Starting phenix.real_space_refine on Mon Jul 6 12:42:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dlu_27516/07_2026/8dlu_27516.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlu_27516/07_2026/8dlu_27516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8dlu_27516/07_2026/8dlu_27516.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dlu_27516/07_2026/8dlu_27516.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dlu_27516/07_2026/8dlu_27516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlu_27516/07_2026/8dlu_27516.map" model { file = "/net/cci-nas-00/data/ceres_data/8dlu_27516/07_2026/8dlu_27516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlu_27516/07_2026/8dlu_27516.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 169 5.16 5 C 22377 2.51 5 N 5759 2.21 5 O 6832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35137 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 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 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 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 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 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 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 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 chiralities: 2 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 chiralities: 8 Chain: "B" 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 chiralities: 8 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 chiralities: 8 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 7.11, per 1000 atoms: 0.20 Number of scatterers: 35137 At special positions: 0 Unit cell: (171, 155, 235, 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 169 16.00 O 6832 8.00 N 5759 7.00 C 22377 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 90 " " NAG D 703 " - " ASN D 103 " " NAG D 704 " - " ASN D 322 " " NAG D 705 " - " ASN D 432 " " NAG D 706 " - " ASN D 546 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " ASN E 546 " " NAG F 1 " - " ASN A 17 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 17 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1074 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 17 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C1074 " " NAG V 1 " - " ASN C1098 " " NAG W 1 " - " ASN C1134 " Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.6 seconds 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8100 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 49 sheets defined 37.7% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 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 370 removed outlier: 4.405A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.511A pdb=" N LYS A 386 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.683A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.903A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.616A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.950A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.537A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.260A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.662A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.054A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.594A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.924A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.072A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.855A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.815A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.896A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.671A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.565A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 616 through 620' Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.570A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.714A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.502A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.901A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.056A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.119A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.811A pdb=" N GLU D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.151A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 Proline residue: D 178 - end of helix removed outlier: 3.683A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 218 through 252 removed outlier: 3.732A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.843A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 301 Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.555A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.706A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 397 through 413 removed outlier: 4.161A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.562A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.397A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.718A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.490A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.836A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'E' and resid 20 through 53 removed outlier: 4.056A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.833A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 4.117A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.649A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 218 through 252 removed outlier: 3.694A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.789A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 301 Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.503A pdb=" N GLY E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.529A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.650A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 397 through 413 removed outlier: 4.200A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.570A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.354A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.698A pdb=" N SER E 502 " --> pdb=" O ASP E 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.482A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.824A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 78 through 79 current: chain 'A' and resid 188 through 197 removed outlier: 6.346A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.934A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.094A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.923A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 163 removed outlier: 9.468A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.342A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.833A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.251A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.183A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.019A 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: 5.114A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.312A 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: 4.278A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.203A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.574A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 711 through 728 current: chain 'A' and resid 1059 through 1078 removed outlier: 3.951A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.321A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.928A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 78 through 79 current: chain 'B' and resid 188 through 197 removed outlier: 6.268A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.129A 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 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 85 current: chain 'B' and resid 116 through 121 removed outlier: 3.819A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.256A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 156 through 172 current: chain 'B' and resid 259 through 260 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 318 removed outlier: 6.745A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.228A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.181A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 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: 6.128A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.368A 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 704 removed outlier: 3.839A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 711 through 728 current: chain 'B' and resid 1059 through 1078 removed outlier: 4.002A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.327A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 78 through 79 current: chain 'C' and resid 188 through 197 removed outlier: 5.957A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.106A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 85 current: chain 'C' and resid 116 through 121 removed outlier: 3.545A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.976A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.055A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 154 through 172 current: chain 'C' and resid 259 through 260 Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.705A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.975A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.836A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.667A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.098A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 711 through 728 current: chain 'C' and resid 1059 through 1078 removed outlier: 3.987A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.385A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.890A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.050A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.347A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.829A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.017A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.336A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1471 hydrogen bonds defined for protein. 4152 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: 8.45 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11138 1.34 - 1.47: 9129 1.47 - 1.59: 15473 1.59 - 1.72: 0 1.72 - 1.84: 238 Bond restraints: 35978 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.52e+00 bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.51e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.97e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.94e+00 ... (remaining 35973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 46768 1.78 - 3.56: 1931 3.56 - 5.34: 173 5.34 - 7.12: 48 7.12 - 8.90: 25 Bond angle restraints: 48945 Sorted by residual: angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.29 -5.59 1.22e+00 6.72e-01 2.10e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.05 -5.35 1.22e+00 6.72e-01 1.92e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.02 -5.32 1.22e+00 6.72e-01 1.90e+01 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.46 128.47 -6.01 1.41e+00 5.03e-01 1.82e+01 angle pdb=" C SER A 359 " pdb=" N ASN A 360 " pdb=" CA ASN A 360 " ideal model delta sigma weight residual 121.54 129.43 -7.89 1.91e+00 2.74e-01 1.71e+01 ... (remaining 48940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 19109 17.88 - 35.76: 1390 35.76 - 53.63: 213 53.63 - 71.51: 65 71.51 - 89.39: 44 Dihedral angle restraints: 20821 sinusoidal: 8241 harmonic: 12580 Sorted by residual: dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual -86.00 -49.39 -36.61 1 1.00e+01 1.00e-02 1.89e+01 dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual -86.00 -49.93 -36.07 1 1.00e+01 1.00e-02 1.84e+01 dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 159.49 20.51 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 20818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4641 0.073 - 0.146: 903 0.146 - 0.218: 78 0.218 - 0.291: 8 0.291 - 0.364: 3 Chirality restraints: 5633 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 5630 not shown) Planarity restraints: 6303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 200 " -0.008 2.00e-02 2.50e+03 5.76e-02 6.63e+01 pdb=" CG TYR B 200 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR B 200 " 0.085 2.00e-02 2.50e+03 pdb=" CD2 TYR B 200 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 200 " -0.086 2.00e-02 2.50e+03 pdb=" CE2 TYR B 200 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 200 " -0.076 2.00e-02 2.50e+03 pdb=" OH TYR B 200 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 36 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C ALA E 36 " -0.056 2.00e-02 2.50e+03 pdb=" O ALA E 36 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU E 37 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 36 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C ALA D 36 " 0.055 2.00e-02 2.50e+03 pdb=" O ALA D 36 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU D 37 " -0.019 2.00e-02 2.50e+03 ... (remaining 6300 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 9634 2.81 - 3.33: 30461 3.33 - 3.86: 60356 3.86 - 4.38: 68717 4.38 - 4.90: 118534 Nonbonded interactions: 287702 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.292 3.040 nonbonded pdb=" ND2 ASN A 360 " pdb=" O GLU B 169 " model vdw 2.298 3.120 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.300 3.040 nonbonded pdb=" OE1 GLN C 52 " pdb=" OG1 THR C 274 " model vdw 2.302 3.040 ... (remaining 287697 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 31.870 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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 : 0.005 0.069 36096 Z= 0.233 Angle : 0.827 15.337 49253 Z= 0.446 Chirality : 0.055 0.364 5633 Planarity : 0.006 0.062 6249 Dihedral : 13.319 89.389 12583 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.08 % Allowed : 3.17 % Favored : 96.75 % 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: 0.19 (0.11), residues: 4260 helix: 1.05 (0.12), residues: 1437 sheet: 0.85 (0.19), residues: 701 loop : -0.76 (0.12), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 460 TYR 0.086 0.002 TYR B 200 PHE 0.030 0.002 PHE A 275 TRP 0.022 0.002 TRP E 69 HIS 0.006 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.23 (35978) covalent geometry : angle 0.79820 / 0.44 (48945) SS BOND : bond 0.00269 / 0.18 ( 46) SS BOND : angle 1.63369 / 1.09 ( 92) hydrogen bonds : bond 0.13079 / 8.45 ( 1471) hydrogen bonds : angle 6.63733 / 4.59 ( 4152) link_BETA1-4 : bond 0.00532 / 0.33 ( 18) link_BETA1-4 : angle 1.41191 / 0.93 ( 54) link_NAG-ASN : bond 0.00712 / 0.37 ( 54) link_NAG-ASN : angle 3.62181 / 2.36 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 409 time to evaluate : 1.283 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: A 170 TYR cc_start: 0.9262 (t80) cc_final: 0.8973 (t80) REVERT: A 229 LEU cc_start: 0.9294 (tp) cc_final: 0.9086 (tp) REVERT: A 981 LEU cc_start: 0.9492 (mm) cc_final: 0.9203 (pp) REVERT: A 1005 GLN cc_start: 0.8270 (mt0) cc_final: 0.7955 (tt0) REVERT: B 79 PHE cc_start: 0.6651 (t80) cc_final: 0.6001 (t80) REVERT: B 88 ASP cc_start: 0.8861 (m-30) cc_final: 0.8350 (p0) REVERT: B 365 TYR cc_start: 0.8521 (m-80) cc_final: 0.8109 (m-80) REVERT: C 135 PHE cc_start: 0.8016 (m-10) cc_final: 0.7737 (m-80) REVERT: C 197 ILE cc_start: 0.9373 (mm) cc_final: 0.9059 (mp) REVERT: C 238 PHE cc_start: 0.7693 (p90) cc_final: 0.7294 (p90) REVERT: C 1005 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8423 (mt0) REVERT: D 27 THR cc_start: 0.4517 (p) cc_final: 0.4268 (t) REVERT: D 31 LYS cc_start: -0.0929 (tptp) cc_final: -0.1292 (mmtt) REVERT: D 126 ILE cc_start: -0.0304 (mt) cc_final: -0.0577 (mt) REVERT: D 290 ASN cc_start: 0.5875 (t0) cc_final: 0.5438 (p0) REVERT: D 306 ARG cc_start: 0.3820 (ttt-90) cc_final: 0.3290 (mtp180) REVERT: D 315 PHE cc_start: 0.0930 (m-80) cc_final: 0.0588 (m-80) REVERT: D 323 MET cc_start: 0.0017 (mmp) cc_final: -0.0832 (mmm) REVERT: D 383 MET cc_start: 0.4765 (mtp) cc_final: 0.3452 (tmm) REVERT: D 480 MET cc_start: 0.0210 (mtp) cc_final: -0.0212 (mtp) REVERT: D 508 ASN cc_start: 0.4634 (m-40) cc_final: 0.4289 (m110) REVERT: D 520 LEU cc_start: 0.6339 (mp) cc_final: 0.6114 (mp) REVERT: D 544 ILE cc_start: -0.0165 (pt) cc_final: -0.0747 (pt) REVERT: D 579 MET cc_start: -0.2557 (ptm) cc_final: -0.2836 (ttt) REVERT: E 152 MET cc_start: 0.2089 (mmm) cc_final: 0.1568 (mmm) REVERT: E 338 ASN cc_start: 0.8077 (t0) cc_final: 0.7774 (p0) REVERT: E 367 ASP cc_start: 0.9440 (m-30) cc_final: 0.9211 (p0) REVERT: E 510 TYR cc_start: 0.8101 (m-80) cc_final: 0.7792 (m-10) outliers start: 3 outliers final: 0 residues processed: 412 average time/residue: 0.2402 time to fit residues: 157.3939 Evaluate side-chains 205 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.0980 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 HIS A 762 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN B 955 ASN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 42 GLN D 96 GLN D 374 HIS ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 ASN E 154 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.124482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.078996 restraints weight = 134269.643| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 4.95 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 36096 Z= 0.269 Angle : 0.663 10.890 49253 Z= 0.333 Chirality : 0.045 0.244 5633 Planarity : 0.004 0.050 6249 Dihedral : 4.326 19.869 4627 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.16 % Allowed : 6.50 % Favored : 92.34 % 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: 0.59 (0.12), residues: 4260 helix: 1.71 (0.13), residues: 1431 sheet: 0.55 (0.19), residues: 682 loop : -0.54 (0.12), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 765 TYR 0.016 0.002 TYR D 183 PHE 0.024 0.002 PHE D 356 TRP 0.016 0.002 TRP E 275 HIS 0.008 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.27 (35978) covalent geometry : angle 0.64052 / 0.33 (48945) SS BOND : bond 0.00544 / 0.23 ( 46) SS BOND : angle 1.22393 / 0.81 ( 92) hydrogen bonds : bond 0.04385 / 2.81 ( 1471) hydrogen bonds : angle 5.35631 / 3.74 ( 4152) link_BETA1-4 : bond 0.00298 / 0.18 ( 18) link_BETA1-4 : angle 1.27220 / 0.84 ( 54) link_NAG-ASN : bond 0.00613 / 0.37 ( 54) link_NAG-ASN : angle 2.86489 / 1.89 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 1.398 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: A 118 LEU cc_start: 0.9418 (tt) cc_final: 0.8952 (mp) REVERT: B 88 ASP cc_start: 0.9046 (m-30) cc_final: 0.8587 (p0) REVERT: B 365 TYR cc_start: 0.8946 (m-80) cc_final: 0.8233 (m-80) REVERT: C 135 PHE cc_start: 0.8457 (m-10) cc_final: 0.7940 (m-80) REVERT: C 238 PHE cc_start: 0.7800 (p90) cc_final: 0.7246 (p90) REVERT: C 240 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8566 (t) REVERT: D 27 THR cc_start: 0.4753 (p) cc_final: 0.4366 (p) REVERT: D 62 MET cc_start: 0.3700 (tmm) cc_final: 0.3307 (ppp) REVERT: D 145 GLU cc_start: 0.1671 (tp30) cc_final: 0.1058 (pt0) REVERT: D 240 LEU cc_start: 0.0775 (tp) cc_final: 0.0492 (pp) REVERT: D 290 ASN cc_start: 0.5917 (t0) cc_final: 0.5121 (p0) REVERT: D 297 MET cc_start: 0.0414 (mtt) cc_final: 0.0059 (mtp) REVERT: D 306 ARG cc_start: 0.4046 (ttt-90) cc_final: 0.3363 (mtp180) REVERT: D 366 MET cc_start: 0.3328 (tpp) cc_final: 0.3008 (tpp) REVERT: D 383 MET cc_start: 0.4273 (mtp) cc_final: 0.3143 (tmm) REVERT: E 338 ASN cc_start: 0.8227 (t0) cc_final: 0.8000 (p0) REVERT: E 367 ASP cc_start: 0.9503 (m-30) cc_final: 0.9267 (p0) REVERT: E 510 TYR cc_start: 0.8331 (m-80) cc_final: 0.8118 (m-10) outliers start: 44 outliers final: 24 residues processed: 238 average time/residue: 0.2107 time to fit residues: 84.7541 Evaluate side-chains 196 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain E residue 341 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 424 optimal weight: 10.0000 chunk 177 optimal weight: 0.9990 chunk 318 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 chunk 365 optimal weight: 30.0000 chunk 268 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 238 optimal weight: 30.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN B 907 ASN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1002 GLN C1005 GLN D 378 HIS ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS E 442 GLN E 552 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.139151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.104709 restraints weight = 165126.265| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 5.58 r_work: 0.3031 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 36096 Z= 0.144 Angle : 0.560 11.253 49253 Z= 0.278 Chirality : 0.043 0.256 5633 Planarity : 0.004 0.046 6249 Dihedral : 4.124 18.926 4627 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.22 % Allowed : 7.61 % Favored : 91.18 % 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: 0.74 (0.12), residues: 4260 helix: 1.89 (0.14), residues: 1422 sheet: 0.57 (0.19), residues: 699 loop : -0.47 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.019 0.001 TYR D 41 PHE 0.020 0.001 PHE C 565 TRP 0.014 0.001 TRP C 436 HIS 0.010 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (35978) covalent geometry : angle 0.53774 / 0.27 (48945) SS BOND : bond 0.00291 / 0.14 ( 46) SS BOND : angle 1.22202 / 0.79 ( 92) hydrogen bonds : bond 0.03968 / 2.54 ( 1471) hydrogen bonds : angle 5.11025 / 3.57 ( 4152) link_BETA1-4 : bond 0.00244 / 0.15 ( 18) link_BETA1-4 : angle 0.91584 / 0.61 ( 54) link_NAG-ASN : bond 0.00522 / 0.28 ( 54) link_NAG-ASN : angle 2.63868 / 1.73 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 180 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9443 (tt) cc_final: 0.9032 (mp) REVERT: A 189 LEU cc_start: 0.9702 (tp) cc_final: 0.9330 (mt) REVERT: B 88 ASP cc_start: 0.9038 (m-30) cc_final: 0.8573 (p0) REVERT: B 365 TYR cc_start: 0.9096 (m-80) cc_final: 0.8488 (m-80) REVERT: C 135 PHE cc_start: 0.7704 (m-10) cc_final: 0.7352 (m-80) REVERT: D 41 TYR cc_start: 0.3759 (t80) cc_final: 0.2934 (t80) REVERT: D 62 MET cc_start: 0.3842 (tmm) cc_final: 0.3596 (ppp) REVERT: D 145 GLU cc_start: 0.1629 (tp30) cc_final: 0.1110 (pt0) REVERT: D 240 LEU cc_start: 0.0561 (tp) cc_final: 0.0244 (pp) REVERT: D 290 ASN cc_start: 0.5658 (t0) cc_final: 0.5235 (p0) REVERT: D 306 ARG cc_start: 0.3829 (ttt-90) cc_final: 0.3345 (mtp180) REVERT: D 366 MET cc_start: 0.4035 (tpp) cc_final: 0.3760 (tpp) REVERT: D 383 MET cc_start: 0.4852 (mtp) cc_final: 0.4137 (tmm) REVERT: E 367 ASP cc_start: 0.9449 (m-30) cc_final: 0.9221 (p0) REVERT: E 510 TYR cc_start: 0.8262 (m-80) cc_final: 0.8005 (m-10) outliers start: 46 outliers final: 26 residues processed: 212 average time/residue: 0.2123 time to fit residues: 76.4474 Evaluate side-chains 190 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain E residue 341 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 161 optimal weight: 3.9990 chunk 398 optimal weight: 5.9990 chunk 373 optimal weight: 7.9990 chunk 349 optimal weight: 50.0000 chunk 357 optimal weight: 0.2980 chunk 421 optimal weight: 10.0000 chunk 307 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 231 optimal weight: 0.8980 chunk 220 optimal weight: 20.0000 chunk 392 optimal weight: 20.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 613 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN D 250 ASN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.127438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.082473 restraints weight = 138251.831| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.99 r_work: 0.3022 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 36096 Z= 0.223 Angle : 0.593 10.966 49253 Z= 0.294 Chirality : 0.043 0.261 5633 Planarity : 0.004 0.043 6249 Dihedral : 4.185 21.545 4627 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.40 % Allowed : 8.40 % Favored : 90.20 % 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: 0.67 (0.12), residues: 4260 helix: 1.84 (0.14), residues: 1428 sheet: 0.32 (0.19), residues: 658 loop : -0.43 (0.13), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 357 TYR 0.016 0.001 TYR D 41 PHE 0.018 0.001 PHE C 106 TRP 0.013 0.001 TRP D 477 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.22 (35978) covalent geometry : angle 0.57228 / 0.29 (48945) SS BOND : bond 0.00288 / 0.15 ( 46) SS BOND : angle 1.14819 / 0.75 ( 92) hydrogen bonds : bond 0.04008 / 2.57 ( 1471) hydrogen bonds : angle 5.06991 / 3.53 ( 4152) link_BETA1-4 : bond 0.00321 / 0.16 ( 18) link_BETA1-4 : angle 1.13777 / 0.73 ( 54) link_NAG-ASN : bond 0.00567 / 0.34 ( 54) link_NAG-ASN : angle 2.57911 / 1.69 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 168 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9479 (tt) cc_final: 0.9070 (mp) REVERT: A 189 LEU cc_start: 0.9573 (tp) cc_final: 0.9161 (mt) REVERT: A 1002 GLN cc_start: 0.9350 (tp40) cc_final: 0.9124 (tp40) REVERT: B 88 ASP cc_start: 0.9041 (m-30) cc_final: 0.8590 (p0) REVERT: B 365 TYR cc_start: 0.9140 (m-80) cc_final: 0.8434 (m-80) REVERT: C 135 PHE cc_start: 0.7876 (m-10) cc_final: 0.7521 (m-80) REVERT: C 238 PHE cc_start: 0.7729 (p90) cc_final: 0.7200 (p90) REVERT: D 145 GLU cc_start: 0.1603 (tp30) cc_final: 0.1082 (pt0) REVERT: D 240 LEU cc_start: 0.0591 (tp) cc_final: 0.0260 (pp) REVERT: D 290 ASN cc_start: 0.5230 (t0) cc_final: 0.4945 (p0) REVERT: D 306 ARG cc_start: 0.3460 (ttt-90) cc_final: 0.2944 (mtp180) REVERT: D 315 PHE cc_start: 0.0252 (OUTLIER) cc_final: -0.0109 (t80) REVERT: D 366 MET cc_start: 0.3809 (tpp) cc_final: 0.3559 (tpp) REVERT: D 383 MET cc_start: 0.5101 (mtp) cc_final: 0.4352 (tmm) REVERT: D 510 TYR cc_start: 0.3338 (OUTLIER) cc_final: 0.3059 (m-80) REVERT: E 323 MET cc_start: 0.9010 (mmp) cc_final: 0.8740 (mmm) REVERT: E 367 ASP cc_start: 0.9356 (m-30) cc_final: 0.9111 (p0) REVERT: E 462 MET cc_start: 0.6693 (ptt) cc_final: 0.6434 (ptt) REVERT: E 510 TYR cc_start: 0.8238 (m-80) cc_final: 0.7969 (m-10) outliers start: 53 outliers final: 35 residues processed: 204 average time/residue: 0.1978 time to fit residues: 69.7798 Evaluate side-chains 193 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain E residue 341 LYS Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 315 optimal weight: 5.9990 chunk 376 optimal weight: 10.0000 chunk 413 optimal weight: 20.0000 chunk 191 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 211 optimal weight: 5.9990 chunk 380 optimal weight: 10.0000 chunk 159 optimal weight: 0.6980 chunk 115 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 218 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 493 GLN A 824 ASN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN C 755 GLN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 535 HIS ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 250 ASN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 586 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.121471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.074555 restraints weight = 137439.490| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 4.03 r_work: 0.2948 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 36096 Z= 0.340 Angle : 0.711 12.308 49253 Z= 0.351 Chirality : 0.046 0.294 5633 Planarity : 0.004 0.046 6249 Dihedral : 4.564 22.355 4627 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.61 % Allowed : 9.33 % Favored : 89.06 % 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: 0.27 (0.12), residues: 4260 helix: 1.54 (0.14), residues: 1413 sheet: -0.11 (0.19), residues: 671 loop : -0.62 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 460 TYR 0.020 0.002 TYR A 269 PHE 0.029 0.002 PHE C 106 TRP 0.024 0.002 TRP D 461 HIS 0.006 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00745 / 0.34 (35978) covalent geometry : angle 0.69159 / 0.35 (48945) SS BOND : bond 0.00311 / 0.19 ( 46) SS BOND : angle 1.17007 / 0.78 ( 92) hydrogen bonds : bond 0.04469 / 2.85 ( 1471) hydrogen bonds : angle 5.35283 / 3.70 ( 4152) link_BETA1-4 : bond 0.00432 / 0.24 ( 18) link_BETA1-4 : angle 1.43667 / 0.92 ( 54) link_NAG-ASN : bond 0.00760 / 0.50 ( 54) link_NAG-ASN : angle 2.74968 / 1.83 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 167 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.9541 (tp) cc_final: 0.9123 (mt) REVERT: A 779 GLN cc_start: 0.9527 (tp40) cc_final: 0.9124 (tm-30) REVERT: A 869 MET cc_start: 0.9367 (mtm) cc_final: 0.9018 (ptp) REVERT: A 1002 GLN cc_start: 0.9384 (tp40) cc_final: 0.9166 (tp40) REVERT: B 88 ASP cc_start: 0.9251 (m-30) cc_final: 0.8829 (p0) REVERT: B 365 TYR cc_start: 0.9145 (m-80) cc_final: 0.8584 (m-80) REVERT: B 369 TYR cc_start: 0.9395 (t80) cc_final: 0.9133 (t80) REVERT: C 135 PHE cc_start: 0.8138 (m-10) cc_final: 0.7608 (m-80) REVERT: C 298 GLU cc_start: 0.9260 (tt0) cc_final: 0.9051 (mt-10) REVERT: C 396 TYR cc_start: 0.6560 (m-80) cc_final: 0.6344 (m-80) REVERT: D 145 GLU cc_start: 0.1603 (tp30) cc_final: 0.1011 (pt0) REVERT: D 240 LEU cc_start: 0.0494 (tp) cc_final: 0.0136 (pp) REVERT: D 306 ARG cc_start: 0.3579 (ttt-90) cc_final: 0.2916 (mtp180) REVERT: D 383 MET cc_start: 0.5415 (mtp) cc_final: 0.4652 (tmm) REVERT: D 480 MET cc_start: -0.0270 (mpp) cc_final: -0.0650 (tpp) REVERT: D 579 MET cc_start: -0.0302 (ptt) cc_final: -0.1231 (mtm) REVERT: E 213 ASP cc_start: 0.8842 (m-30) cc_final: 0.8542 (t0) REVERT: E 367 ASP cc_start: 0.9361 (m-30) cc_final: 0.9032 (p0) REVERT: E 462 MET cc_start: 0.6665 (ptt) cc_final: 0.6335 (ptt) REVERT: E 510 TYR cc_start: 0.8488 (m-80) cc_final: 0.8209 (m-10) outliers start: 61 outliers final: 31 residues processed: 210 average time/residue: 0.1982 time to fit residues: 71.7477 Evaluate side-chains 186 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain E residue 341 LYS Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 280 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 140 optimal weight: 9.9990 chunk 299 optimal weight: 0.9980 chunk 297 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 347 optimal weight: 20.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 762 GLN B 978 ASN D 102 GLN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.137425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.103355 restraints weight = 163941.647| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 5.76 r_work: 0.3000 rms_B_bonded: 5.17 restraints_weight: 2.0000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 36096 Z= 0.115 Angle : 0.547 11.145 49253 Z= 0.270 Chirality : 0.043 0.267 5633 Planarity : 0.003 0.040 6249 Dihedral : 4.166 17.750 4627 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.08 % Allowed : 10.09 % Favored : 88.82 % 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: 0.57 (0.13), residues: 4260 helix: 1.86 (0.14), residues: 1416 sheet: -0.00 (0.20), residues: 649 loop : -0.47 (0.13), residues: 2195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 514 TYR 0.013 0.001 TYR C1067 PHE 0.021 0.001 PHE B 175 TRP 0.021 0.001 TRP C 436 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (35978) covalent geometry : angle 0.53063 / 0.27 (48945) SS BOND : bond 0.00229 / 0.12 ( 46) SS BOND : angle 0.87926 / 0.58 ( 92) hydrogen bonds : bond 0.03693 / 2.35 ( 1471) hydrogen bonds : angle 4.97091 / 3.45 ( 4152) link_BETA1-4 : bond 0.00303 / 0.21 ( 18) link_BETA1-4 : angle 0.92653 / 0.60 ( 54) link_NAG-ASN : bond 0.00472 / 0.25 ( 54) link_NAG-ASN : angle 2.29726 / 1.52 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.9695 (tp) cc_final: 0.9272 (mt) REVERT: A 869 MET cc_start: 0.9269 (mtm) cc_final: 0.8978 (ptp) REVERT: B 88 ASP cc_start: 0.9235 (m-30) cc_final: 0.8705 (p0) REVERT: B 365 TYR cc_start: 0.9081 (m-80) cc_final: 0.8424 (m-80) REVERT: B 369 TYR cc_start: 0.9274 (t80) cc_final: 0.9010 (t80) REVERT: C 135 PHE cc_start: 0.7796 (m-10) cc_final: 0.7362 (m-80) REVERT: D 145 GLU cc_start: 0.1507 (tp30) cc_final: 0.0953 (pt0) REVERT: D 240 LEU cc_start: 0.0376 (tp) cc_final: -0.0054 (pp) REVERT: D 306 ARG cc_start: 0.3723 (ttt-90) cc_final: 0.3178 (mtp180) REVERT: D 383 MET cc_start: 0.5370 (mtp) cc_final: 0.4702 (tmm) REVERT: D 480 MET cc_start: -0.0340 (mpp) cc_final: -0.0882 (tpp) REVERT: D 579 MET cc_start: 0.0485 (ptt) cc_final: 0.0124 (mtm) REVERT: E 62 MET cc_start: 0.8668 (ppp) cc_final: 0.8468 (ppp) REVERT: E 213 ASP cc_start: 0.8832 (m-30) cc_final: 0.8544 (t0) REVERT: E 367 ASP cc_start: 0.9420 (m-30) cc_final: 0.9139 (p0) REVERT: E 408 MET cc_start: 0.8006 (mmm) cc_final: 0.7745 (mmm) REVERT: E 510 TYR cc_start: 0.8638 (m-80) cc_final: 0.8403 (m-10) outliers start: 41 outliers final: 23 residues processed: 200 average time/residue: 0.1947 time to fit residues: 66.8990 Evaluate side-chains 181 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain E residue 341 LYS Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 232 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 308 optimal weight: 0.0000 chunk 389 optimal weight: 9.9990 chunk 224 optimal weight: 2.9990 chunk 301 optimal weight: 2.9990 chunk 278 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 383 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 306 optimal weight: 1.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 580 GLN D 76 GLN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 524 GLN E 493 HIS ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.122796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.080127 restraints weight = 142498.648| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.77 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 36096 Z= 0.183 Angle : 0.572 10.579 49253 Z= 0.280 Chirality : 0.043 0.273 5633 Planarity : 0.003 0.040 6249 Dihedral : 4.107 18.632 4627 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.14 % Allowed : 10.62 % Favored : 88.24 % 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: 0.59 (0.13), residues: 4260 helix: 1.88 (0.14), residues: 1417 sheet: -0.04 (0.19), residues: 669 loop : -0.43 (0.13), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 514 TYR 0.029 0.001 TYR D 510 PHE 0.027 0.001 PHE C 238 TRP 0.015 0.001 TRP C 436 HIS 0.004 0.001 HIS D 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (35978) covalent geometry : angle 0.55534 / 0.28 (48945) SS BOND : bond 0.00222 / 0.12 ( 46) SS BOND : angle 0.83495 / 0.56 ( 92) hydrogen bonds : bond 0.03741 / 2.38 ( 1471) hydrogen bonds : angle 4.94819 / 3.43 ( 4152) link_BETA1-4 : bond 0.00283 / 0.17 ( 18) link_BETA1-4 : angle 1.12106 / 0.73 ( 54) link_NAG-ASN : bond 0.00523 / 0.31 ( 54) link_NAG-ASN : angle 2.33219 / 1.54 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.9579 (tp) cc_final: 0.9162 (mt) REVERT: A 1002 GLN cc_start: 0.9130 (tp40) cc_final: 0.8799 (tp40) REVERT: B 88 ASP cc_start: 0.9084 (m-30) cc_final: 0.8690 (p0) REVERT: B 365 TYR cc_start: 0.8804 (m-80) cc_final: 0.8319 (m-80) REVERT: B 369 TYR cc_start: 0.8849 (t80) cc_final: 0.8612 (t80) REVERT: C 135 PHE cc_start: 0.8140 (m-10) cc_final: 0.7659 (m-80) REVERT: C 245 HIS cc_start: 0.7457 (OUTLIER) cc_final: 0.7115 (t-170) REVERT: C 979 ASP cc_start: 0.8939 (t0) cc_final: 0.8716 (t0) REVERT: D 145 GLU cc_start: 0.1335 (tp30) cc_final: 0.0788 (pt0) REVERT: D 240 LEU cc_start: 0.0889 (tp) cc_final: 0.0333 (pp) REVERT: D 306 ARG cc_start: 0.4002 (ttt-90) cc_final: 0.3454 (mtp180) REVERT: D 383 MET cc_start: 0.5186 (mtp) cc_final: 0.3055 (tmm) REVERT: D 480 MET cc_start: -0.0014 (mpp) cc_final: -0.1053 (tpp) REVERT: D 579 MET cc_start: -0.1850 (ptt) cc_final: -0.2588 (mtm) REVERT: E 213 ASP cc_start: 0.8681 (m-30) cc_final: 0.8272 (t0) REVERT: E 367 ASP cc_start: 0.9352 (m-30) cc_final: 0.9052 (p0) REVERT: E 408 MET cc_start: 0.7770 (mmm) cc_final: 0.7497 (mmm) REVERT: E 510 TYR cc_start: 0.8503 (m-80) cc_final: 0.8160 (m-10) outliers start: 43 outliers final: 27 residues processed: 196 average time/residue: 0.1890 time to fit residues: 63.1995 Evaluate side-chains 181 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain E residue 341 LYS Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 351 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 chunk 193 optimal weight: 0.8980 chunk 150 optimal weight: 9.9990 chunk 241 optimal weight: 20.0000 chunk 224 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 405 optimal weight: 7.9990 chunk 40 optimal weight: 30.0000 chunk 103 optimal weight: 1.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS D 76 GLN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 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 = 0.4308 r_free = 0.4308 target = 0.123697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.080884 restraints weight = 142169.077| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.74 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 36096 Z= 0.215 Angle : 0.586 12.907 49253 Z= 0.288 Chirality : 0.043 0.277 5633 Planarity : 0.004 0.040 6249 Dihedral : 4.149 18.207 4627 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.98 % Allowed : 11.10 % Favored : 87.93 % 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: 0.53 (0.13), residues: 4260 helix: 1.83 (0.14), residues: 1417 sheet: -0.05 (0.20), residues: 647 loop : -0.47 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 357 TYR 0.027 0.001 TYR D 510 PHE 0.026 0.001 PHE D 356 TRP 0.013 0.001 TRP C 436 HIS 0.005 0.001 HIS D 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (35978) covalent geometry : angle 0.57068 / 0.29 (48945) SS BOND : bond 0.00214 / 0.13 ( 46) SS BOND : angle 0.82024 / 0.55 ( 92) hydrogen bonds : bond 0.03804 / 2.43 ( 1471) hydrogen bonds : angle 5.00024 / 3.47 ( 4152) link_BETA1-4 : bond 0.00212 / 0.13 ( 18) link_BETA1-4 : angle 1.08576 / 0.71 ( 54) link_NAG-ASN : bond 0.00524 / 0.32 ( 54) link_NAG-ASN : angle 2.31637 / 1.54 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1002 GLN cc_start: 0.9147 (tp40) cc_final: 0.8863 (tp40) REVERT: B 88 ASP cc_start: 0.9136 (m-30) cc_final: 0.8713 (p0) REVERT: B 365 TYR cc_start: 0.8875 (m-80) cc_final: 0.8396 (m-80) REVERT: B 369 TYR cc_start: 0.8874 (t80) cc_final: 0.8631 (t80) REVERT: C 135 PHE cc_start: 0.8205 (m-80) cc_final: 0.7692 (m-80) REVERT: C 245 HIS cc_start: 0.7423 (OUTLIER) cc_final: 0.7098 (t-170) REVERT: C 396 TYR cc_start: 0.6607 (m-80) cc_final: 0.6363 (m-10) REVERT: C 979 ASP cc_start: 0.8980 (t0) cc_final: 0.8757 (t0) REVERT: D 102 GLN cc_start: 0.2877 (OUTLIER) cc_final: 0.2278 (tm-30) REVERT: D 145 GLU cc_start: 0.1396 (tp30) cc_final: 0.0843 (pt0) REVERT: D 240 LEU cc_start: 0.0874 (tp) cc_final: 0.0320 (pp) REVERT: D 306 ARG cc_start: 0.4000 (ttt-90) cc_final: 0.3499 (mtp180) REVERT: D 480 MET cc_start: -0.0020 (mpp) cc_final: -0.1080 (tpt) REVERT: D 484 ILE cc_start: 0.1105 (mt) cc_final: 0.0853 (mm) REVERT: D 579 MET cc_start: -0.1803 (ptt) cc_final: -0.2571 (mtm) REVERT: E 62 MET cc_start: 0.8615 (ppp) cc_final: 0.8396 (ppp) REVERT: E 213 ASP cc_start: 0.8770 (m-30) cc_final: 0.8318 (t0) REVERT: E 367 ASP cc_start: 0.9376 (m-30) cc_final: 0.9064 (p0) REVERT: E 408 MET cc_start: 0.7867 (mmm) cc_final: 0.7620 (mmm) REVERT: E 462 MET cc_start: 0.6616 (ptt) cc_final: 0.6315 (ptt) REVERT: E 510 TYR cc_start: 0.8518 (m-80) cc_final: 0.8176 (m-10) outliers start: 37 outliers final: 30 residues processed: 187 average time/residue: 0.1992 time to fit residues: 63.7939 Evaluate side-chains 185 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain E residue 341 LYS Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 414 optimal weight: 10.0000 chunk 349 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 324 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 296 optimal weight: 1.9990 chunk 209 optimal weight: 0.0770 chunk 137 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 378 optimal weight: 2.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 GLN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.135750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.099856 restraints weight = 164191.146| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 5.77 r_work: 0.2971 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 36096 Z= 0.218 Angle : 0.595 11.401 49253 Z= 0.293 Chirality : 0.043 0.278 5633 Planarity : 0.004 0.040 6249 Dihedral : 4.167 20.810 4627 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.08 % Allowed : 11.28 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.52 (0.13), residues: 4260 helix: 1.83 (0.14), residues: 1417 sheet: -0.09 (0.20), residues: 648 loop : -0.48 (0.13), residues: 2195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 246 TYR 0.036 0.001 TYR B 904 PHE 0.023 0.001 PHE C 238 TRP 0.013 0.001 TRP C 436 HIS 0.015 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.22 (35978) covalent geometry : angle 0.57993 / 0.29 (48945) SS BOND : bond 0.00209 / 0.12 ( 46) SS BOND : angle 0.80695 / 0.54 ( 92) hydrogen bonds : bond 0.03804 / 2.42 ( 1471) hydrogen bonds : angle 5.01568 / 3.48 ( 4152) link_BETA1-4 : bond 0.00210 / 0.12 ( 18) link_BETA1-4 : angle 1.10580 / 0.72 ( 54) link_NAG-ASN : bond 0.00524 / 0.32 ( 54) link_NAG-ASN : angle 2.31283 / 1.55 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 1.176 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: A 869 MET cc_start: 0.9247 (mtm) cc_final: 0.8893 (ptp) REVERT: A 1002 GLN cc_start: 0.9407 (tp40) cc_final: 0.9169 (tp40) REVERT: B 88 ASP cc_start: 0.9218 (m-30) cc_final: 0.8781 (p0) REVERT: B 365 TYR cc_start: 0.9135 (m-80) cc_final: 0.8594 (m-80) REVERT: B 369 TYR cc_start: 0.9250 (t80) cc_final: 0.8978 (t80) REVERT: C 135 PHE cc_start: 0.8094 (m-80) cc_final: 0.7556 (m-80) REVERT: C 245 HIS cc_start: 0.7354 (OUTLIER) cc_final: 0.7055 (t-170) REVERT: C 396 TYR cc_start: 0.6603 (m-80) cc_final: 0.6369 (m-10) REVERT: C 979 ASP cc_start: 0.9106 (t0) cc_final: 0.8855 (t0) REVERT: D 145 GLU cc_start: 0.1769 (tp30) cc_final: 0.1167 (pt0) REVERT: D 240 LEU cc_start: 0.0100 (tp) cc_final: -0.0313 (pp) REVERT: D 297 MET cc_start: -0.1703 (OUTLIER) cc_final: -0.2241 (mtp) REVERT: D 306 ARG cc_start: 0.4048 (ttt-90) cc_final: 0.3723 (mtp180) REVERT: D 480 MET cc_start: -0.0482 (mpp) cc_final: -0.1190 (tpt) REVERT: D 579 MET cc_start: 0.0366 (ptt) cc_final: -0.0469 (mtm) REVERT: E 62 MET cc_start: 0.8647 (ppp) cc_final: 0.8416 (ppp) REVERT: E 213 ASP cc_start: 0.8985 (m-30) cc_final: 0.8695 (t0) REVERT: E 367 ASP cc_start: 0.9422 (m-30) cc_final: 0.9100 (p0) REVERT: E 408 MET cc_start: 0.8089 (mmm) cc_final: 0.7872 (mmm) REVERT: E 462 MET cc_start: 0.6886 (ptt) cc_final: 0.6608 (ptt) REVERT: E 510 TYR cc_start: 0.8755 (m-80) cc_final: 0.8531 (m-10) outliers start: 41 outliers final: 33 residues processed: 189 average time/residue: 0.1858 time to fit residues: 60.1934 Evaluate side-chains 185 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain E residue 163 TRP Chi-restraints excluded: chain E residue 341 LYS Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 404 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 359 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 377 optimal weight: 0.0270 chunk 223 optimal weight: 4.9990 chunk 399 optimal weight: 5.9990 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.136251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.101702 restraints weight = 164858.590| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 5.36 r_work: 0.2976 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 36096 Z= 0.164 Angle : 0.561 11.300 49253 Z= 0.276 Chirality : 0.043 0.275 5633 Planarity : 0.003 0.040 6249 Dihedral : 4.068 19.288 4627 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.90 % Allowed : 11.47 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.59 (0.13), residues: 4260 helix: 1.87 (0.14), residues: 1423 sheet: -0.04 (0.20), residues: 644 loop : -0.44 (0.13), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 319 TYR 0.024 0.001 TYR B 904 PHE 0.030 0.001 PHE E 315 TRP 0.023 0.001 TRP C 436 HIS 0.012 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (35978) covalent geometry : angle 0.54581 / 0.27 (48945) SS BOND : bond 0.00180 / 0.10 ( 46) SS BOND : angle 0.75749 / 0.51 ( 92) hydrogen bonds : bond 0.03622 / 2.31 ( 1471) hydrogen bonds : angle 4.92370 / 3.41 ( 4152) link_BETA1-4 : bond 0.00245 / 0.14 ( 18) link_BETA1-4 : angle 0.97607 / 0.64 ( 54) link_NAG-ASN : bond 0.00446 / 0.26 ( 54) link_NAG-ASN : angle 2.20706 / 1.48 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.9312 (mtm) cc_final: 0.8882 (ptp) REVERT: A 1002 GLN cc_start: 0.9382 (tp40) cc_final: 0.9149 (tp40) REVERT: B 88 ASP cc_start: 0.9314 (m-30) cc_final: 0.8781 (p0) REVERT: B 365 TYR cc_start: 0.9151 (m-80) cc_final: 0.8542 (m-80) REVERT: B 369 TYR cc_start: 0.9270 (t80) cc_final: 0.8994 (t80) REVERT: C 135 PHE cc_start: 0.8210 (m-80) cc_final: 0.7621 (m-80) REVERT: C 979 ASP cc_start: 0.9094 (t0) cc_final: 0.8881 (t0) REVERT: D 145 GLU cc_start: 0.1765 (tp30) cc_final: 0.1169 (pt0) REVERT: D 240 LEU cc_start: 0.0222 (tp) cc_final: -0.0216 (pp) REVERT: D 297 MET cc_start: -0.2119 (OUTLIER) cc_final: -0.2655 (mtp) REVERT: D 306 ARG cc_start: 0.3955 (ttt-90) cc_final: 0.3649 (mtp180) REVERT: D 480 MET cc_start: -0.0327 (mpp) cc_final: -0.0747 (tpt) REVERT: D 579 MET cc_start: 0.0437 (ptt) cc_final: -0.0458 (mtm) REVERT: E 62 MET cc_start: 0.8679 (ppp) cc_final: 0.8426 (ppp) REVERT: E 213 ASP cc_start: 0.9018 (m-30) cc_final: 0.8731 (t0) REVERT: E 367 ASP cc_start: 0.9416 (m-30) cc_final: 0.9085 (p0) REVERT: E 408 MET cc_start: 0.8066 (mmm) cc_final: 0.7803 (mmm) REVERT: E 462 MET cc_start: 0.6684 (ptt) cc_final: 0.6370 (ptt) REVERT: E 510 TYR cc_start: 0.8716 (m-80) cc_final: 0.8498 (m-80) outliers start: 34 outliers final: 29 residues processed: 180 average time/residue: 0.2087 time to fit residues: 64.0660 Evaluate side-chains 183 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain E residue 163 TRP Chi-restraints excluded: chain E residue 341 LYS Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 388 optimal weight: 0.9980 chunk 308 optimal weight: 0.5980 chunk 44 optimal weight: 9.9990 chunk 39 optimal weight: 50.0000 chunk 158 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 32 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 415 optimal weight: 2.9990 chunk 344 optimal weight: 20.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.136314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.102083 restraints weight = 163838.923| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 5.61 r_work: 0.3030 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36096 Z= 0.152 Angle : 0.555 11.128 49253 Z= 0.273 Chirality : 0.043 0.274 5633 Planarity : 0.003 0.040 6249 Dihedral : 4.025 18.360 4627 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.87 % Allowed : 11.47 % Favored : 87.66 % 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: 0.62 (0.13), residues: 4260 helix: 1.90 (0.14), residues: 1421 sheet: -0.01 (0.20), residues: 644 loop : -0.42 (0.13), residues: 2195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.023 0.001 TYR B 904 PHE 0.020 0.001 PHE C 238 TRP 0.017 0.001 TRP C 436 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (35978) covalent geometry : angle 0.54072 / 0.27 (48945) SS BOND : bond 0.00174 / 0.10 ( 46) SS BOND : angle 0.74021 / 0.50 ( 92) hydrogen bonds : bond 0.03596 / 2.30 ( 1471) hydrogen bonds : angle 4.89793 / 3.40 ( 4152) link_BETA1-4 : bond 0.00235 / 0.13 ( 18) link_BETA1-4 : angle 0.98523 / 0.65 ( 54) link_NAG-ASN : bond 0.00443 / 0.25 ( 54) link_NAG-ASN : angle 2.18592 / 1.46 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13555.16 seconds wall clock time: 231 minutes 23.40 seconds (13883.40 seconds total)