc_final: 0.6477 (tpp-160) REVERT: A 153 MET cc_start: 0.4323 (ppp) cc_final: 0.4115 (pmm) REVERT: A 200 TYR cc_start: 0.6125 (OUTLIER) cc_final: 0.5222 (m-80) REVERT: A 560 LEU cc_start: 0.8676 (mm) cc_final: 0.8354 (mp) REVERT: A 979 ASP cc_start: 0.7822 (t0) cc_final: 0.7557 (t0) REVERT: A 985 ASP cc_start: 0.7701 (p0) cc_final: 0.7281 (p0) REVERT: A 988 GLU cc_start: 0.8269 (mp0) cc_final: 0.7990 (mp0) REVERT: B 55 PHE cc_start: 0.7563 (m-80) cc_final: 0.7310 (m-80) REVERT: B 237 ARG cc_start: 0.8763 (mtp180) cc_final: 0.8484 (mtm110) REVERT: B 238 PHE cc_start: 0.7264 (p90) cc_final: 0.6955 (p90) REVERT: B 740 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7718 (tpp) REVERT: B 934 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8422 (mp) REVERT: C 302 THR cc_start: 0.9392 (OUTLIER) cc_final: 0.9128 (p) REVERT: C 353 TRP cc_start: 0.8345 (p-90) cc_final: 0.7967 (p-90) REVERT: C 516 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6722 (tm-30) REVERT: C 983 ARG cc_start: 0.7710 (ttm-80) cc_final: 0.6849 (tpm170) REVERT: C 990 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7429 (mt-10) REVERT: C 1031 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7996 (mt-10) REVERT: C 1142 GLN cc_start: 0.8769 (tp40) cc_final: 0.8385 (tm-30) outliers start: 52 outliers final: 36 residues processed: 192 average time/residue: 0.9939 time to fit residues: 228.8925 Evaluate side-chains 194 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 151 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 255 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 121 optimal weight: 0.0770 chunk 177 optimal weight: 9.9990 chunk 267 optimal weight: 0.0980 chunk 246 optimal weight: 0.8980 chunk 213 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 762 GLN A 965 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.6973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22435 Z= 0.174 Angle : 0.553 11.915 30510 Z= 0.278 Chirality : 0.045 0.282 3659 Planarity : 0.004 0.040 3857 Dihedral : 4.640 52.964 4089 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.10 % Allowed : 16.23 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.16), residues: 2645 helix: 2.16 (0.21), residues: 641 sheet: 0.39 (0.20), residues: 618 loop : -0.36 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 104 HIS 0.004 0.001 HIS A 954 PHE 0.029 0.001 PHE C 592 TYR 0.020 0.001 TYR B1067 ARG 0.003 0.000 ARG A 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 158 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8441 (tm-30) cc_final: 0.8192 (tm-30) REVERT: A 97 LYS cc_start: 0.5865 (OUTLIER) cc_final: 0.4740 (mptp) REVERT: A 200 TYR cc_start: 0.6057 (OUTLIER) cc_final: 0.5201 (m-80) REVERT: A 560 LEU cc_start: 0.8649 (mm) cc_final: 0.8342 (mp) REVERT: A 964 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8326 (mttt) REVERT: A 979 ASP cc_start: 0.7791 (t0) cc_final: 0.7533 (t0) REVERT: A 985 ASP cc_start: 0.7723 (p0) cc_final: 0.7177 (p0) REVERT: A 988 GLU cc_start: 0.8268 (mp0) cc_final: 0.8013 (mp0) REVERT: B 55 PHE cc_start: 0.7554 (m-80) cc_final: 0.7308 (m-80) REVERT: B 237 ARG cc_start: 0.8815 (mtp180) cc_final: 0.8516 (mtm110) REVERT: B 238 PHE cc_start: 0.7279 (p90) cc_final: 0.6969 (p90) REVERT: B 740 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7706 (tpp) REVERT: B 934 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8389 (mp) REVERT: C 302 THR cc_start: 0.9391 (OUTLIER) cc_final: 0.9128 (p) REVERT: C 353 TRP cc_start: 0.8348 (p-90) cc_final: 0.7996 (p-90) REVERT: C 516 GLU cc_start: 0.6990 (pp20) cc_final: 0.6726 (tm-30) REVERT: C 990 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7410 (mt-10) REVERT: C 1031 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: C 1142 GLN cc_start: 0.8784 (tp40) cc_final: 0.8413 (tm-30) outliers start: 50 outliers final: 33 residues processed: 189 average time/residue: 0.9838 time to fit residues: 224.0755 Evaluate side-chains 187 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 147 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 227 optimal weight: 0.0970 chunk 65 optimal weight: 0.3980 chunk 196 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 59 optimal weight: 0.4980 chunk 213 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 219 optimal weight: 0.4980 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 187 optimal weight: 6.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 762 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.132380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.082020 restraints weight = 44404.519| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.97 r_work: 0.3058 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.7048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22435 Z= 0.170 Angle : 0.557 13.781 30510 Z= 0.277 Chirality : 0.045 0.320 3659 Planarity : 0.004 0.056 3857 Dihedral : 4.588 52.915 4089 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.81 % Allowed : 16.57 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.16), residues: 2645 helix: 2.13 (0.20), residues: 641 sheet: 0.44 (0.20), residues: 618 loop : -0.34 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 104 HIS 0.004 0.001 HIS A 954 PHE 0.030 0.001 PHE A 133 TYR 0.020 0.001 TYR B1067 ARG 0.004 0.000 ARG B 995 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6726.28 seconds wall clock time: 121 minutes 22.25 seconds (7282.25 seconds total)