Starting phenix.real_space_refine on Fri Mar 6 22:52:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g70_29792/03_2026/8g70_29792.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g70_29792/03_2026/8g70_29792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g70_29792/03_2026/8g70_29792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g70_29792/03_2026/8g70_29792.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g70_29792/03_2026/8g70_29792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g70_29792/03_2026/8g70_29792.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 912 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 159 5.16 5 C 21767 2.51 5 N 5742 2.21 5 O 6769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34437 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1083, 8462 Classifications: {'peptide': 1083} Link IDs: {'PTRANS': 59, 'TRANS': 1023} Chain breaks: 4 Chain: "B" Number of atoms: 8493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8493 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 58, 'TRANS': 1028} Chain breaks: 4 Chain: "D" Number of atoms: 8467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8467 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 59, 'TRANS': 1024} Chain breaks: 4 Chain: "E" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 881 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "H" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 881 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "I" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 881 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "G" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 893 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "F" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 893 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "K" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 893 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "N" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 974 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "O" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 877 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "M" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 877 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} 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: "C" 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: "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: "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: "V" 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: "W" 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: "X" 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: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 223 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 17 Chain: "D" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 8.01, per 1000 atoms: 0.23 Number of scatterers: 34437 At special positions: 0 Unit cell: (172.64, 173.525, 186.805, 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 159 16.00 O 6769 8.00 N 5742 7.00 C 21767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, 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 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.06 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.02 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 94 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 95 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG J 1 " - " NAG J 2 " " NAG L 1 " - " NAG L 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 V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 17 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 74 " " NAG A1310 " - " ASN A 165 " " NAG A1311 " - " ASN A 603 " " NAG A1312 " - " ASN A 149 " " NAG A1313 " - " ASN A 282 " " NAG A1314 " - " ASN A 234 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 717 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B 17 " " NAG B1309 " - " ASN B 61 " " NAG B1310 " - " ASN B 74 " " NAG B1311 " - " ASN B 165 " " NAG B1312 " - " ASN B 282 " " NAG B1313 " - " ASN B 122 " " NAG B1314 " - " ASN B 149 " " NAG B1315 " - " ASN B 343 " " NAG B1316 " - " ASN B 331 " " NAG C 1 " - " ASN A 801 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 122 " " NAG D1303 " - " ASN D 282 " " NAG D1304 " - " ASN D 331 " " NAG D1305 " - " ASN D 616 " " NAG D1306 " - " ASN D 657 " " NAG D1307 " - " ASN D 709 " " NAG D1308 " - " ASN D1074 " " NAG D1309 " - " ASN D 17 " " NAG D1310 " - " ASN D 74 " " NAG D1311 " - " ASN D 165 " " NAG D1312 " - " ASN D 343 " " NAG D1313 " - " ASN D 603 " " NAG D1314 " - " ASN D 149 " " NAG D1315 " - " ASN D 234 " " NAG J 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG P 1 " - " ASN A 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN D 717 " " NAG U 1 " - " ASN D 801 " " NAG V 1 " - " ASN D1098 " " NAG W 1 " - " ASN D1134 " " NAG X 1 " - " ASN A 122 " Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.3 seconds 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7948 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 76 sheets defined 19.9% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.847A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.045A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.049A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.667A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.786A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.859A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.089A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.519A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.543A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.742A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.116A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.414A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.934A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.101A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 619 through 624 removed outlier: 4.036A pdb=" N ALA B 623 " --> pdb=" O GLU B 619 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 619 through 624' Processing helix chain 'B' and resid 636 through 640 removed outlier: 3.743A pdb=" N SER B 640 " --> pdb=" O SER B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.545A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) 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: 3.663A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.550A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.769A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 4.374A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 7.236A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.512A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.828A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.026A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.933A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 343 Processing helix chain 'D' and resid 364 through 370 removed outlier: 4.209A pdb=" N LEU D 368 " --> pdb=" O ASP D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 411 removed outlier: 3.935A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA D 411 " --> pdb=" O ARG D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 737 through 743 Processing helix chain 'D' and resid 746 through 754 removed outlier: 3.991A pdb=" N SER D 750 " --> pdb=" O SER D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 783 Processing helix chain 'D' and resid 816 through 825 Processing helix chain 'D' and resid 866 through 885 Processing helix chain 'D' and resid 886 through 890 Processing helix chain 'D' and resid 897 through 910 Processing helix chain 'D' and resid 912 through 941 removed outlier: 4.313A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS D 921 " --> pdb=" O TYR D 917 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR D 941 " --> pdb=" O SER D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.968A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU D 962 " --> pdb=" O ALA D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 984 removed outlier: 3.597A pdb=" N ILE D 980 " --> pdb=" O VAL D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.845A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1147 removed outlier: 4.106A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.882A pdb=" N THR H 90 " --> pdb=" O ASP H 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 90 Processing helix chain 'G' and resid 60 through 63 Processing helix chain 'G' and resid 85 through 89 removed outlier: 3.636A pdb=" N THR G 89 " --> pdb=" O PRO G 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 63 removed outlier: 4.236A pdb=" N LYS F 63 " --> pdb=" O ASP F 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 60 through 63' Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.597A pdb=" N THR F 89 " --> pdb=" O PRO F 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 89 Processing helix chain 'K' and resid 99 through 103 removed outlier: 4.347A pdb=" N GLY K 102 " --> pdb=" O PRO K 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'O' and resid 86 through 90 Processing helix chain 'M' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 4.151A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.397A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.619A pdb=" N GLY D 566 " --> pdb=" O ALA D 575 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 50 removed outlier: 4.041A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.936A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 13.137A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.671A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.472A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 10.435A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.152A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.838A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.635A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.591A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.543A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.912A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.057A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.678A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.944A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.194A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.855A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.855A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.886A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 68 through 70 Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.552A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.219A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.962A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B 140 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.958A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.961A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.605A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE B 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 355 through 358 Processing sheet with id=AD1, first strand: chain 'B' and resid 355 through 358 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.847A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 653 through 655 removed outlier: 6.607A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.169A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.601A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.549A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'D' and resid 27 through 30 removed outlier: 4.660A pdb=" N ALA D 27 " --> pdb=" O TRP D 64 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 10.052A pdb=" N HIS D 207 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 9.890A pdb=" N LEU D 223 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL D 36 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 48 through 55 removed outlier: 4.004A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 68 through 69 removed outlier: 4.156A pdb=" N ARG D 78 " --> pdb=" O HIS D 69 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.812A pdb=" N GLU D 154 " --> pdb=" O TYR D 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.865A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE D 128 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N PHE D 168 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL D 130 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N CYS D 166 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER D 162 " --> pdb=" O GLN D 134 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.306A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 650 " --> pdb=" O PHE D 643 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE D 643 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 356 through 358 Processing sheet with id=AE7, first strand: chain 'D' and resid 452 through 453 Processing sheet with id=AE8, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.794A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.329A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA D 672 " --> pdb=" O PRO D 665 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 711 through 715 Processing sheet with id=AF2, first strand: chain 'D' and resid 718 through 728 removed outlier: 6.841A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'D' and resid 1120 through 1122 Processing sheet with id=AF5, first strand: chain 'D' and resid 1094 through 1097 Processing sheet with id=AF6, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AF7, first strand: chain 'E' and resid 11 through 13 removed outlier: 3.637A pdb=" N ALA E 91 " --> pdb=" O VAL E 110 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN E 39 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU E 33 " --> pdb=" O ARG E 98 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N MET E 34 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N THR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 11 through 13 removed outlier: 3.637A pdb=" N ALA E 91 " --> pdb=" O VAL E 110 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA E 97 " --> pdb=" O TYR E 103 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 17 through 20 Processing sheet with id=AG1, first strand: chain 'H' and resid 11 through 13 removed outlier: 7.289A pdb=" N VAL H 12 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN H 58 " --> pdb=" O THR H 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 17 through 18 Processing sheet with id=AG3, first strand: chain 'H' and resid 69 through 70 Processing sheet with id=AG4, first strand: chain 'I' and resid 4 through 5 removed outlier: 3.730A pdb=" N GLN I 5 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS I 22 " --> pdb=" O VAL I 78 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 11 through 13 removed outlier: 6.942A pdb=" N VAL I 12 " --> pdb=" O SER I 113 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG I 98 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU I 33 " --> pdb=" O ARG I 98 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N MET I 34 " --> pdb=" O THR I 50 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N THR I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 11 through 13 removed outlier: 6.942A pdb=" N VAL I 12 " --> pdb=" O SER I 113 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 17 through 18 Processing sheet with id=AG8, first strand: chain 'G' and resid 18 through 22 removed outlier: 4.087A pdb=" N VAL G 77 " --> pdb=" O CYS G 22 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 56 through 58 removed outlier: 6.326A pdb=" N TRP G 35 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN G 49 " --> pdb=" O MET G 33 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET G 33 " --> pdb=" O GLN G 49 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 18 through 21 Processing sheet with id=AH2, first strand: chain 'F' and resid 56 through 58 removed outlier: 4.728A pdb=" N LEU F 46 " --> pdb=" O ARG F 37 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ARG F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 17 through 22 removed outlier: 3.824A pdb=" N VAL K 77 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 57 through 58 removed outlier: 5.829A pdb=" N LEU K 46 " --> pdb=" O ARG K 37 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AH6, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.852A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG N 38 " --> pdb=" O GLY N 47 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLY N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'O' and resid 4 through 7 removed outlier: 3.518A pdb=" N VAL O 78 " --> pdb=" O CYS O 22 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR O 68 " --> pdb=" O GLN O 81 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'O' and resid 10 through 11 removed outlier: 3.736A pdb=" N THR O 112 " --> pdb=" O GLY O 10 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'O' and resid 10 through 11 removed outlier: 3.736A pdb=" N THR O 112 " --> pdb=" O GLY O 10 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.506A pdb=" N GLN M 5 " --> pdb=" O ALA M 23 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA M 23 " --> pdb=" O GLN M 5 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.506A pdb=" N GLN M 5 " --> pdb=" O ALA M 23 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA M 23 " --> pdb=" O GLN M 5 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS M 79 " --> pdb=" O THR M 70 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 10 through 11 removed outlier: 3.622A pdb=" N THR M 112 " --> pdb=" O GLY M 10 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 10 through 11 removed outlier: 3.622A pdb=" N THR M 112 " --> pdb=" O GLY M 10 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA M 97 " --> pdb=" O TYR M 104 " (cutoff:3.500A) 1244 hydrogen bonds defined for protein. 3273 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: 9.62 Time building geometry restraints manager: 3.76 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: 11051 1.34 - 1.47: 8928 1.47 - 1.59: 15015 1.59 - 1.71: 2 1.71 - 1.84: 211 Bond restraints: 35207 Sorted by residual: bond pdb=" N ALA B 903 " pdb=" CA ALA B 903 " ideal model delta sigma weight residual 1.457 1.556 -0.099 1.29e-02 6.01e+03 5.88e+01 bond pdb=" CG PRO D 384 " pdb=" CD PRO D 384 " ideal model delta sigma weight residual 1.503 1.339 0.164 3.40e-02 8.65e+02 2.32e+01 bond pdb=" CB PRO B 209 " pdb=" CG PRO B 209 " ideal model delta sigma weight residual 1.492 1.685 -0.193 5.00e-02 4.00e+02 1.49e+01 bond pdb=" N PRO D 384 " pdb=" CD PRO D 384 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.39e+01 bond pdb=" CG PRO B 209 " pdb=" CD PRO B 209 " ideal model delta sigma weight residual 1.503 1.388 0.115 3.40e-02 8.65e+02 1.14e+01 ... (remaining 35202 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 47644 3.37 - 6.73: 188 6.73 - 10.10: 29 10.10 - 13.47: 6 13.47 - 16.83: 2 Bond angle restraints: 47869 Sorted by residual: angle pdb=" CA PRO D 384 " pdb=" N PRO D 384 " pdb=" CD PRO D 384 " ideal model delta sigma weight residual 112.00 95.17 16.83 1.40e+00 5.10e-01 1.45e+02 angle pdb=" CA PRO B 209 " pdb=" N PRO B 209 " pdb=" CD PRO B 209 " ideal model delta sigma weight residual 112.00 97.05 14.95 1.40e+00 5.10e-01 1.14e+02 angle pdb=" CA PRO B 892 " pdb=" N PRO B 892 " pdb=" CD PRO B 892 " ideal model delta sigma weight residual 112.00 99.83 12.17 1.40e+00 5.10e-01 7.56e+01 angle pdb=" N PRO D 384 " pdb=" CD PRO D 384 " pdb=" CG PRO D 384 " ideal model delta sigma weight residual 103.20 91.95 11.25 1.50e+00 4.44e-01 5.62e+01 angle pdb=" CA PRO D 225 " pdb=" N PRO D 225 " pdb=" CD PRO D 225 " ideal model delta sigma weight residual 112.00 103.01 8.99 1.40e+00 5.10e-01 4.13e+01 ... (remaining 47864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 19280 17.88 - 35.76: 1880 35.76 - 53.64: 502 53.64 - 71.52: 86 71.52 - 89.40: 29 Dihedral angle restraints: 21777 sinusoidal: 9349 harmonic: 12428 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -0.40 -85.60 1 1.00e+01 1.00e-02 8.86e+01 dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 94 " pdb=" CB CYS G 94 " ideal model delta sinusoidal sigma weight residual 93.00 12.69 80.31 1 1.00e+01 1.00e-02 7.98e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -14.54 -71.46 1 1.00e+01 1.00e-02 6.55e+01 ... (remaining 21774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.170: 5523 0.170 - 0.340: 18 0.340 - 0.509: 3 0.509 - 0.679: 0 0.679 - 0.849: 1 Chirality restraints: 5545 Sorted by residual: chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.55 -0.85 2.00e-01 2.50e+01 1.80e+01 chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" C1 NAG A1311 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1311 " pdb=" O5 NAG A1311 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.32e+00 ... (remaining 5542 not shown) Planarity restraints: 6176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 383 " 0.120 5.00e-02 4.00e+02 1.64e-01 4.30e+01 pdb=" N PRO D 384 " -0.283 5.00e-02 4.00e+02 pdb=" CA PRO D 384 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO D 384 " 0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " 0.040 2.00e-02 2.50e+03 5.73e-02 4.11e+01 pdb=" CG ASN A 234 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " -0.100 2.00e-02 2.50e+03 pdb=" C1 NAG A1314 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 891 " -0.098 5.00e-02 4.00e+02 1.38e-01 3.04e+01 pdb=" N PRO B 892 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO B 892 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO B 892 " -0.070 5.00e-02 4.00e+02 ... (remaining 6173 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.80: 2 1.80 - 2.57: 357 2.57 - 3.35: 41977 3.35 - 4.12: 81348 4.12 - 4.90: 144666 Nonbonded interactions: 268350 Sorted by model distance: nonbonded pdb=" CD1 TRP D 152 " pdb=" OE1 GLU D 154 " model vdw 1.019 3.260 nonbonded pdb=" NE1 TRP D 152 " pdb=" OE1 GLU D 154 " model vdw 1.775 3.120 nonbonded pdb=" OE1 GLN B 607 " pdb=" OG SER B 691 " model vdw 1.912 3.040 nonbonded pdb=" CG2 ILE B 896 " pdb=" NE2 GLN B 901 " model vdw 2.033 3.540 nonbonded pdb=" CD1 TRP D 152 " pdb=" CD GLU D 154 " model vdw 2.109 3.490 ... (remaining 268345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 178 or resid 184 through 622 or resid 632 throu \ gh 1307 or (resid 1308 and (name C1 or name C2 or name C3 or name C4 or name C5 \ or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 or name O6 or \ name O7 )) or resid 1309 through 1314)) selection = (chain 'B' and (resid 14 through 178 or resid 184 through 622 or resid 632 throu \ gh 676 or resid 690 through 827 or resid 855 through 1314)) selection = (chain 'D' and (resid 14 through 622 or resid 632 through 676 or resid 690 throu \ gh 827 or resid 855 through 1307 or (resid 1308 and (name C1 or name C2 or name \ C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 \ or name O5 or name O6 or name O7 )) or resid 1309 through 1314)) } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'L' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'O' } 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: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 33.950 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.193 35326 Z= 0.188 Angle : 0.734 25.884 48176 Z= 0.364 Chirality : 0.049 0.849 5545 Planarity : 0.005 0.164 6119 Dihedral : 14.949 89.395 13679 Min Nonbonded Distance : 1.019 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.02 % Favored : 94.62 % Rotamer: Outliers : 0.51 % Allowed : 20.96 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.13), residues: 4259 helix: 1.35 (0.21), residues: 676 sheet: -0.16 (0.16), residues: 1037 loop : -1.22 (0.12), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 905 TYR 0.042 0.001 TYR D 505 PHE 0.030 0.001 PHE A 392 TRP 0.043 0.001 TRP D 353 HIS 0.012 0.001 HIS K 95 Details of bonding type rmsd covalent geometry : bond 0.00405 (35207) covalent geometry : angle 0.68658 (47869) SS BOND : bond 0.00516 ( 50) SS BOND : angle 1.07485 ( 100) hydrogen bonds : bond 0.16748 ( 1187) hydrogen bonds : angle 7.54299 ( 3273) link_BETA1-4 : bond 0.00459 ( 12) link_BETA1-4 : angle 1.47220 ( 36) link_NAG-ASN : bond 0.01752 ( 57) link_NAG-ASN : angle 4.33737 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 328 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 987 PRO cc_start: 0.8625 (Cg_exo) cc_final: 0.8413 (Cg_endo) REVERT: B 189 LEU cc_start: 0.8521 (tp) cc_final: 0.8296 (pt) REVERT: D 275 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7902 (m-80) REVERT: D 1106 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8257 (pt0) REVERT: G 37 ARG cc_start: 0.5248 (ptp-170) cc_final: 0.4961 (ttm170) REVERT: F 33 MET cc_start: 0.5004 (mmm) cc_final: 0.4568 (mmm) outliers start: 19 outliers final: 10 residues processed: 342 average time/residue: 0.2142 time to fit residues: 122.4564 Evaluate side-chains 305 residues out of total 3711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 293 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 1106 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 493 GLN A1142 GLN B 81 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 655 HIS D1106 GLN I 3 GLN ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 HIS ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.178416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.117744 restraints weight = 65869.452| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.93 r_work: 0.3349 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 35326 Z= 0.226 Angle : 0.713 20.671 48176 Z= 0.357 Chirality : 0.049 0.546 5545 Planarity : 0.005 0.066 6119 Dihedral : 7.239 57.291 6116 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.68 % Favored : 93.97 % Rotamer: Outliers : 4.02 % Allowed : 19.02 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.13), residues: 4259 helix: 1.34 (0.20), residues: 691 sheet: -0.23 (0.15), residues: 1085 loop : -1.39 (0.12), residues: 2483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 66 TYR 0.025 0.002 TYR D 265 PHE 0.022 0.002 PHE B 133 TRP 0.018 0.002 TRP D 353 HIS 0.011 0.002 HIS D 207 Details of bonding type rmsd covalent geometry : bond 0.00540 (35207) covalent geometry : angle 0.67157 (47869) SS BOND : bond 0.00493 ( 50) SS BOND : angle 1.29455 ( 100) hydrogen bonds : bond 0.05772 ( 1187) hydrogen bonds : angle 6.12643 ( 3273) link_BETA1-4 : bond 0.00346 ( 12) link_BETA1-4 : angle 1.10138 ( 36) link_NAG-ASN : bond 0.00657 ( 57) link_NAG-ASN : angle 3.97581 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 309 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7550 (tp30) cc_final: 0.7282 (mm-30) REVERT: B 153 MET cc_start: 0.6838 (mmp) cc_final: 0.6620 (mmp) REVERT: B 979 ASP cc_start: 0.8560 (t0) cc_final: 0.8301 (t0) REVERT: D 275 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8254 (m-80) REVERT: D 398 ASP cc_start: 0.7508 (m-30) cc_final: 0.7113 (m-30) REVERT: D 775 ASP cc_start: 0.9006 (OUTLIER) cc_final: 0.8655 (m-30) REVERT: E 98 ARG cc_start: 0.8136 (ttp-110) cc_final: 0.7913 (ttm-80) REVERT: G 60 ASP cc_start: 0.7030 (OUTLIER) cc_final: 0.6453 (p0) REVERT: G 66 PHE cc_start: 0.6322 (m-80) cc_final: 0.6048 (m-10) REVERT: F 11 LEU cc_start: 0.4361 (OUTLIER) cc_final: 0.3801 (mm) REVERT: F 36 TYR cc_start: 0.6821 (t80) cc_final: 0.6592 (t80) REVERT: F 106 ASP cc_start: 0.5079 (p0) cc_final: 0.4753 (p0) REVERT: K 78 TYR cc_start: 0.7186 (OUTLIER) cc_final: 0.6920 (t80) REVERT: N 103 ARG cc_start: 0.3014 (OUTLIER) cc_final: 0.2427 (ttt180) outliers start: 149 outliers final: 79 residues processed: 431 average time/residue: 0.2075 time to fit residues: 149.7861 Evaluate side-chains 373 residues out of total 3711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 288 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 775 ASP Chi-restraints excluded: chain D residue 786 LYS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 57 HIS Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 78 TYR Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 108 TRP Chi-restraints excluded: chain N residue 103 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 251 optimal weight: 0.5980 chunk 376 optimal weight: 40.0000 chunk 227 optimal weight: 9.9990 chunk 294 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 286 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 chunk 160 optimal weight: 0.6980 chunk 410 optimal weight: 20.0000 chunk 384 optimal weight: 30.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 613 GLN B 52 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 804 GLN B 901 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 ASN D 607 GLN G 71 HIS ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 107 GLN ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.186107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.127746 restraints weight = 64413.611| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 4.39 r_work: 0.3377 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 35326 Z= 0.127 Angle : 0.636 19.889 48176 Z= 0.314 Chirality : 0.047 0.537 5545 Planarity : 0.004 0.060 6119 Dihedral : 6.398 54.928 6104 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.79 % Favored : 94.86 % Rotamer: Outliers : 3.91 % Allowed : 19.24 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.13), residues: 4259 helix: 1.63 (0.20), residues: 691 sheet: -0.16 (0.16), residues: 1047 loop : -1.33 (0.12), residues: 2521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 53 TYR 0.020 0.001 TYR F 36 PHE 0.016 0.001 PHE A 823 TRP 0.017 0.001 TRP D 104 HIS 0.008 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00287 (35207) covalent geometry : angle 0.59268 (47869) SS BOND : bond 0.00361 ( 50) SS BOND : angle 1.26331 ( 100) hydrogen bonds : bond 0.04813 ( 1187) hydrogen bonds : angle 5.68045 ( 3273) link_BETA1-4 : bond 0.00453 ( 12) link_BETA1-4 : angle 1.13048 ( 36) link_NAG-ASN : bond 0.00657 ( 57) link_NAG-ASN : angle 3.80491 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 323 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.8995 (tpp) cc_final: 0.8648 (ttm) REVERT: B 134 GLN cc_start: 0.7038 (tp40) cc_final: 0.6730 (tp40) REVERT: B 979 ASP cc_start: 0.8631 (t0) cc_final: 0.8309 (t0) REVERT: D 398 ASP cc_start: 0.7603 (m-30) cc_final: 0.7048 (m-30) REVERT: E 43 LYS cc_start: 0.5784 (OUTLIER) cc_final: 0.5396 (mptt) REVERT: E 98 ARG cc_start: 0.8161 (ttp-110) cc_final: 0.7960 (ttm-80) REVERT: G 60 ASP cc_start: 0.7029 (OUTLIER) cc_final: 0.6454 (p0) REVERT: G 92 TYR cc_start: 0.5268 (m-80) cc_final: 0.5021 (m-80) REVERT: F 36 TYR cc_start: 0.6676 (t80) cc_final: 0.6392 (t80) REVERT: F 106 ASP cc_start: 0.4888 (p0) cc_final: 0.4439 (p0) REVERT: K 45 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6975 (tp30) REVERT: K 78 TYR cc_start: 0.7135 (OUTLIER) cc_final: 0.6924 (t80) REVERT: N 103 ARG cc_start: 0.2998 (OUTLIER) cc_final: 0.2649 (ttt180) outliers start: 145 outliers final: 78 residues processed: 437 average time/residue: 0.1976 time to fit residues: 145.6350 Evaluate side-chains 371 residues out of total 3711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 288 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 786 LYS Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 78 TYR Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 96 LEU Chi-restraints excluded: chain K residue 108 TRP Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain N residue 103 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 198 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 263 optimal weight: 10.0000 chunk 174 optimal weight: 0.9980 chunk 213 optimal weight: 3.9990 chunk 337 optimal weight: 0.0270 chunk 42 optimal weight: 1.9990 chunk 250 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 255 optimal weight: 5.9990 overall best weight: 2.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN B 52 GLN B 949 GLN D 146 HIS ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 GLN D1142 GLN F 13 GLN ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.186648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.139102 restraints weight = 63166.041| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 5.07 r_work: 0.3343 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 35326 Z= 0.168 Angle : 0.662 19.992 48176 Z= 0.327 Chirality : 0.048 0.542 5545 Planarity : 0.004 0.059 6119 Dihedral : 5.965 53.933 6095 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.64 % Favored : 94.04 % Rotamer: Outliers : 5.23 % Allowed : 19.05 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.13), residues: 4259 helix: 1.54 (0.20), residues: 698 sheet: -0.15 (0.16), residues: 1068 loop : -1.37 (0.12), residues: 2493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 19 TYR 0.022 0.001 TYR D 265 PHE 0.026 0.002 PHE B 133 TRP 0.024 0.001 TRP D 436 HIS 0.011 0.001 HIS D 207 Details of bonding type rmsd covalent geometry : bond 0.00394 (35207) covalent geometry : angle 0.62084 (47869) SS BOND : bond 0.00605 ( 50) SS BOND : angle 1.37671 ( 100) hydrogen bonds : bond 0.05021 ( 1187) hydrogen bonds : angle 5.57506 ( 3273) link_BETA1-4 : bond 0.00391 ( 12) link_BETA1-4 : angle 1.09574 ( 36) link_NAG-ASN : bond 0.00653 ( 57) link_NAG-ASN : angle 3.76448 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 304 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7125 (pt) REVERT: A 558 LYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6688 (pttt) REVERT: A 1029 MET cc_start: 0.9002 (tpp) cc_final: 0.8651 (ttm) REVERT: B 737 ASP cc_start: 0.8016 (t70) cc_final: 0.7751 (t70) REVERT: B 979 ASP cc_start: 0.8746 (t0) cc_final: 0.8388 (t0) REVERT: D 160 TYR cc_start: 0.7915 (p90) cc_final: 0.7377 (p90) REVERT: D 324 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6631 (tt0) REVERT: D 398 ASP cc_start: 0.7570 (m-30) cc_final: 0.7136 (m-30) REVERT: E 43 LYS cc_start: 0.5729 (OUTLIER) cc_final: 0.5390 (mptt) REVERT: E 66 ARG cc_start: 0.6979 (mtm-85) cc_final: 0.6545 (mtm-85) REVERT: E 81 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7019 (mp-120) REVERT: G 81 MET cc_start: 0.5462 (OUTLIER) cc_final: 0.5182 (ptp) REVERT: F 11 LEU cc_start: 0.4265 (OUTLIER) cc_final: 0.3717 (mm) REVERT: F 36 TYR cc_start: 0.6705 (t80) cc_final: 0.6319 (t80) REVERT: F 106 ASP cc_start: 0.5058 (p0) cc_final: 0.4726 (p0) REVERT: K 45 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7082 (tp30) REVERT: K 78 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.6987 (t80) REVERT: N 103 ARG cc_start: 0.2914 (OUTLIER) cc_final: 0.2713 (ttt180) outliers start: 194 outliers final: 119 residues processed: 458 average time/residue: 0.2022 time to fit residues: 157.0948 Evaluate side-chains 418 residues out of total 3711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 289 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 786 LYS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 78 TYR Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 96 LEU Chi-restraints excluded: chain K residue 108 TRP Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain N residue 103 ARG Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain M residue 50 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 375 optimal weight: 5.9990 chunk 318 optimal weight: 0.0870 chunk 299 optimal weight: 0.9990 chunk 300 optimal weight: 0.8980 chunk 224 optimal weight: 9.9990 chunk 220 optimal weight: 7.9990 chunk 287 optimal weight: 4.9990 chunk 239 optimal weight: 20.0000 chunk 362 optimal weight: 4.9990 chunk 222 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN B 52 GLN B 81 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 ASN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.183235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.123454 restraints weight = 64421.041| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.76 r_work: 0.3363 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 35326 Z= 0.164 Angle : 0.665 19.758 48176 Z= 0.327 Chirality : 0.048 0.521 5545 Planarity : 0.004 0.062 6119 Dihedral : 5.796 54.196 6095 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.49 % Favored : 94.18 % Rotamer: Outliers : 5.07 % Allowed : 19.48 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.13), residues: 4259 helix: 1.53 (0.20), residues: 697 sheet: -0.19 (0.16), residues: 1059 loop : -1.36 (0.12), residues: 2503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 53 TYR 0.022 0.001 TYR D 265 PHE 0.020 0.002 PHE E 29 TRP 0.034 0.001 TRP D 436 HIS 0.008 0.001 HIS D 207 Details of bonding type rmsd covalent geometry : bond 0.00385 (35207) covalent geometry : angle 0.62438 (47869) SS BOND : bond 0.00444 ( 50) SS BOND : angle 1.42915 ( 100) hydrogen bonds : bond 0.04992 ( 1187) hydrogen bonds : angle 5.47192 ( 3273) link_BETA1-4 : bond 0.00417 ( 12) link_BETA1-4 : angle 1.09896 ( 36) link_NAG-ASN : bond 0.00655 ( 57) link_NAG-ASN : angle 3.72794 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 309 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.7485 (pttt) cc_final: 0.7280 (pttt) REVERT: A 176 LEU cc_start: 0.8431 (pt) cc_final: 0.7883 (mt) REVERT: A 558 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6676 (pttt) REVERT: A 751 ASN cc_start: 0.8151 (m-40) cc_final: 0.7950 (m-40) REVERT: A 1029 MET cc_start: 0.9032 (tpp) cc_final: 0.8718 (ttm) REVERT: B 153 MET cc_start: 0.6959 (mmp) cc_final: 0.6707 (mmp) REVERT: B 737 ASP cc_start: 0.8129 (t70) cc_final: 0.7685 (t70) REVERT: B 900 MET cc_start: 0.8850 (ttm) cc_final: 0.8573 (mtp) REVERT: B 979 ASP cc_start: 0.8749 (t0) cc_final: 0.8418 (t0) REVERT: D 160 TYR cc_start: 0.7856 (p90) cc_final: 0.7370 (p90) REVERT: D 324 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6509 (tt0) REVERT: D 398 ASP cc_start: 0.7589 (m-30) cc_final: 0.7113 (m-30) REVERT: D 409 GLN cc_start: 0.6194 (mt0) cc_final: 0.5937 (tm-30) REVERT: D 651 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8690 (pt) REVERT: E 43 LYS cc_start: 0.5739 (OUTLIER) cc_final: 0.5419 (mppt) REVERT: E 66 ARG cc_start: 0.6960 (mtm-85) cc_final: 0.6539 (mtm-85) REVERT: E 81 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7031 (mp-120) REVERT: G 81 MET cc_start: 0.5561 (mpp) cc_final: 0.5085 (ptp) REVERT: F 11 LEU cc_start: 0.4142 (OUTLIER) cc_final: 0.3639 (mm) REVERT: F 36 TYR cc_start: 0.6843 (t80) cc_final: 0.6478 (t80) REVERT: F 106 ASP cc_start: 0.5021 (p0) cc_final: 0.4735 (p0) REVERT: K 45 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7203 (tp30) REVERT: K 46 LEU cc_start: 0.7920 (tp) cc_final: 0.7585 (pp) REVERT: K 78 TYR cc_start: 0.7213 (OUTLIER) cc_final: 0.6988 (t80) REVERT: N 103 ARG cc_start: 0.2977 (OUTLIER) cc_final: 0.2753 (ttt180) outliers start: 188 outliers final: 132 residues processed: 458 average time/residue: 0.2019 time to fit residues: 156.6494 Evaluate side-chains 425 residues out of total 3711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 284 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 786 LYS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 78 TYR Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 96 LEU Chi-restraints excluded: chain K residue 108 TRP Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain N residue 103 ARG Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 51 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 35 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 332 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 151 optimal weight: 40.0000 chunk 44 optimal weight: 0.5980 chunk 381 optimal weight: 9.9990 chunk 375 optimal weight: 6.9990 chunk 386 optimal weight: 8.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 394 ASN A1048 HIS B 49 HIS B 52 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 GLN E 5 GLN E 39 GLN G 13 GLN ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.177276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.117442 restraints weight = 65915.315| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.95 r_work: 0.3312 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 35326 Z= 0.269 Angle : 0.763 20.253 48176 Z= 0.378 Chirality : 0.051 0.563 5545 Planarity : 0.005 0.070 6119 Dihedral : 6.247 52.119 6095 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.95 % Favored : 92.74 % Rotamer: Outliers : 6.22 % Allowed : 19.37 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.13), residues: 4259 helix: 1.15 (0.20), residues: 698 sheet: -0.33 (0.16), residues: 1090 loop : -1.53 (0.12), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 355 TYR 0.034 0.002 TYR D 265 PHE 0.031 0.002 PHE E 29 TRP 0.024 0.002 TRP D 436 HIS 0.012 0.002 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00644 (35207) covalent geometry : angle 0.72446 (47869) SS BOND : bond 0.00544 ( 50) SS BOND : angle 1.56404 ( 100) hydrogen bonds : bond 0.06053 ( 1187) hydrogen bonds : angle 5.73935 ( 3273) link_BETA1-4 : bond 0.00423 ( 12) link_BETA1-4 : angle 1.21914 ( 36) link_NAG-ASN : bond 0.00688 ( 57) link_NAG-ASN : angle 3.92089 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 231 poor density : 299 time to evaluate : 1.307 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 97 LYS cc_start: 0.7552 (pttt) cc_final: 0.7329 (pttt) REVERT: A 249 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6973 (pt) REVERT: A 394 ASN cc_start: 0.4275 (OUTLIER) cc_final: 0.2650 (m-40) REVERT: A 558 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6994 (pttt) REVERT: A 969 ASN cc_start: 0.8551 (t0) cc_final: 0.7900 (t0) REVERT: A 1029 MET cc_start: 0.9115 (tpp) cc_final: 0.8775 (ttm) REVERT: A 1092 GLU cc_start: 0.8532 (pm20) cc_final: 0.8147 (pm20) REVERT: B 153 MET cc_start: 0.7235 (mmp) cc_final: 0.6986 (mmp) REVERT: B 277 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8917 (mt) REVERT: B 737 ASP cc_start: 0.8068 (t70) cc_final: 0.7779 (t70) REVERT: B 979 ASP cc_start: 0.8862 (t0) cc_final: 0.8556 (t0) REVERT: B 988 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8177 (pm20) REVERT: D 160 TYR cc_start: 0.7571 (p90) cc_final: 0.7264 (p90) REVERT: D 275 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8190 (m-80) REVERT: D 324 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6683 (tt0) REVERT: D 398 ASP cc_start: 0.7756 (m-30) cc_final: 0.7361 (m-30) REVERT: D 409 GLN cc_start: 0.6373 (mt0) cc_final: 0.6107 (tm-30) REVERT: D 569 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8345 (mm) REVERT: D 651 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8851 (pt) REVERT: D 869 MET cc_start: 0.8815 (mmt) cc_final: 0.8307 (mtt) REVERT: E 1 GLN cc_start: 0.6282 (mt0) cc_final: 0.5100 (tp-100) REVERT: E 43 LYS cc_start: 0.5849 (OUTLIER) cc_final: 0.5441 (mppt) REVERT: E 81 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7116 (mp-120) REVERT: H 58 ASN cc_start: 0.7856 (m-40) cc_final: 0.7347 (t0) REVERT: H 98 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7854 (ptp-170) REVERT: I 21 SER cc_start: 0.8333 (t) cc_final: 0.8087 (p) REVERT: G 81 MET cc_start: 0.5696 (OUTLIER) cc_final: 0.5323 (ptp) REVERT: F 11 LEU cc_start: 0.4020 (OUTLIER) cc_final: 0.3558 (mm) REVERT: F 36 TYR cc_start: 0.7012 (t80) cc_final: 0.6562 (t80) REVERT: F 106 ASP cc_start: 0.5400 (p0) cc_final: 0.5168 (p0) REVERT: F 107 TYR cc_start: 0.5808 (m-80) cc_final: 0.5555 (m-80) REVERT: K 46 LEU cc_start: 0.8075 (tp) cc_final: 0.7654 (pp) REVERT: K 78 TYR cc_start: 0.7272 (OUTLIER) cc_final: 0.6997 (t80) outliers start: 231 outliers final: 170 residues processed: 491 average time/residue: 0.2001 time to fit residues: 166.8812 Evaluate side-chains 461 residues out of total 3711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 276 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 265 TYR Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 786 LYS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 979 ASP Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1006 THR Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 78 TYR Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 108 TRP Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 82 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 17 optimal weight: 0.9980 chunk 39 optimal weight: 0.0060 chunk 313 optimal weight: 0.8980 chunk 201 optimal weight: 0.6980 chunk 222 optimal weight: 1.9990 chunk 196 optimal weight: 0.8980 chunk 276 optimal weight: 0.0870 chunk 32 optimal weight: 0.9990 chunk 346 optimal weight: 6.9990 chunk 262 optimal weight: 0.0670 chunk 379 optimal weight: 10.0000 overall best weight: 0.3512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 394 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN B 52 GLN B 901 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 58 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.182139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.123677 restraints weight = 66261.728| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 3.75 r_work: 0.3467 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 35326 Z= 0.117 Angle : 0.651 18.570 48176 Z= 0.318 Chirality : 0.047 0.529 5545 Planarity : 0.004 0.082 6119 Dihedral : 5.559 55.700 6095 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.74 % Favored : 94.93 % Rotamer: Outliers : 3.75 % Allowed : 22.02 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.13), residues: 4259 helix: 1.65 (0.20), residues: 698 sheet: -0.16 (0.16), residues: 1103 loop : -1.37 (0.12), residues: 2458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 66 TYR 0.016 0.001 TYR D1067 PHE 0.024 0.001 PHE B 133 TRP 0.022 0.001 TRP D 353 HIS 0.007 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00250 (35207) covalent geometry : angle 0.61187 (47869) SS BOND : bond 0.00383 ( 50) SS BOND : angle 1.22283 ( 100) hydrogen bonds : bond 0.04485 ( 1187) hydrogen bonds : angle 5.28326 ( 3273) link_BETA1-4 : bond 0.00428 ( 12) link_BETA1-4 : angle 1.14924 ( 36) link_NAG-ASN : bond 0.00680 ( 57) link_NAG-ASN : angle 3.66193 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 312 time to evaluate : 1.344 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 97 LYS cc_start: 0.7494 (pttt) cc_final: 0.7278 (pttt) REVERT: A 249 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7092 (pt) REVERT: A 552 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7969 (mt) REVERT: A 751 ASN cc_start: 0.8304 (m-40) cc_final: 0.8070 (m-40) REVERT: A 1092 GLU cc_start: 0.8442 (pm20) cc_final: 0.8032 (pm20) REVERT: B 153 MET cc_start: 0.7148 (mmp) cc_final: 0.6672 (mmp) REVERT: B 155 SER cc_start: 0.7066 (OUTLIER) cc_final: 0.6800 (t) REVERT: B 737 ASP cc_start: 0.7891 (t70) cc_final: 0.7524 (t70) REVERT: B 979 ASP cc_start: 0.8764 (t0) cc_final: 0.8496 (t0) REVERT: B 1138 TYR cc_start: 0.7882 (t80) cc_final: 0.7616 (t80) REVERT: D 200 TYR cc_start: 0.7859 (m-80) cc_final: 0.7646 (m-80) REVERT: D 323 THR cc_start: 0.7651 (p) cc_final: 0.7294 (t) REVERT: D 398 ASP cc_start: 0.7698 (m-30) cc_final: 0.7273 (m-30) REVERT: D 409 GLN cc_start: 0.6456 (mt0) cc_final: 0.6065 (tm-30) REVERT: D 651 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8660 (pt) REVERT: E 1 GLN cc_start: 0.6296 (mt0) cc_final: 0.5062 (tp-100) REVERT: E 43 LYS cc_start: 0.5831 (OUTLIER) cc_final: 0.5420 (mppt) REVERT: E 66 ARG cc_start: 0.6554 (mtm-85) cc_final: 0.6258 (mtm-85) REVERT: E 81 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.6972 (mp-120) REVERT: E 108 THR cc_start: 0.7493 (t) cc_final: 0.7202 (m) REVERT: H 58 ASN cc_start: 0.7813 (m-40) cc_final: 0.7319 (t0) REVERT: G 81 MET cc_start: 0.5611 (mpp) cc_final: 0.5132 (ptp) REVERT: F 36 TYR cc_start: 0.7068 (t80) cc_final: 0.6521 (t80) REVERT: F 107 TYR cc_start: 0.5700 (m-80) cc_final: 0.5440 (m-80) REVERT: K 33 MET cc_start: 0.6874 (mmm) cc_final: 0.6656 (mmm) REVERT: K 78 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.6996 (t80) outliers start: 139 outliers final: 99 residues processed: 420 average time/residue: 0.2051 time to fit residues: 145.9901 Evaluate side-chains 396 residues out of total 3711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 290 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 78 TYR Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 108 TRP Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 51 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 95 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 350 optimal weight: 20.0000 chunk 373 optimal weight: 5.9990 chunk 342 optimal weight: 10.0000 chunk 82 optimal weight: 0.0770 chunk 69 optimal weight: 6.9990 chunk 204 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 354 optimal weight: 8.9990 chunk 402 optimal weight: 7.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 644 GLN A 690 GLN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.177041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.115086 restraints weight = 65973.251| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.93 r_work: 0.3345 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 35326 Z= 0.275 Angle : 0.769 20.182 48176 Z= 0.380 Chirality : 0.051 0.550 5545 Planarity : 0.005 0.083 6119 Dihedral : 6.034 52.009 6095 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.79 % Favored : 92.93 % Rotamer: Outliers : 4.45 % Allowed : 21.64 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.13), residues: 4259 helix: 1.22 (0.20), residues: 697 sheet: -0.36 (0.16), residues: 1056 loop : -1.49 (0.12), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 66 TYR 0.034 0.002 TYR D 265 PHE 0.034 0.002 PHE E 29 TRP 0.037 0.002 TRP D 436 HIS 0.013 0.002 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00658 (35207) covalent geometry : angle 0.73284 (47869) SS BOND : bond 0.00527 ( 50) SS BOND : angle 1.57713 ( 100) hydrogen bonds : bond 0.05933 ( 1187) hydrogen bonds : angle 5.61916 ( 3273) link_BETA1-4 : bond 0.00391 ( 12) link_BETA1-4 : angle 1.18739 ( 36) link_NAG-ASN : bond 0.00684 ( 57) link_NAG-ASN : angle 3.83572 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 289 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7039 (pt) REVERT: A 394 ASN cc_start: 0.3901 (OUTLIER) cc_final: 0.3687 (t0) REVERT: A 969 ASN cc_start: 0.8598 (t0) cc_final: 0.8294 (t0) REVERT: A 1092 GLU cc_start: 0.8577 (pm20) cc_final: 0.8170 (pm20) REVERT: B 153 MET cc_start: 0.7320 (mmp) cc_final: 0.6865 (mmp) REVERT: B 155 SER cc_start: 0.7151 (OUTLIER) cc_final: 0.6863 (t) REVERT: B 277 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8919 (mt) REVERT: B 737 ASP cc_start: 0.8096 (t70) cc_final: 0.7687 (t70) REVERT: B 979 ASP cc_start: 0.8857 (t0) cc_final: 0.8564 (t0) REVERT: D 324 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7092 (pt0) REVERT: D 342 PHE cc_start: 0.6625 (t80) cc_final: 0.6340 (t80) REVERT: D 374 PHE cc_start: 0.5387 (m-10) cc_final: 0.5174 (m-10) REVERT: D 398 ASP cc_start: 0.7757 (m-30) cc_final: 0.7323 (m-30) REVERT: D 409 GLN cc_start: 0.6686 (mt0) cc_final: 0.6340 (tm-30) REVERT: D 651 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8806 (pt) REVERT: D 869 MET cc_start: 0.8746 (mmt) cc_final: 0.8256 (mtt) REVERT: E 1 GLN cc_start: 0.6344 (mt0) cc_final: 0.5105 (tp-100) REVERT: E 66 ARG cc_start: 0.6835 (mtm-85) cc_final: 0.6484 (mtm-85) REVERT: E 81 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7022 (mp-120) REVERT: H 58 ASN cc_start: 0.7963 (m-40) cc_final: 0.7367 (t0) REVERT: G 81 MET cc_start: 0.5727 (OUTLIER) cc_final: 0.5331 (ptp) REVERT: K 33 MET cc_start: 0.6930 (mmm) cc_final: 0.6704 (mmm) REVERT: K 78 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.6990 (t80) outliers start: 165 outliers final: 137 residues processed: 424 average time/residue: 0.1979 time to fit residues: 143.5445 Evaluate side-chains 418 residues out of total 3711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 272 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 786 LYS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 979 ASP Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1006 THR Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 78 TYR Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 108 TRP Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 51 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 411 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 324 optimal weight: 0.0370 chunk 192 optimal weight: 0.6980 chunk 170 optimal weight: 0.9980 chunk 272 optimal weight: 5.9990 chunk 378 optimal weight: 10.0000 chunk 121 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 354 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN B 52 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.184861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.125361 restraints weight = 64592.283| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.87 r_work: 0.3419 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35326 Z= 0.118 Angle : 0.663 18.540 48176 Z= 0.323 Chirality : 0.047 0.487 5545 Planarity : 0.004 0.081 6119 Dihedral : 5.577 55.209 6095 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.56 % Favored : 95.16 % Rotamer: Outliers : 3.42 % Allowed : 22.64 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.13), residues: 4259 helix: 1.62 (0.20), residues: 697 sheet: -0.22 (0.16), residues: 1052 loop : -1.36 (0.12), residues: 2510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 646 TYR 0.021 0.001 TYR K 105 PHE 0.026 0.001 PHE B 133 TRP 0.033 0.001 TRP D 436 HIS 0.008 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00257 (35207) covalent geometry : angle 0.62441 (47869) SS BOND : bond 0.00374 ( 50) SS BOND : angle 1.18862 ( 100) hydrogen bonds : bond 0.04603 ( 1187) hydrogen bonds : angle 5.25515 ( 3273) link_BETA1-4 : bond 0.00472 ( 12) link_BETA1-4 : angle 1.13557 ( 36) link_NAG-ASN : bond 0.00688 ( 57) link_NAG-ASN : angle 3.67702 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 299 time to evaluate : 1.276 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 249 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7093 (pt) REVERT: A 552 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7909 (mt) REVERT: A 969 ASN cc_start: 0.8507 (t0) cc_final: 0.7882 (t0) REVERT: A 1092 GLU cc_start: 0.8452 (pm20) cc_final: 0.8042 (pm20) REVERT: B 153 MET cc_start: 0.7253 (mmp) cc_final: 0.6801 (mmp) REVERT: B 155 SER cc_start: 0.7098 (OUTLIER) cc_final: 0.6797 (t) REVERT: B 737 ASP cc_start: 0.7916 (t70) cc_final: 0.7543 (t70) REVERT: B 979 ASP cc_start: 0.8773 (t0) cc_final: 0.8482 (t0) REVERT: D 323 THR cc_start: 0.7740 (p) cc_final: 0.7376 (t) REVERT: D 342 PHE cc_start: 0.6618 (t80) cc_final: 0.6193 (t80) REVERT: D 398 ASP cc_start: 0.7723 (m-30) cc_final: 0.7255 (m-30) REVERT: D 409 GLN cc_start: 0.6585 (mt0) cc_final: 0.6218 (tm-30) REVERT: D 651 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8664 (pt) REVERT: D 869 MET cc_start: 0.8663 (mmt) cc_final: 0.8340 (mtt) REVERT: E 1 GLN cc_start: 0.6275 (mt0) cc_final: 0.4985 (tp-100) REVERT: E 66 ARG cc_start: 0.6685 (mtm-85) cc_final: 0.6403 (mtm-85) REVERT: E 81 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.6973 (mp-120) REVERT: E 108 THR cc_start: 0.7573 (t) cc_final: 0.7285 (m) REVERT: H 58 ASN cc_start: 0.7932 (m-40) cc_final: 0.7385 (t0) REVERT: I 48 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8103 (t) REVERT: G 81 MET cc_start: 0.5596 (mpp) cc_final: 0.5205 (ptp) REVERT: F 33 MET cc_start: 0.6187 (mmm) cc_final: 0.5827 (mmm) REVERT: F 36 TYR cc_start: 0.7087 (t80) cc_final: 0.6531 (t80) REVERT: K 33 MET cc_start: 0.6790 (mmm) cc_final: 0.6574 (mmm) outliers start: 127 outliers final: 98 residues processed: 401 average time/residue: 0.2011 time to fit residues: 137.5203 Evaluate side-chains 391 residues out of total 3711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 287 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 96 LEU Chi-restraints excluded: chain K residue 108 TRP Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 197 optimal weight: 6.9990 chunk 366 optimal weight: 1.9990 chunk 387 optimal weight: 20.0000 chunk 301 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 352 optimal weight: 8.9990 chunk 416 optimal weight: 20.0000 chunk 93 optimal weight: 0.8980 chunk 271 optimal weight: 7.9990 chunk 336 optimal weight: 0.6980 chunk 191 optimal weight: 0.0470 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 690 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN ** D 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.182239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.119630 restraints weight = 66549.999| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 4.03 r_work: 0.3428 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35326 Z= 0.130 Angle : 0.659 19.009 48176 Z= 0.319 Chirality : 0.047 0.488 5545 Planarity : 0.004 0.081 6119 Dihedral : 5.416 54.478 6095 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.35 % Favored : 94.36 % Rotamer: Outliers : 3.13 % Allowed : 23.01 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.13), residues: 4259 helix: 1.70 (0.21), residues: 696 sheet: -0.17 (0.16), residues: 1065 loop : -1.32 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 19 TYR 0.029 0.001 TYR K 78 PHE 0.021 0.001 PHE D 392 TRP 0.032 0.001 TRP D 436 HIS 0.008 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00297 (35207) covalent geometry : angle 0.62125 (47869) SS BOND : bond 0.00393 ( 50) SS BOND : angle 1.23632 ( 100) hydrogen bonds : bond 0.04534 ( 1187) hydrogen bonds : angle 5.18502 ( 3273) link_BETA1-4 : bond 0.00436 ( 12) link_BETA1-4 : angle 1.14917 ( 36) link_NAG-ASN : bond 0.00728 ( 57) link_NAG-ASN : angle 3.61959 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8518 Ramachandran restraints generated. 4259 Oldfield, 0 Emsley, 4259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 291 time to evaluate : 1.373 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 249 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.7013 (pt) REVERT: A 1092 GLU cc_start: 0.8418 (pm20) cc_final: 0.8001 (pm20) REVERT: B 153 MET cc_start: 0.7287 (mmp) cc_final: 0.6771 (mmp) REVERT: B 155 SER cc_start: 0.7040 (OUTLIER) cc_final: 0.6791 (t) REVERT: B 737 ASP cc_start: 0.7885 (t70) cc_final: 0.7533 (t70) REVERT: B 979 ASP cc_start: 0.8779 (t0) cc_final: 0.8513 (t0) REVERT: D 323 THR cc_start: 0.7854 (p) cc_final: 0.7487 (t) REVERT: D 324 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7039 (pt0) REVERT: D 398 ASP cc_start: 0.7752 (m-30) cc_final: 0.7301 (m-30) REVERT: D 409 GLN cc_start: 0.6541 (mt0) cc_final: 0.6192 (tm-30) REVERT: D 651 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8643 (pt) REVERT: D 869 MET cc_start: 0.8636 (mmt) cc_final: 0.8352 (mtt) REVERT: E 1 GLN cc_start: 0.6250 (mt0) cc_final: 0.4952 (tp-100) REVERT: E 66 ARG cc_start: 0.6750 (mtm-85) cc_final: 0.6518 (mtm-85) REVERT: H 58 ASN cc_start: 0.8024 (m-40) cc_final: 0.7486 (t0) REVERT: I 48 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8089 (t) REVERT: G 33 MET cc_start: 0.5250 (tpp) cc_final: 0.4925 (tpp) REVERT: G 81 MET cc_start: 0.5606 (mpp) cc_final: 0.5105 (ptp) REVERT: F 33 MET cc_start: 0.6185 (mmm) cc_final: 0.5821 (mmm) REVERT: F 36 TYR cc_start: 0.7104 (t80) cc_final: 0.6541 (t80) outliers start: 116 outliers final: 106 residues processed: 382 average time/residue: 0.2024 time to fit residues: 131.8464 Evaluate side-chains 391 residues out of total 3711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 280 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 443 SER Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 96 HIS Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 96 LEU Chi-restraints excluded: chain K residue 108 TRP Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 335 optimal weight: 9.9990 chunk 413 optimal weight: 10.0000 chunk 389 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 195 optimal weight: 0.8980 chunk 278 optimal weight: 0.9990 chunk 344 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 318 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN B 52 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.180687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.124451 restraints weight = 65542.593| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.99 r_work: 0.3404 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.325 35326 Z= 0.204 Angle : 0.821 59.198 48176 Z= 0.448 Chirality : 0.049 1.029 5545 Planarity : 0.005 0.188 6119 Dihedral : 5.415 54.543 6095 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.35 % Favored : 94.36 % Rotamer: Outliers : 3.21 % Allowed : 23.23 % Favored : 73.57 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.13), residues: 4259 helix: 1.70 (0.21), residues: 696 sheet: -0.17 (0.16), residues: 1065 loop : -1.32 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 19 TYR 0.026 0.001 TYR K 78 PHE 0.018 0.001 PHE E 29 TRP 0.028 0.001 TRP D 436 HIS 0.008 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00456 (35207) covalent geometry : angle 0.79235 (47869) SS BOND : bond 0.00387 ( 50) SS BOND : angle 1.22582 ( 100) hydrogen bonds : bond 0.04559 ( 1187) hydrogen bonds : angle 5.18476 ( 3273) link_BETA1-4 : bond 0.00477 ( 12) link_BETA1-4 : angle 1.15523 ( 36) link_NAG-ASN : bond 0.00716 ( 57) link_NAG-ASN : angle 3.62152 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9903.25 seconds wall clock time: 170 minutes 10.21 seconds (10210.21 seconds total)