Starting phenix.real_space_refine on Fri Mar 6 18:45:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nd7_12278/03_2026/7nd7_12278.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nd7_12278/03_2026/7nd7_12278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nd7_12278/03_2026/7nd7_12278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nd7_12278/03_2026/7nd7_12278.map" model { file = "/net/cci-nas-00/data/ceres_data/7nd7_12278/03_2026/7nd7_12278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nd7_12278/03_2026/7nd7_12278.cif" } resolution = 3.6 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= 0.002 sd= 0.026 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 4620 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 138 5.16 5 C 18767 2.51 5 N 4858 2.21 5 O 5828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s 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: 29591 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "B" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "C" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 800 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "F" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "G" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 800 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "J" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "K" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 800 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "Y" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.87, per 1000 atoms: 0.23 Number of scatterers: 29591 At special positions: 0 Unit cell: (139.4, 137.76, 198.44, 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 138 16.00 O 5828 8.00 N 4858 7.00 C 18767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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=2.02 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 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG I 1 " - " NAG I 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " BETA1-6 " NAG Y 1 " - " FUC Y 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Z 1 " - " FUC Z 3 " " NAG a 1 " - " FUC a 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " " NAG Y 1 " - " ASN H 59 " " NAG Z 1 " - " ASN F 59 " " NAG a 1 " - " ASN J 59 " Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.5 seconds 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6858 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 63 sheets defined 23.0% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.848A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.404A 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: 3.631A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.686A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.138A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.886A 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 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.650A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.101A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) 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 371 removed outlier: 3.834A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.401A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.627A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.694A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.102A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.870A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.650A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.097A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.821A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.401A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.635A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.700A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.153A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.896A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.655A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.090A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 81 through 85 Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.611A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.007A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 52 removed outlier: 4.122A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.164A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.742A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.228A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.672A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.267A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.128A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.898A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.642A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.642A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.622A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.614A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.136A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.185A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.753A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.250A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.698A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.280A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.564A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.848A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.697A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.697A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.668A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.619A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 52 removed outlier: 7.026A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.215A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.714A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.257A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.249A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.564A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.536A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.536A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.639A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF2, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.662A pdb=" N TYR H 33 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.957A pdb=" N TYR H 111 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N MET H 100 " --> pdb=" O PHE H 109 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE H 109 " --> pdb=" O MET H 100 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.504A pdb=" N ALA L 86 " --> pdb=" O LEU L 107 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.504A pdb=" N ALA L 86 " --> pdb=" O LEU L 107 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AF7, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AF8, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.724A pdb=" N TYR F 33 " --> pdb=" O ASP F 99 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.984A pdb=" N TYR F 111 " --> pdb=" O ARG F 98 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N MET F 100 " --> pdb=" O PHE F 109 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N PHE F 109 " --> pdb=" O MET F 100 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.178A pdb=" N GLN G 39 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU G 48 " --> pdb=" O GLN G 39 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 9 through 12 Processing sheet with id=AG3, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AG4, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AG5, first strand: chain 'J' and resid 10 through 12 removed outlier: 4.710A pdb=" N TYR J 33 " --> pdb=" O ASP J 99 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.974A pdb=" N TYR J 111 " --> pdb=" O ARG J 98 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N MET J 100 " --> pdb=" O PHE J 109 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N PHE J 109 " --> pdb=" O MET J 100 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.170A pdb=" N GLN K 39 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU K 48 " --> pdb=" O GLN K 39 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 9 through 12 Processing sheet with id=AG9, first strand: chain 'K' and resid 18 through 23 1237 hydrogen bonds defined for protein. 3294 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: 8.75 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9406 1.35 - 1.47: 7716 1.47 - 1.59: 12942 1.59 - 1.71: 1 1.71 - 1.83: 183 Bond restraints: 30248 Sorted by residual: bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.77e+00 bond pdb=" C1 NAG W 2 " pdb=" O5 NAG W 2 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.67e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.60e+00 bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.59e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.57e+00 ... (remaining 30243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 40911 2.93 - 5.87: 217 5.87 - 8.80: 8 8.80 - 11.73: 0 11.73 - 14.67: 1 Bond angle restraints: 41137 Sorted by residual: angle pdb=" C GLY C 526 " pdb=" N PRO C 527 " pdb=" CD PRO C 527 " ideal model delta sigma weight residual 125.00 110.33 14.67 4.10e+00 5.95e-02 1.28e+01 angle pdb=" C VAL K 53 " pdb=" N SER K 54 " pdb=" CA SER K 54 " ideal model delta sigma weight residual 121.99 116.76 5.23 1.56e+00 4.11e-01 1.12e+01 angle pdb=" CA TYR C 904 " pdb=" CB TYR C 904 " pdb=" CG TYR C 904 " ideal model delta sigma weight residual 113.90 119.73 -5.83 1.80e+00 3.09e-01 1.05e+01 angle pdb=" CA TYR A 904 " pdb=" CB TYR A 904 " pdb=" CG TYR A 904 " ideal model delta sigma weight residual 113.90 119.71 -5.81 1.80e+00 3.09e-01 1.04e+01 angle pdb=" CA CYS C 760 " pdb=" CB CYS C 760 " pdb=" SG CYS C 760 " ideal model delta sigma weight residual 114.40 121.79 -7.39 2.30e+00 1.89e-01 1.03e+01 ... (remaining 41132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 17771 17.54 - 35.09: 736 35.09 - 52.63: 161 52.63 - 70.18: 76 70.18 - 87.72: 30 Dihedral angle restraints: 18774 sinusoidal: 8076 harmonic: 10698 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -168.83 82.83 1 1.00e+01 1.00e-02 8.40e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -168.56 82.56 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -168.39 82.39 1 1.00e+01 1.00e-02 8.33e+01 ... (remaining 18771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3691 0.049 - 0.099: 843 0.099 - 0.148: 277 0.148 - 0.197: 3 0.197 - 0.247: 9 Chirality restraints: 4823 Sorted by residual: chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN F 59 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN H 59 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA GLU K 52 " pdb=" N GLU K 52 " pdb=" C GLU K 52 " pdb=" CB GLU K 52 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 4820 not shown) Planarity restraints: 5273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 526 " -0.107 5.00e-02 4.00e+02 1.64e-01 4.29e+01 pdb=" N PRO C 527 " 0.283 5.00e-02 4.00e+02 pdb=" CA PRO C 527 " -0.094 5.00e-02 4.00e+02 pdb=" CD PRO C 527 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 526 " -0.058 5.00e-02 4.00e+02 8.79e-02 1.24e+01 pdb=" N PRO B 527 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 881 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C THR A 881 " -0.060 2.00e-02 2.50e+03 pdb=" O THR A 881 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE A 882 " 0.020 2.00e-02 2.50e+03 ... (remaining 5270 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4376 2.76 - 3.30: 27242 3.30 - 3.83: 49572 3.83 - 4.37: 58626 4.37 - 4.90: 101890 Nonbonded interactions: 241706 Sorted by model distance: nonbonded pdb=" O LEU B 492 " pdb=" ND2 ASN F 54 " model vdw 2.229 3.120 nonbonded pdb=" OG SER B1123 " pdb=" OD1 ASN C 914 " model vdw 2.270 3.040 nonbonded pdb=" OG SER A1123 " pdb=" OD1 ASN B 914 " model vdw 2.298 3.040 nonbonded pdb=" O LEU C 492 " pdb=" ND2 ASN J 54 " model vdw 2.302 3.120 nonbonded pdb=" O LEU A 492 " pdb=" ND2 ASN H 54 " model vdw 2.304 3.120 ... (remaining 241701 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 27 through 1308) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'Y' selection = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.930 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.100 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 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 0.097 30357 Z= 0.177 Angle : 0.638 14.667 41419 Z= 0.345 Chirality : 0.046 0.247 4823 Planarity : 0.004 0.164 5230 Dihedral : 11.283 87.722 11781 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.65 % Favored : 96.15 % Rotamer: Outliers : 0.38 % Allowed : 2.19 % Favored : 97.43 % 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: -0.12 (0.13), residues: 3639 helix: 0.18 (0.18), residues: 711 sheet: 0.10 (0.15), residues: 1041 loop : -0.15 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 815 TYR 0.017 0.001 TYR A1067 PHE 0.020 0.001 PHE B 329 TRP 0.011 0.001 TRP J 50 HIS 0.007 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00373 (30248) covalent geometry : angle 0.63223 (41137) SS BOND : bond 0.00309 ( 45) SS BOND : angle 1.11081 ( 90) hydrogen bonds : bond 0.18512 ( 1181) hydrogen bonds : angle 7.88916 ( 3294) link_BETA1-4 : bond 0.00257 ( 18) link_BETA1-4 : angle 1.06442 ( 54) link_BETA1-6 : bond 0.00631 ( 3) link_BETA1-6 : angle 1.47857 ( 9) link_NAG-ASN : bond 0.00195 ( 43) link_NAG-ASN : angle 1.37431 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 757 time to evaluate : 1.042 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: 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: 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 54 LEU cc_start: 0.8615 (mt) cc_final: 0.8080 (mp) REVERT: A 392 PHE cc_start: 0.7065 (m-80) cc_final: 0.6843 (m-80) REVERT: A 513 LEU cc_start: 0.8680 (mt) cc_final: 0.8450 (mp) REVERT: A 902 MET cc_start: 0.7829 (mmm) cc_final: 0.7048 (mmm) REVERT: A 904 TYR cc_start: 0.5283 (m-10) cc_final: 0.4916 (m-10) REVERT: A 1037 SER cc_start: 0.7037 (t) cc_final: 0.6807 (t) REVERT: A 1122 VAL cc_start: 0.8289 (t) cc_final: 0.8089 (p) REVERT: B 88 ASP cc_start: 0.8350 (m-30) cc_final: 0.8129 (t0) REVERT: B 269 TYR cc_start: 0.6673 (m-80) cc_final: 0.6401 (m-80) REVERT: B 490 PHE cc_start: 0.8061 (t80) cc_final: 0.7201 (t80) REVERT: B 492 LEU cc_start: 0.8762 (mt) cc_final: 0.8405 (mt) REVERT: B 513 LEU cc_start: 0.8869 (mt) cc_final: 0.8635 (mp) REVERT: B 756 TYR cc_start: 0.8622 (m-80) cc_final: 0.8133 (m-80) REVERT: B 1029 MET cc_start: 0.8235 (tpp) cc_final: 0.7958 (tpp) REVERT: C 54 LEU cc_start: 0.8581 (mt) cc_final: 0.8056 (mt) REVERT: C 92 PHE cc_start: 0.6167 (t80) cc_final: 0.5161 (t80) REVERT: C 396 TYR cc_start: 0.5856 (m-80) cc_final: 0.4702 (m-10) REVERT: C 398 ASP cc_start: 0.6748 (m-30) cc_final: 0.6461 (m-30) REVERT: C 902 MET cc_start: 0.7392 (mmm) cc_final: 0.6622 (mmm) REVERT: H 76 ILE cc_start: 0.8989 (pt) cc_final: 0.8743 (pt) outliers start: 12 outliers final: 0 residues processed: 767 average time/residue: 0.2026 time to fit residues: 241.8504 Evaluate side-chains 373 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.0970 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 450 ASN B1010 GLN B1011 GLN C 321 GLN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 762 GLN C 872 GLN C1010 GLN C1106 GLN C1135 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.188036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.149047 restraints weight = 57148.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.143701 restraints weight = 69513.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.140477 restraints weight = 50701.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.140082 restraints weight = 50427.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.141163 restraints weight = 42131.410| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 30357 Z= 0.163 Angle : 0.670 10.880 41419 Z= 0.344 Chirality : 0.047 0.210 4823 Planarity : 0.005 0.147 5230 Dihedral : 6.506 55.994 5295 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.84 % Favored : 98.13 % Rotamer: Outliers : 2.07 % Allowed : 9.20 % Favored : 88.73 % 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: 0.46 (0.13), residues: 3639 helix: 1.56 (0.20), residues: 699 sheet: 0.37 (0.15), residues: 1017 loop : -0.13 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1014 TYR 0.022 0.002 TYR F 60 PHE 0.030 0.002 PHE C 515 TRP 0.023 0.002 TRP A 104 HIS 0.005 0.001 HIS J 35 Details of bonding type rmsd covalent geometry : bond 0.00381 (30248) covalent geometry : angle 0.65711 (41137) SS BOND : bond 0.00314 ( 45) SS BOND : angle 1.98339 ( 90) hydrogen bonds : bond 0.04540 ( 1181) hydrogen bonds : angle 6.49070 ( 3294) link_BETA1-4 : bond 0.00523 ( 18) link_BETA1-4 : angle 1.15912 ( 54) link_BETA1-6 : bond 0.00724 ( 3) link_BETA1-6 : angle 1.36673 ( 9) link_NAG-ASN : bond 0.00353 ( 43) link_NAG-ASN : angle 1.68302 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 428 time to evaluate : 1.092 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8202 (p) cc_final: 0.7846 (t) REVERT: A 269 TYR cc_start: 0.6947 (m-80) cc_final: 0.6677 (m-80) REVERT: A 492 LEU cc_start: 0.8763 (mt) cc_final: 0.8445 (tp) REVERT: A 606 ASN cc_start: 0.8330 (OUTLIER) cc_final: 0.7895 (t0) REVERT: A 902 MET cc_start: 0.7818 (mmm) cc_final: 0.6995 (mmm) REVERT: A 904 TYR cc_start: 0.5188 (m-10) cc_final: 0.4968 (m-10) REVERT: A 1037 SER cc_start: 0.7561 (t) cc_final: 0.7304 (t) REVERT: B 88 ASP cc_start: 0.8012 (m-30) cc_final: 0.7656 (t0) REVERT: B 293 LEU cc_start: 0.8239 (tt) cc_final: 0.7664 (tt) REVERT: B 490 PHE cc_start: 0.7997 (t80) cc_final: 0.7206 (t80) REVERT: B 492 LEU cc_start: 0.8775 (mt) cc_final: 0.8516 (mt) REVERT: B 756 TYR cc_start: 0.8800 (m-80) cc_final: 0.8090 (m-80) REVERT: C 42 VAL cc_start: 0.9112 (OUTLIER) cc_final: 0.8748 (m) REVERT: C 902 MET cc_start: 0.7109 (mmm) cc_final: 0.6595 (mmm) REVERT: C 945 LEU cc_start: 0.8827 (mm) cc_final: 0.8595 (mt) REVERT: F 73 ASP cc_start: 0.7064 (t0) cc_final: 0.6676 (t0) REVERT: J 73 ASP cc_start: 0.7001 (t0) cc_final: 0.6540 (t0) outliers start: 66 outliers final: 33 residues processed: 473 average time/residue: 0.1999 time to fit residues: 148.2588 Evaluate side-chains 366 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 331 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain K residue 3 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 16 optimal weight: 4.9990 chunk 232 optimal weight: 0.0170 chunk 138 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 256 optimal weight: 6.9990 chunk 163 optimal weight: 0.7980 chunk 261 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 450 ASN B 613 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** 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 = 0.4568 r_free = 0.4568 target = 0.186640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.148274 restraints weight = 57237.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.140518 restraints weight = 69013.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.137462 restraints weight = 65397.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.138476 restraints weight = 50708.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.138989 restraints weight = 41244.333| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 30357 Z= 0.148 Angle : 0.629 9.427 41419 Z= 0.318 Chirality : 0.046 0.312 4823 Planarity : 0.004 0.128 5230 Dihedral : 6.124 58.957 5295 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.20 % Favored : 97.77 % Rotamer: Outliers : 2.00 % Allowed : 11.49 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3639 helix: 1.52 (0.20), residues: 714 sheet: 0.37 (0.15), residues: 1029 loop : -0.12 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 466 TYR 0.019 0.002 TYR B 369 PHE 0.022 0.001 PHE C 515 TRP 0.031 0.002 TRP C 104 HIS 0.005 0.001 HIS G 98 Details of bonding type rmsd covalent geometry : bond 0.00341 (30248) covalent geometry : angle 0.62054 (41137) SS BOND : bond 0.00497 ( 45) SS BOND : angle 1.38347 ( 90) hydrogen bonds : bond 0.04055 ( 1181) hydrogen bonds : angle 6.22174 ( 3294) link_BETA1-4 : bond 0.00349 ( 18) link_BETA1-4 : angle 1.08606 ( 54) link_BETA1-6 : bond 0.00646 ( 3) link_BETA1-6 : angle 1.43910 ( 9) link_NAG-ASN : bond 0.00380 ( 43) link_NAG-ASN : angle 1.53301 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 352 time to evaluate : 1.086 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8200 (p) cc_final: 0.7846 (t) REVERT: A 269 TYR cc_start: 0.7032 (m-80) cc_final: 0.6820 (m-80) REVERT: A 606 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.7943 (t0) REVERT: A 740 MET cc_start: 0.8062 (ttt) cc_final: 0.7801 (ttm) REVERT: A 902 MET cc_start: 0.7873 (mmm) cc_final: 0.7061 (mmm) REVERT: A 1037 SER cc_start: 0.7661 (t) cc_final: 0.7389 (t) REVERT: B 90 VAL cc_start: 0.8140 (m) cc_final: 0.7837 (t) REVERT: B 269 TYR cc_start: 0.6961 (m-80) cc_final: 0.6631 (m-80) REVERT: B 466 ARG cc_start: 0.6600 (mtp180) cc_final: 0.6256 (mtp85) REVERT: B 490 PHE cc_start: 0.7842 (t80) cc_final: 0.7125 (t80) REVERT: B 492 LEU cc_start: 0.8767 (mt) cc_final: 0.8550 (mt) REVERT: B 756 TYR cc_start: 0.8771 (m-80) cc_final: 0.8065 (m-80) REVERT: C 42 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8702 (m) REVERT: C 189 LEU cc_start: 0.7895 (tp) cc_final: 0.7623 (tt) REVERT: C 291 CYS cc_start: 0.6177 (m) cc_final: 0.5886 (m) REVERT: C 492 LEU cc_start: 0.8420 (mt) cc_final: 0.8193 (tp) REVERT: C 787 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7808 (mp10) REVERT: C 902 MET cc_start: 0.7251 (mmm) cc_final: 0.6673 (mmm) REVERT: C 945 LEU cc_start: 0.8821 (mm) cc_final: 0.8544 (mt) REVERT: H 73 ASP cc_start: 0.6538 (t0) cc_final: 0.6312 (t0) REVERT: F 70 MET cc_start: 0.1956 (mtt) cc_final: 0.1133 (mtp) REVERT: F 73 ASP cc_start: 0.7460 (t0) cc_final: 0.7117 (t0) REVERT: G 3 VAL cc_start: 0.5209 (OUTLIER) cc_final: 0.4999 (p) REVERT: J 70 MET cc_start: 0.1672 (mtt) cc_final: 0.0840 (mtt) REVERT: J 73 ASP cc_start: 0.6952 (t0) cc_final: 0.6620 (t0) REVERT: K 41 HIS cc_start: 0.5642 (OUTLIER) cc_final: 0.4949 (m90) outliers start: 64 outliers final: 38 residues processed: 399 average time/residue: 0.1954 time to fit residues: 123.8266 Evaluate side-chains 365 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 322 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 41 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 12 optimal weight: 0.7980 chunk 323 optimal weight: 8.9990 chunk 150 optimal weight: 0.0870 chunk 200 optimal weight: 10.0000 chunk 265 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 272 optimal weight: 0.9980 chunk 331 optimal weight: 30.0000 chunk 29 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A1005 GLN B 52 GLN C 52 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.185500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.147240 restraints weight = 57076.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.141581 restraints weight = 77315.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.139070 restraints weight = 65460.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.139402 restraints weight = 60696.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.139964 restraints weight = 46568.713| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30357 Z= 0.147 Angle : 0.599 9.873 41419 Z= 0.304 Chirality : 0.045 0.254 4823 Planarity : 0.004 0.048 5230 Dihedral : 5.765 57.346 5295 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.92 % Favored : 98.05 % Rotamer: Outliers : 2.28 % Allowed : 11.86 % Favored : 85.85 % 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: 0.45 (0.14), residues: 3639 helix: 1.56 (0.20), residues: 717 sheet: 0.27 (0.15), residues: 1071 loop : -0.10 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 38 TYR 0.024 0.002 TYR L 89 PHE 0.026 0.001 PHE F 109 TRP 0.019 0.002 TRP J 36 HIS 0.011 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00344 (30248) covalent geometry : angle 0.59117 (41137) SS BOND : bond 0.00716 ( 45) SS BOND : angle 1.28914 ( 90) hydrogen bonds : bond 0.03847 ( 1181) hydrogen bonds : angle 6.03124 ( 3294) link_BETA1-4 : bond 0.00337 ( 18) link_BETA1-4 : angle 1.06594 ( 54) link_BETA1-6 : bond 0.00583 ( 3) link_BETA1-6 : angle 1.53836 ( 9) link_NAG-ASN : bond 0.00251 ( 43) link_NAG-ASN : angle 1.41634 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 343 time to evaluate : 1.134 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: 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: symmetry clash REVERT: A 33 THR cc_start: 0.8196 (p) cc_final: 0.7864 (t) REVERT: A 606 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.7915 (t0) REVERT: A 902 MET cc_start: 0.8131 (mmm) cc_final: 0.7429 (mmm) REVERT: A 1037 SER cc_start: 0.7883 (t) cc_final: 0.7041 (p) REVERT: B 90 VAL cc_start: 0.8137 (m) cc_final: 0.7842 (t) REVERT: B 357 ARG cc_start: 0.7678 (ttp80) cc_final: 0.7459 (ttp80) REVERT: B 490 PHE cc_start: 0.7741 (t80) cc_final: 0.7118 (t80) REVERT: B 756 TYR cc_start: 0.8795 (m-80) cc_final: 0.8047 (m-80) REVERT: B 948 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8159 (mt) REVERT: C 109 THR cc_start: 0.7331 (p) cc_final: 0.7129 (p) REVERT: C 189 LEU cc_start: 0.7701 (tp) cc_final: 0.7457 (tt) REVERT: C 492 LEU cc_start: 0.8418 (mt) cc_final: 0.8202 (tp) REVERT: C 902 MET cc_start: 0.7642 (mmm) cc_final: 0.6807 (mmm) REVERT: L 49 MET cc_start: 0.3853 (tpp) cc_final: 0.3571 (ttm) REVERT: G 3 VAL cc_start: 0.5119 (OUTLIER) cc_final: 0.4837 (p) outliers start: 73 outliers final: 48 residues processed: 400 average time/residue: 0.1960 time to fit residues: 125.8071 Evaluate side-chains 348 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 297 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 32 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 230 optimal weight: 0.5980 chunk 301 optimal weight: 5.9990 chunk 206 optimal weight: 4.9990 chunk 348 optimal weight: 4.9990 chunk 282 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 322 optimal weight: 0.8980 chunk 254 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 493 GLN B 955 ASN C 52 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.185084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.143845 restraints weight = 57369.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.139650 restraints weight = 68179.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.134025 restraints weight = 46865.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.134486 restraints weight = 48527.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.135097 restraints weight = 40895.250| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 30357 Z= 0.144 Angle : 0.595 13.102 41419 Z= 0.302 Chirality : 0.045 0.232 4823 Planarity : 0.004 0.080 5230 Dihedral : 5.502 55.702 5295 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.23 % Favored : 97.75 % Rotamer: Outliers : 2.66 % Allowed : 12.46 % Favored : 84.88 % 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: 0.47 (0.14), residues: 3639 helix: 1.74 (0.21), residues: 696 sheet: 0.31 (0.16), residues: 1047 loop : -0.16 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1107 TYR 0.016 0.002 TYR A1067 PHE 0.016 0.001 PHE B 192 TRP 0.014 0.002 TRP C 886 HIS 0.004 0.001 HIS G 98 Details of bonding type rmsd covalent geometry : bond 0.00337 (30248) covalent geometry : angle 0.58456 (41137) SS BOND : bond 0.00432 ( 45) SS BOND : angle 1.78219 ( 90) hydrogen bonds : bond 0.03786 ( 1181) hydrogen bonds : angle 5.93800 ( 3294) link_BETA1-4 : bond 0.00294 ( 18) link_BETA1-4 : angle 1.05764 ( 54) link_BETA1-6 : bond 0.00555 ( 3) link_BETA1-6 : angle 1.51885 ( 9) link_NAG-ASN : bond 0.00229 ( 43) link_NAG-ASN : angle 1.35524 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 330 time to evaluate : 1.103 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: 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: symmetry clash revert: symmetry clash REVERT: A 204 TYR cc_start: 0.8202 (m-80) cc_final: 0.7844 (m-80) REVERT: A 269 TYR cc_start: 0.6797 (m-80) cc_final: 0.6588 (m-80) REVERT: A 492 LEU cc_start: 0.8812 (mm) cc_final: 0.8560 (tp) REVERT: A 606 ASN cc_start: 0.8459 (t0) cc_final: 0.7954 (t0) REVERT: A 902 MET cc_start: 0.8352 (mmm) cc_final: 0.7775 (mmm) REVERT: A 1037 SER cc_start: 0.7995 (t) cc_final: 0.7687 (t) REVERT: B 90 VAL cc_start: 0.8115 (m) cc_final: 0.7890 (t) REVERT: B 269 TYR cc_start: 0.6999 (m-80) cc_final: 0.6556 (m-80) REVERT: B 301 CYS cc_start: 0.7439 (OUTLIER) cc_final: 0.7180 (m) REVERT: B 357 ARG cc_start: 0.7804 (ttp80) cc_final: 0.7219 (ttp80) REVERT: B 490 PHE cc_start: 0.8015 (t80) cc_final: 0.7298 (t80) REVERT: B 492 LEU cc_start: 0.8241 (mt) cc_final: 0.7812 (mm) REVERT: B 756 TYR cc_start: 0.8840 (m-80) cc_final: 0.8163 (m-80) REVERT: B 948 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8112 (mt) REVERT: B 1005 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7452 (tp40) REVERT: C 109 THR cc_start: 0.7255 (p) cc_final: 0.7048 (p) REVERT: C 189 LEU cc_start: 0.7964 (tp) cc_final: 0.7743 (tt) REVERT: C 332 ILE cc_start: 0.7431 (mp) cc_final: 0.7129 (tp) REVERT: C 492 LEU cc_start: 0.8574 (mt) cc_final: 0.8308 (tp) REVERT: C 740 MET cc_start: 0.8212 (ttt) cc_final: 0.7931 (ttt) REVERT: C 902 MET cc_start: 0.7778 (mmm) cc_final: 0.6851 (mmm) REVERT: C 992 GLN cc_start: 0.7993 (mp10) cc_final: 0.7716 (mp10) REVERT: L 34 TYR cc_start: 0.0704 (m-80) cc_final: 0.0268 (m-80) REVERT: L 49 MET cc_start: 0.4287 (tpp) cc_final: 0.3503 (ttm) REVERT: G 3 VAL cc_start: 0.5977 (OUTLIER) cc_final: 0.5703 (p) REVERT: J 81 MET cc_start: 0.7655 (mmm) cc_final: 0.6929 (mmm) REVERT: K 37 TRP cc_start: 0.4879 (m100) cc_final: 0.3767 (m100) REVERT: K 41 HIS cc_start: 0.5704 (OUTLIER) cc_final: 0.5018 (m90) REVERT: K 49 MET cc_start: 0.6364 (ppp) cc_final: 0.6137 (mtt) outliers start: 85 outliers final: 60 residues processed: 396 average time/residue: 0.1978 time to fit residues: 124.8279 Evaluate side-chains 356 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 292 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 41 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 23 optimal weight: 6.9990 chunk 291 optimal weight: 1.9990 chunk 336 optimal weight: 6.9990 chunk 276 optimal weight: 0.9990 chunk 312 optimal weight: 6.9990 chunk 211 optimal weight: 9.9990 chunk 120 optimal weight: 0.7980 chunk 238 optimal weight: 10.0000 chunk 184 optimal weight: 0.5980 chunk 365 optimal weight: 30.0000 chunk 266 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** 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 = 0.4525 r_free = 0.4525 target = 0.182828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.146775 restraints weight = 56982.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.144863 restraints weight = 84697.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.143905 restraints weight = 63852.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.143577 restraints weight = 58231.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.143010 restraints weight = 54702.178| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 30357 Z= 0.190 Angle : 0.618 11.041 41419 Z= 0.315 Chirality : 0.046 0.220 4823 Planarity : 0.004 0.058 5230 Dihedral : 5.447 53.233 5295 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.58 % Favored : 97.39 % Rotamer: Outliers : 2.57 % Allowed : 13.27 % Favored : 84.16 % 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: 0.38 (0.14), residues: 3639 helix: 1.38 (0.20), residues: 714 sheet: 0.30 (0.16), residues: 1044 loop : -0.13 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 38 TYR 0.020 0.002 TYR A1067 PHE 0.019 0.002 PHE B1089 TRP 0.016 0.002 TRP C 886 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00449 (30248) covalent geometry : angle 0.60918 (41137) SS BOND : bond 0.00469 ( 45) SS BOND : angle 1.53934 ( 90) hydrogen bonds : bond 0.03880 ( 1181) hydrogen bonds : angle 5.89376 ( 3294) link_BETA1-4 : bond 0.00287 ( 18) link_BETA1-4 : angle 1.08678 ( 54) link_BETA1-6 : bond 0.00539 ( 3) link_BETA1-6 : angle 1.51915 ( 9) link_NAG-ASN : bond 0.00265 ( 43) link_NAG-ASN : angle 1.41608 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 306 time to evaluate : 1.117 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: 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 606 ASN cc_start: 0.8368 (t0) cc_final: 0.7925 (t0) REVERT: A 902 MET cc_start: 0.8601 (mmm) cc_final: 0.7540 (mmm) REVERT: A 1037 SER cc_start: 0.7958 (t) cc_final: 0.6927 (p) REVERT: B 90 VAL cc_start: 0.8202 (m) cc_final: 0.7923 (t) REVERT: B 357 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7334 (ttp80) REVERT: B 490 PHE cc_start: 0.7126 (t80) cc_final: 0.6906 (t80) REVERT: B 948 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8127 (mt) REVERT: C 231 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7565 (tt) REVERT: C 291 CYS cc_start: 0.6104 (m) cc_final: 0.5636 (m) REVERT: L 34 TYR cc_start: 0.0123 (m-80) cc_final: -0.0326 (m-80) REVERT: L 49 MET cc_start: 0.4003 (tpp) cc_final: 0.2724 (ttm) REVERT: G 3 VAL cc_start: 0.4895 (OUTLIER) cc_final: 0.4666 (p) outliers start: 82 outliers final: 64 residues processed: 370 average time/residue: 0.1983 time to fit residues: 118.0400 Evaluate side-chains 352 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 285 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 32 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 365 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 chunk 296 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 287 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 210 optimal weight: 20.0000 chunk 94 optimal weight: 0.7980 chunk 149 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** K 40 GLN ** 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 = 0.4530 r_free = 0.4530 target = 0.183273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.144608 restraints weight = 57135.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.141112 restraints weight = 79402.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.136768 restraints weight = 60565.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.135873 restraints weight = 62551.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.136360 restraints weight = 54982.829| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30357 Z= 0.145 Angle : 0.586 11.071 41419 Z= 0.298 Chirality : 0.045 0.201 4823 Planarity : 0.004 0.048 5230 Dihedral : 5.291 51.068 5295 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.53 % Favored : 97.44 % Rotamer: Outliers : 2.54 % Allowed : 14.33 % Favored : 83.13 % 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: 0.40 (0.14), residues: 3639 helix: 1.48 (0.21), residues: 708 sheet: 0.28 (0.16), residues: 1038 loop : -0.12 (0.15), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 67 TYR 0.017 0.002 TYR B 369 PHE 0.020 0.001 PHE J 64 TRP 0.018 0.002 TRP C 886 HIS 0.005 0.001 HIS K 98 Details of bonding type rmsd covalent geometry : bond 0.00338 (30248) covalent geometry : angle 0.57755 (41137) SS BOND : bond 0.00378 ( 45) SS BOND : angle 1.37053 ( 90) hydrogen bonds : bond 0.03687 ( 1181) hydrogen bonds : angle 5.81071 ( 3294) link_BETA1-4 : bond 0.00275 ( 18) link_BETA1-4 : angle 1.05286 ( 54) link_BETA1-6 : bond 0.00570 ( 3) link_BETA1-6 : angle 1.47040 ( 9) link_NAG-ASN : bond 0.00217 ( 43) link_NAG-ASN : angle 1.33648 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 301 time to evaluate : 1.046 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: 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 606 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.7930 (t0) REVERT: A 902 MET cc_start: 0.8443 (mmm) cc_final: 0.7322 (mmm) REVERT: A 1037 SER cc_start: 0.8104 (t) cc_final: 0.7192 (p) REVERT: B 88 ASP cc_start: 0.7923 (t0) cc_final: 0.7431 (t0) REVERT: B 90 VAL cc_start: 0.8160 (m) cc_final: 0.7889 (t) REVERT: B 269 TYR cc_start: 0.6987 (m-80) cc_final: 0.6741 (m-80) REVERT: B 490 PHE cc_start: 0.7926 (t80) cc_final: 0.7212 (t80) REVERT: B 492 LEU cc_start: 0.8389 (mm) cc_final: 0.7904 (tp) REVERT: B 756 TYR cc_start: 0.8863 (m-80) cc_final: 0.8204 (m-80) REVERT: B 948 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8073 (mt) REVERT: C 231 ILE cc_start: 0.7808 (mm) cc_final: 0.7593 (tt) REVERT: C 291 CYS cc_start: 0.6296 (m) cc_final: 0.5846 (m) REVERT: C 902 MET cc_start: 0.8188 (mmm) cc_final: 0.7442 (mmm) REVERT: L 34 TYR cc_start: 0.0391 (m-80) cc_final: 0.0010 (m-80) REVERT: L 49 MET cc_start: 0.4587 (tpp) cc_final: 0.3377 (ttm) REVERT: G 3 VAL cc_start: 0.5599 (OUTLIER) cc_final: 0.5367 (p) REVERT: J 100 MET cc_start: 0.1651 (tpt) cc_final: 0.1202 (tpt) outliers start: 81 outliers final: 68 residues processed: 362 average time/residue: 0.1929 time to fit residues: 112.5561 Evaluate side-chains 356 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 285 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 32 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 112 optimal weight: 4.9990 chunk 336 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 79 optimal weight: 0.0870 chunk 82 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN B 394 ASN B 450 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 450 ASN ** K 40 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 = 0.4518 r_free = 0.4518 target = 0.182267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.145169 restraints weight = 57227.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.142168 restraints weight = 85157.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.138790 restraints weight = 68370.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.139003 restraints weight = 63447.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.138834 restraints weight = 49511.459| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 30357 Z= 0.176 Angle : 0.609 12.425 41419 Z= 0.309 Chirality : 0.046 0.209 4823 Planarity : 0.004 0.047 5230 Dihedral : 5.277 50.847 5295 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.94 % Favored : 97.03 % Rotamer: Outliers : 2.85 % Allowed : 14.40 % Favored : 82.75 % 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: 0.33 (0.14), residues: 3639 helix: 1.37 (0.20), residues: 708 sheet: 0.26 (0.16), residues: 1008 loop : -0.17 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 56 TYR 0.020 0.002 TYR A 265 PHE 0.031 0.002 PHE C 392 TRP 0.019 0.002 TRP C 886 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00416 (30248) covalent geometry : angle 0.60095 (41137) SS BOND : bond 0.00356 ( 45) SS BOND : angle 1.35303 ( 90) hydrogen bonds : bond 0.03758 ( 1181) hydrogen bonds : angle 5.78571 ( 3294) link_BETA1-4 : bond 0.00264 ( 18) link_BETA1-4 : angle 1.06696 ( 54) link_BETA1-6 : bond 0.00543 ( 3) link_BETA1-6 : angle 1.53260 ( 9) link_NAG-ASN : bond 0.00240 ( 43) link_NAG-ASN : angle 1.37117 ( 129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 293 time to evaluate : 1.020 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: 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 492 LEU cc_start: 0.7790 (tp) cc_final: 0.7541 (tp) REVERT: A 606 ASN cc_start: 0.8373 (t0) cc_final: 0.7937 (t0) REVERT: A 902 MET cc_start: 0.8662 (mmm) cc_final: 0.7471 (mmm) REVERT: B 88 ASP cc_start: 0.8003 (t0) cc_final: 0.7493 (t0) REVERT: B 90 VAL cc_start: 0.8159 (m) cc_final: 0.7830 (t) REVERT: B 466 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.6429 (mtp85) REVERT: B 490 PHE cc_start: 0.7646 (t80) cc_final: 0.7099 (t80) REVERT: B 492 LEU cc_start: 0.8095 (mm) cc_final: 0.7731 (tp) REVERT: B 948 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8079 (mt) REVERT: C 291 CYS cc_start: 0.5911 (m) cc_final: 0.5569 (m) REVERT: C 902 MET cc_start: 0.8214 (mmm) cc_final: 0.7411 (mmm) REVERT: L 34 TYR cc_start: 0.0453 (m-80) cc_final: 0.0105 (m-80) REVERT: L 49 MET cc_start: 0.3809 (tpp) cc_final: 0.2831 (ttm) REVERT: F 67 ARG cc_start: 0.4360 (ptp90) cc_final: 0.3417 (ptt-90) REVERT: F 104 MET cc_start: 0.5372 (OUTLIER) cc_final: 0.4517 (tmm) REVERT: G 3 VAL cc_start: 0.5056 (OUTLIER) cc_final: 0.4845 (p) outliers start: 91 outliers final: 74 residues processed: 356 average time/residue: 0.1873 time to fit residues: 108.0254 Evaluate side-chains 360 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 282 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 104 MET Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 32 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 33 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 187 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 180 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** 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 = 0.4508 r_free = 0.4508 target = 0.181287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.143487 restraints weight = 57174.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.139954 restraints weight = 89009.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.138157 restraints weight = 71420.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.137796 restraints weight = 66327.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.137800 restraints weight = 57936.737| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 30357 Z= 0.221 Angle : 0.650 11.919 41419 Z= 0.330 Chirality : 0.047 0.217 4823 Planarity : 0.004 0.058 5230 Dihedral : 5.381 50.529 5295 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.30 % Favored : 96.67 % Rotamer: Outliers : 2.72 % Allowed : 14.99 % Favored : 82.28 % 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: 0.20 (0.14), residues: 3639 helix: 1.20 (0.20), residues: 708 sheet: 0.20 (0.16), residues: 990 loop : -0.23 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 56 TYR 0.028 0.002 TYR B 451 PHE 0.050 0.002 PHE C 392 TRP 0.033 0.002 TRP B 104 HIS 0.008 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00524 (30248) covalent geometry : angle 0.64251 (41137) SS BOND : bond 0.00443 ( 45) SS BOND : angle 1.39962 ( 90) hydrogen bonds : bond 0.03911 ( 1181) hydrogen bonds : angle 5.83802 ( 3294) link_BETA1-4 : bond 0.00255 ( 18) link_BETA1-4 : angle 1.08409 ( 54) link_BETA1-6 : bond 0.00526 ( 3) link_BETA1-6 : angle 1.56741 ( 9) link_NAG-ASN : bond 0.00294 ( 43) link_NAG-ASN : angle 1.42912 ( 129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 290 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: 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: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.7881 (tp) cc_final: 0.7617 (tp) REVERT: A 606 ASN cc_start: 0.8412 (t0) cc_final: 0.8018 (t0) REVERT: A 902 MET cc_start: 0.8646 (mmm) cc_final: 0.7432 (mmm) REVERT: B 90 VAL cc_start: 0.8287 (m) cc_final: 0.7944 (t) REVERT: B 490 PHE cc_start: 0.7475 (t80) cc_final: 0.7181 (t80) REVERT: B 492 LEU cc_start: 0.8124 (mm) cc_final: 0.7744 (tp) REVERT: B 948 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8042 (mt) REVERT: C 291 CYS cc_start: 0.6150 (m) cc_final: 0.5807 (m) REVERT: C 773 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7880 (pt0) REVERT: C 902 MET cc_start: 0.7843 (mmm) cc_final: 0.7304 (mmm) REVERT: H 104 MET cc_start: 0.2680 (tpt) cc_final: 0.2111 (tpt) REVERT: L 34 TYR cc_start: 0.0540 (m-80) cc_final: 0.0150 (m-80) REVERT: L 49 MET cc_start: 0.3866 (tpp) cc_final: 0.2890 (ttm) REVERT: F 67 ARG cc_start: 0.4387 (ptp90) cc_final: 0.3760 (ptt-90) REVERT: F 104 MET cc_start: 0.5337 (OUTLIER) cc_final: 0.4488 (tmm) REVERT: G 41 HIS cc_start: 0.5314 (m90) cc_final: 0.5041 (m-70) outliers start: 87 outliers final: 74 residues processed: 353 average time/residue: 0.1921 time to fit residues: 111.4629 Evaluate side-chains 352 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 275 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 104 MET Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 32 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 310 optimal weight: 20.0000 chunk 274 optimal weight: 0.5980 chunk 251 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 265 optimal weight: 0.6980 chunk 342 optimal weight: 10.0000 chunk 211 optimal weight: 2.9990 chunk 210 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 87 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 450 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN K 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.181375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.144786 restraints weight = 57288.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.143031 restraints weight = 81852.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.141253 restraints weight = 65051.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.140702 restraints weight = 60120.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.139802 restraints weight = 54215.388| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 30357 Z= 0.174 Angle : 0.631 15.740 41419 Z= 0.316 Chirality : 0.046 0.237 4823 Planarity : 0.004 0.068 5230 Dihedral : 5.304 51.061 5295 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.97 % Favored : 97.00 % Rotamer: Outliers : 2.44 % Allowed : 15.52 % Favored : 82.03 % 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: 0.18 (0.14), residues: 3639 helix: 1.30 (0.20), residues: 708 sheet: 0.23 (0.16), residues: 972 loop : -0.32 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 56 TYR 0.020 0.002 TYR C 365 PHE 0.051 0.002 PHE C 392 TRP 0.040 0.002 TRP B 104 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00416 (30248) covalent geometry : angle 0.62452 (41137) SS BOND : bond 0.00393 ( 45) SS BOND : angle 1.29280 ( 90) hydrogen bonds : bond 0.03740 ( 1181) hydrogen bonds : angle 5.76807 ( 3294) link_BETA1-4 : bond 0.00266 ( 18) link_BETA1-4 : angle 1.04254 ( 54) link_BETA1-6 : bond 0.00500 ( 3) link_BETA1-6 : angle 1.47994 ( 9) link_NAG-ASN : bond 0.00238 ( 43) link_NAG-ASN : angle 1.35156 ( 129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 289 time to evaluate : 1.158 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: 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 606 ASN cc_start: 0.8407 (t0) cc_final: 0.8010 (t0) REVERT: A 902 MET cc_start: 0.8664 (mmm) cc_final: 0.7474 (mmm) REVERT: B 319 ARG cc_start: 0.5995 (OUTLIER) cc_final: 0.5687 (tpt-90) REVERT: B 490 PHE cc_start: 0.7353 (t80) cc_final: 0.7148 (t80) REVERT: B 492 LEU cc_start: 0.8042 (mm) cc_final: 0.7744 (tp) REVERT: B 608 VAL cc_start: 0.8960 (OUTLIER) cc_final: 0.8482 (t) REVERT: B 948 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8075 (mt) REVERT: C 291 CYS cc_start: 0.6188 (m) cc_final: 0.5840 (m) REVERT: C 902 MET cc_start: 0.8156 (mmm) cc_final: 0.7474 (mmm) REVERT: H 104 MET cc_start: 0.2527 (tpt) cc_final: 0.1964 (tpt) REVERT: L 49 MET cc_start: 0.3747 (tpp) cc_final: 0.2774 (ttm) REVERT: F 67 ARG cc_start: 0.3983 (ptp90) cc_final: 0.3616 (ptt-90) REVERT: G 41 HIS cc_start: 0.4829 (m90) cc_final: 0.4451 (m-70) outliers start: 78 outliers final: 68 residues processed: 342 average time/residue: 0.1932 time to fit residues: 107.9981 Evaluate side-chains 347 residues out of total 3195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 276 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 40 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 250 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 168 optimal weight: 0.0980 chunk 169 optimal weight: 0.6980 chunk 328 optimal weight: 3.9990 chunk 273 optimal weight: 0.7980 chunk 173 optimal weight: 0.6980 chunk 32 optimal weight: 0.0980 chunk 31 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 301 optimal weight: 0.0270 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.181699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.145176 restraints weight = 57811.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.142129 restraints weight = 81752.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.138759 restraints weight = 69038.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.139117 restraints weight = 64624.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.138284 restraints weight = 51219.413| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.194 30357 Z= 0.286 Angle : 0.818 59.200 41419 Z= 0.472 Chirality : 0.048 0.843 4823 Planarity : 0.006 0.214 5230 Dihedral : 5.313 51.074 5295 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.97 % Favored : 97.00 % Rotamer: Outliers : 2.38 % Allowed : 15.74 % Favored : 81.88 % Cbeta Deviations : 0.09 % 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: 0.18 (0.14), residues: 3639 helix: 1.33 (0.21), residues: 708 sheet: 0.21 (0.16), residues: 972 loop : -0.32 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 44 TYR 0.038 0.002 TYR B 269 PHE 0.067 0.002 PHE A 194 TRP 0.131 0.003 TRP A 104 HIS 0.366 0.005 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00554 (30248) covalent geometry : angle 0.80763 (41137) SS BOND : bond 0.00399 ( 45) SS BOND : angle 1.26807 ( 90) hydrogen bonds : bond 0.03724 ( 1181) hydrogen bonds : angle 5.78710 ( 3294) link_BETA1-4 : bond 0.00282 ( 18) link_BETA1-4 : angle 0.99459 ( 54) link_BETA1-6 : bond 0.00299 ( 3) link_BETA1-6 : angle 1.32565 ( 9) link_NAG-ASN : bond 0.00440 ( 43) link_NAG-ASN : angle 2.29588 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5261.28 seconds wall clock time: 92 minutes 6.94 seconds (5526.94 seconds total)