Starting phenix.real_space_refine on Fri Feb 6 22:30:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sxz_25511/02_2026/7sxz_25511.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sxz_25511/02_2026/7sxz_25511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sxz_25511/02_2026/7sxz_25511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sxz_25511/02_2026/7sxz_25511.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sxz_25511/02_2026/7sxz_25511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sxz_25511/02_2026/7sxz_25511.map" } resolution = 2.61 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= 0.039 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 132 5.16 5 C 18191 2.51 5 N 4679 2.21 5 O 5581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28583 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 6555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6555 Classifications: {'peptide': 841} Link IDs: {'PTRANS': 45, 'TRANS': 795} Chain breaks: 8 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: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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 dihedrals: 24 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 6.58, per 1000 atoms: 0.23 Number of scatterers: 28583 At special positions: 0 Unit cell: (141, 158, 236, 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 132 16.00 O 5581 8.00 N 4679 7.00 C 18191 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 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 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 D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 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 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 1 " - " ASN A 17 " " 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 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 17 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1074 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN C 17 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1074 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C1134 " Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.3 seconds 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6604 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 42 sheets defined 33.2% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.890A 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: 3.640A 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: 3.942A 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: 3.564A 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 1032 removed outlier: 4.265A 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 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.697A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.084A 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: 3.609A 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: 3.927A 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: 4.047A 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: 3.839A 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: 3.842A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.895A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.611A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.549A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.972A 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: 3.598A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.549A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.888A 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 removed outlier: 3.503A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.118A 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 'E' and resid 20 through 53 removed outlier: 4.153A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 4.114A 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: 3.823A 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: 4.084A 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 146 through 155 removed outlier: 3.988A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.706A 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: 3.700A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.854A 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: 3.796A 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 318 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.548A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.684A 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: 4.252A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.949A 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: 3.529A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.388A 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: 3.768A 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: 4.447A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.571A 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: 3.875A 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: 6.306A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.782A 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: 4.108A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.029A 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: 4.178A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.932A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.651A 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: 9.490A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.361A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.279A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.881A 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 319 removed outlier: 5.210A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.993A 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) Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.108A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.596A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, 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: 3.848A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.312A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.911A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB5, first strand: chain 'B' and resid 27 through 30 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: 6.342A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.008A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB7, 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: 11.407A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.004A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.295A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.041A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.515A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 154 through 172 current: chain 'B' and resid 259 through 260 Processing sheet with id=AB8, first strand: chain 'B' and resid 311 through 318 removed outlier: 6.708A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.146A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.250A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.123A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.820A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC7, 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: 3.886A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.259A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD1, 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: 5.938A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.124A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, 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: 3.585A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.230A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 9.913A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.265A 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=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.695A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.841A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.863A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.535A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.030A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE1, 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: 3.912A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.327A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.752A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.939A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.333A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1148 hydrogen bonds defined for protein. 3228 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: 7.01 Time building geometry restraints manager: 3.13 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: 9009 1.34 - 1.47: 7369 1.47 - 1.59: 12683 1.59 - 1.72: 0 1.72 - 1.84: 180 Bond restraints: 29241 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.93e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.55e+00 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.48e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.47e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.38e+00 ... (remaining 29236 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 38351 2.01 - 4.02: 1285 4.02 - 6.03: 112 6.03 - 8.04: 28 8.04 - 10.05: 11 Bond angle restraints: 39787 Sorted by residual: angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.82 129.36 -6.54 1.42e+00 4.96e-01 2.12e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.27 -5.57 1.22e+00 6.72e-01 2.08e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.23 -5.53 1.22e+00 6.72e-01 2.05e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 115.88 -5.18 1.22e+00 6.72e-01 1.81e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 122.06 -7.96 2.00e+00 2.50e-01 1.58e+01 ... (remaining 39782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 16803 17.92 - 35.85: 1178 35.85 - 53.77: 177 53.77 - 71.70: 58 71.70 - 89.62: 36 Dihedral angle restraints: 18252 sinusoidal: 8006 harmonic: 10246 Sorted by residual: 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 180.00 154.55 25.45 0 5.00e+00 4.00e-02 2.59e+01 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 -46.34 -39.66 1 1.00e+01 1.00e-02 2.21e+01 dihedral pdb=" CA PHE C 515 " pdb=" C PHE C 515 " pdb=" N GLU C 516 " pdb=" CA GLU C 516 " ideal model delta harmonic sigma weight residual 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 18249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3762 0.071 - 0.143: 799 0.143 - 0.214: 85 0.214 - 0.286: 6 0.286 - 0.357: 1 Chirality restraints: 4653 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB VAL B 576 " pdb=" CA VAL B 576 " pdb=" CG1 VAL B 576 " pdb=" CG2 VAL B 576 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 4650 not shown) Planarity restraints: 5116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 394 " -0.035 2.00e-02 2.50e+03 7.13e-02 5.08e+01 pdb=" CG ASN C 394 " 0.123 2.00e-02 2.50e+03 pdb=" OD1 ASN C 394 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN C 394 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 36 " 0.021 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C ALA E 36 " -0.072 2.00e-02 2.50e+03 pdb=" O ALA E 36 " 0.027 2.00e-02 2.50e+03 pdb=" N GLU E 37 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 169 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.47e+00 pdb=" C ARG E 169 " -0.053 2.00e-02 2.50e+03 pdb=" O ARG E 169 " 0.020 2.00e-02 2.50e+03 pdb=" N SER E 170 " 0.018 2.00e-02 2.50e+03 ... (remaining 5113 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 7451 2.80 - 3.33: 24622 3.33 - 3.85: 49344 3.85 - 4.38: 56706 4.38 - 4.90: 97196 Nonbonded interactions: 235319 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.291 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.292 3.040 nonbonded pdb=" OE1 GLN A 115 " pdb=" OG1 THR A 167 " model vdw 2.301 3.040 nonbonded pdb=" OD1 ASN A 540 " pdb=" OG1 THR A 549 " model vdw 2.305 3.040 ... (remaining 235314 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.960 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.710 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 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 0.058 29345 Z= 0.240 Angle : 0.853 15.325 40059 Z= 0.453 Chirality : 0.057 0.357 4653 Planarity : 0.006 0.071 5070 Dihedral : 12.887 89.619 11528 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.13), residues: 3465 helix: 0.71 (0.14), residues: 1003 sheet: 0.55 (0.19), residues: 688 loop : -0.78 (0.13), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 328 TYR 0.033 0.002 TYR A 200 PHE 0.034 0.002 PHE A 238 TRP 0.027 0.002 TRP B 886 HIS 0.007 0.001 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00490 (29241) covalent geometry : angle 0.81923 (39787) SS BOND : bond 0.00282 ( 40) SS BOND : angle 1.59772 ( 80) hydrogen bonds : bond 0.12446 ( 1148) hydrogen bonds : angle 6.79532 ( 3228) link_BETA1-4 : bond 0.00563 ( 18) link_BETA1-4 : angle 1.87566 ( 54) link_NAG-ASN : bond 0.00666 ( 46) link_NAG-ASN : angle 3.83602 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 PHE cc_start: 0.5120 (m-10) cc_final: 0.4360 (m-10) REVERT: A 270 LEU cc_start: 0.8657 (mt) cc_final: 0.8428 (mm) REVERT: A 1029 MET cc_start: 0.9141 (tpp) cc_final: 0.8908 (tpp) REVERT: B 54 LEU cc_start: 0.9228 (mp) cc_final: 0.8804 (tp) REVERT: B 88 ASP cc_start: 0.8933 (m-30) cc_final: 0.8649 (p0) REVERT: B 153 MET cc_start: 0.5775 (ptt) cc_final: 0.4789 (pmt) REVERT: B 369 TYR cc_start: 0.8443 (t80) cc_final: 0.8080 (t80) REVERT: B 370 ASN cc_start: 0.8908 (m-40) cc_final: 0.7823 (p0) REVERT: C 565 PHE cc_start: 0.8149 (p90) cc_final: 0.7895 (p90) REVERT: E 341 LYS cc_start: 0.7989 (mmtt) cc_final: 0.7729 (ptpp) REVERT: E 480 MET cc_start: 0.1418 (mtp) cc_final: 0.0929 (mpp) REVERT: E 559 ARG cc_start: 0.7420 (ptm-80) cc_final: 0.7186 (ttp80) outliers start: 0 outliers final: 2 residues processed: 290 average time/residue: 0.7082 time to fit residues: 237.4983 Evaluate side-chains 132 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain C residue 360 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.0010 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.9980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 926 GLN A1011 GLN B 115 GLN B 173 GLN B 354 ASN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 901 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1011 GLN E 374 HIS E 578 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.127489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.073121 restraints weight = 85958.848| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 4.27 r_work: 0.3091 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29345 Z= 0.120 Angle : 0.573 10.937 40059 Z= 0.289 Chirality : 0.044 0.251 4653 Planarity : 0.004 0.055 5070 Dihedral : 5.345 52.924 5109 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.97 % Allowed : 7.61 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.44 (0.13), residues: 3465 helix: 1.68 (0.16), residues: 1023 sheet: 0.55 (0.19), residues: 663 loop : -0.62 (0.13), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 765 TYR 0.018 0.001 TYR B 351 PHE 0.023 0.001 PHE A 238 TRP 0.021 0.002 TRP C 353 HIS 0.005 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00259 (29241) covalent geometry : angle 0.54436 (39787) SS BOND : bond 0.00184 ( 40) SS BOND : angle 1.01855 ( 80) hydrogen bonds : bond 0.04220 ( 1148) hydrogen bonds : angle 5.44935 ( 3228) link_BETA1-4 : bond 0.00327 ( 18) link_BETA1-4 : angle 0.96245 ( 54) link_NAG-ASN : bond 0.00608 ( 46) link_NAG-ASN : angle 3.00796 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5537 (ptt) cc_final: 0.5254 (ppp) REVERT: A 168 PHE cc_start: 0.7922 (t80) cc_final: 0.7556 (OUTLIER) REVERT: A 200 TYR cc_start: 0.8299 (m-80) cc_final: 0.7984 (m-80) REVERT: A 1005 GLN cc_start: 0.8854 (tt0) cc_final: 0.8576 (tt0) REVERT: A 1029 MET cc_start: 0.9491 (tpp) cc_final: 0.9289 (tpp) REVERT: B 54 LEU cc_start: 0.9467 (mp) cc_final: 0.8852 (tp) REVERT: B 88 ASP cc_start: 0.9211 (m-30) cc_final: 0.8549 (p0) REVERT: B 153 MET cc_start: 0.5725 (ptt) cc_final: 0.4722 (pmt) REVERT: B 369 TYR cc_start: 0.8625 (t80) cc_final: 0.8271 (t80) REVERT: B 370 ASN cc_start: 0.8887 (m-40) cc_final: 0.7922 (p0) REVERT: B 451 TYR cc_start: 0.5908 (m-80) cc_final: 0.5583 (m-80) REVERT: B 1002 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7637 (tm-30) REVERT: C 565 PHE cc_start: 0.7964 (p90) cc_final: 0.7417 (p90) REVERT: C 957 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8219 (tm-30) REVERT: E 474 MET cc_start: 0.1499 (mmm) cc_final: 0.0255 (mmm) REVERT: E 559 ARG cc_start: 0.7452 (ptm-80) cc_final: 0.7179 (ttp-110) outliers start: 30 outliers final: 11 residues processed: 170 average time/residue: 0.6244 time to fit residues: 125.0919 Evaluate side-chains 128 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 37 optimal weight: 0.9980 chunk 287 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 294 optimal weight: 20.0000 chunk 226 optimal weight: 20.0000 chunk 141 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 824 ASN B 580 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 824 ASN C1002 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 524 GLN E 552 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.136539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.094877 restraints weight = 103759.556| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 5.47 r_work: 0.2986 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29345 Z= 0.195 Angle : 0.582 10.986 40059 Z= 0.290 Chirality : 0.044 0.265 4653 Planarity : 0.004 0.039 5070 Dihedral : 5.014 51.886 5105 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.13 % Allowed : 8.26 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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 (0.14), residues: 3465 helix: 1.97 (0.16), residues: 1027 sheet: 0.48 (0.20), residues: 625 loop : -0.51 (0.13), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 567 TYR 0.023 0.002 TYR B 365 PHE 0.020 0.002 PHE C 106 TRP 0.017 0.002 TRP A 886 HIS 0.004 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00440 (29241) covalent geometry : angle 0.55680 (39787) SS BOND : bond 0.00333 ( 40) SS BOND : angle 0.96795 ( 80) hydrogen bonds : bond 0.04249 ( 1148) hydrogen bonds : angle 5.22041 ( 3228) link_BETA1-4 : bond 0.00224 ( 18) link_BETA1-4 : angle 1.14750 ( 54) link_NAG-ASN : bond 0.00671 ( 46) link_NAG-ASN : angle 2.79659 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 1.049 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 153 MET cc_start: 0.5383 (ptt) cc_final: 0.5003 (ppp) REVERT: A 168 PHE cc_start: 0.8301 (t80) cc_final: 0.7978 (t80) REVERT: A 170 TYR cc_start: 0.8832 (t80) cc_final: 0.8560 (t80) REVERT: A 200 TYR cc_start: 0.8143 (m-80) cc_final: 0.7923 (m-80) REVERT: A 329 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7870 (m-10) REVERT: A 773 GLU cc_start: 0.8843 (tt0) cc_final: 0.8491 (tt0) REVERT: A 1002 GLN cc_start: 0.9053 (tp40) cc_final: 0.8794 (tp-100) REVERT: A 1005 GLN cc_start: 0.8910 (tt0) cc_final: 0.8667 (tt0) REVERT: A 1010 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8603 (mp10) REVERT: B 54 LEU cc_start: 0.9475 (mp) cc_final: 0.8823 (tp) REVERT: B 88 ASP cc_start: 0.9208 (m-30) cc_final: 0.8515 (p0) REVERT: B 153 MET cc_start: 0.5836 (ptt) cc_final: 0.4885 (pmt) REVERT: B 369 TYR cc_start: 0.8707 (t80) cc_final: 0.8345 (t80) REVERT: B 370 ASN cc_start: 0.8955 (m-40) cc_final: 0.8010 (p0) REVERT: B 425 LEU cc_start: 0.6356 (mm) cc_final: 0.6110 (mp) REVERT: B 451 TYR cc_start: 0.6164 (m-80) cc_final: 0.5813 (m-80) REVERT: B 1002 GLN cc_start: 0.8282 (tm-30) cc_final: 0.7667 (tm-30) REVERT: C 130 VAL cc_start: 0.8373 (t) cc_final: 0.8068 (p) REVERT: E 474 MET cc_start: 0.0565 (mmm) cc_final: 0.0178 (mmm) REVERT: E 559 ARG cc_start: 0.7666 (ptm-80) cc_final: 0.7369 (ttp-110) REVERT: E 579 MET cc_start: 0.5538 (tpp) cc_final: 0.4826 (tpt) REVERT: E 606 TRP cc_start: 0.1717 (p90) cc_final: 0.1220 (p90) REVERT: E 613 TYR cc_start: 0.4943 (t80) cc_final: 0.4503 (m-10) outliers start: 35 outliers final: 12 residues processed: 156 average time/residue: 0.5644 time to fit residues: 105.5767 Evaluate side-chains 133 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 176 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 134 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 215 optimal weight: 0.1980 chunk 120 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 chunk 277 optimal weight: 0.8980 chunk 212 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN B 907 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.137416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.096321 restraints weight = 103117.790| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 5.33 r_work: 0.3034 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 29345 Z= 0.108 Angle : 0.524 13.661 40059 Z= 0.257 Chirality : 0.043 0.267 4653 Planarity : 0.003 0.049 5070 Dihedral : 4.747 52.572 5105 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.04 % Allowed : 8.94 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.75 (0.14), residues: 3465 helix: 2.19 (0.16), residues: 1025 sheet: 0.34 (0.20), residues: 614 loop : -0.42 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 452 TYR 0.023 0.001 TYR B 351 PHE 0.024 0.001 PHE A 157 TRP 0.017 0.001 TRP E 594 HIS 0.004 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00236 (29241) covalent geometry : angle 0.50052 (39787) SS BOND : bond 0.00177 ( 40) SS BOND : angle 0.84454 ( 80) hydrogen bonds : bond 0.03708 ( 1148) hydrogen bonds : angle 4.97438 ( 3228) link_BETA1-4 : bond 0.00315 ( 18) link_BETA1-4 : angle 0.89263 ( 54) link_NAG-ASN : bond 0.00571 ( 46) link_NAG-ASN : angle 2.61584 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5421 (ptt) cc_final: 0.5170 (ppp) REVERT: A 168 PHE cc_start: 0.8275 (t80) cc_final: 0.7862 (t80) REVERT: A 773 GLU cc_start: 0.8794 (tt0) cc_final: 0.8496 (tt0) REVERT: A 1002 GLN cc_start: 0.9060 (tp40) cc_final: 0.8735 (tp-100) REVERT: B 54 LEU cc_start: 0.9444 (mp) cc_final: 0.8781 (tp) REVERT: B 88 ASP cc_start: 0.9225 (m-30) cc_final: 0.8517 (p0) REVERT: B 153 MET cc_start: 0.5815 (ptt) cc_final: 0.4937 (pmt) REVERT: B 369 TYR cc_start: 0.8751 (t80) cc_final: 0.8387 (t80) REVERT: B 370 ASN cc_start: 0.8952 (m-40) cc_final: 0.8043 (p0) REVERT: B 425 LEU cc_start: 0.6433 (mm) cc_final: 0.6158 (mp) REVERT: B 451 TYR cc_start: 0.6230 (m-80) cc_final: 0.5893 (m-80) REVERT: B 1002 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7728 (tm-30) REVERT: C 130 VAL cc_start: 0.8276 (t) cc_final: 0.8009 (p) REVERT: C 245 HIS cc_start: 0.6806 (OUTLIER) cc_final: 0.6383 (m-70) REVERT: C 957 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8483 (tm-30) REVERT: C 993 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8734 (mp) REVERT: E 140 GLU cc_start: 0.1260 (OUTLIER) cc_final: 0.0895 (tt0) REVERT: E 358 ILE cc_start: 0.2941 (OUTLIER) cc_final: 0.2589 (mt) REVERT: E 553 LYS cc_start: 0.7112 (mptt) cc_final: 0.6865 (ttpt) REVERT: E 559 ARG cc_start: 0.7694 (ptm-80) cc_final: 0.7315 (ttp-110) REVERT: E 579 MET cc_start: 0.5918 (tpp) cc_final: 0.5150 (tpt) REVERT: E 606 TRP cc_start: 0.1657 (p90) cc_final: 0.1166 (p90) REVERT: E 613 TYR cc_start: 0.4806 (t80) cc_final: 0.4379 (m-10) outliers start: 32 outliers final: 12 residues processed: 151 average time/residue: 0.5840 time to fit residues: 106.3178 Evaluate side-chains 135 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 46 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 221 optimal weight: 20.0000 chunk 122 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 265 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 247 optimal weight: 0.8980 chunk 266 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN A 955 ASN B 824 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.125228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.072113 restraints weight = 82531.043| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 4.80 r_work: 0.2948 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 29345 Z= 0.286 Angle : 0.634 11.176 40059 Z= 0.314 Chirality : 0.046 0.268 4653 Planarity : 0.004 0.043 5070 Dihedral : 5.157 54.084 5105 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.13 % Allowed : 9.82 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.56 (0.14), residues: 3465 helix: 2.06 (0.16), residues: 1025 sheet: -0.05 (0.19), residues: 702 loop : -0.45 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 452 TYR 0.025 0.002 TYR B 351 PHE 0.025 0.002 PHE C 106 TRP 0.019 0.002 TRP E 594 HIS 0.005 0.001 HIS E 265 Details of bonding type rmsd covalent geometry : bond 0.00644 (29241) covalent geometry : angle 0.61042 (39787) SS BOND : bond 0.00257 ( 40) SS BOND : angle 0.88161 ( 80) hydrogen bonds : bond 0.04545 ( 1148) hydrogen bonds : angle 5.24929 ( 3228) link_BETA1-4 : bond 0.00419 ( 18) link_BETA1-4 : angle 1.36952 ( 54) link_NAG-ASN : bond 0.00780 ( 46) link_NAG-ASN : angle 2.83764 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.8337 (t80) cc_final: 0.8044 (t80) REVERT: A 200 TYR cc_start: 0.8569 (m-80) cc_final: 0.8247 (m-10) REVERT: A 329 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7970 (m-80) REVERT: A 773 GLU cc_start: 0.8848 (tt0) cc_final: 0.8518 (tt0) REVERT: A 1002 GLN cc_start: 0.9195 (tp40) cc_final: 0.8800 (tp40) REVERT: A 1010 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8564 (mp10) REVERT: B 88 ASP cc_start: 0.9170 (m-30) cc_final: 0.8778 (p0) REVERT: B 153 MET cc_start: 0.6070 (ptt) cc_final: 0.5076 (pmt) REVERT: B 369 TYR cc_start: 0.8748 (t80) cc_final: 0.8411 (t80) REVERT: B 370 ASN cc_start: 0.8996 (m-40) cc_final: 0.8118 (p0) REVERT: B 425 LEU cc_start: 0.6501 (mm) cc_final: 0.6214 (mp) REVERT: B 451 TYR cc_start: 0.6240 (m-80) cc_final: 0.5931 (m-80) REVERT: B 740 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8372 (tmm) REVERT: C 130 VAL cc_start: 0.8424 (t) cc_final: 0.8100 (p) REVERT: C 245 HIS cc_start: 0.6644 (OUTLIER) cc_final: 0.6149 (m-70) REVERT: E 140 GLU cc_start: 0.1026 (OUTLIER) cc_final: 0.0641 (tt0) REVERT: E 323 MET cc_start: 0.4074 (mpp) cc_final: 0.3792 (mpp) REVERT: E 553 LYS cc_start: 0.7244 (mptt) cc_final: 0.7022 (ttpt) REVERT: E 559 ARG cc_start: 0.7769 (ptm-80) cc_final: 0.7533 (ttp80) REVERT: E 579 MET cc_start: 0.6357 (tpp) cc_final: 0.5797 (tpt) REVERT: E 606 TRP cc_start: 0.1932 (p90) cc_final: 0.1573 (p90) REVERT: E 613 TYR cc_start: 0.4948 (t80) cc_final: 0.4579 (m-10) outliers start: 35 outliers final: 15 residues processed: 138 average time/residue: 0.5920 time to fit residues: 99.0007 Evaluate side-chains 127 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 288 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 232 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 284 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN C1002 GLN ** C1010 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 = 0.4521 r_free = 0.4521 target = 0.136258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.095336 restraints weight = 103013.399| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 5.22 r_work: 0.2979 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29345 Z= 0.125 Angle : 0.533 11.522 40059 Z= 0.262 Chirality : 0.043 0.274 4653 Planarity : 0.003 0.037 5070 Dihedral : 4.880 53.113 5105 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.87 % Allowed : 10.63 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.72 (0.14), residues: 3465 helix: 2.29 (0.16), residues: 1019 sheet: -0.07 (0.19), residues: 668 loop : -0.34 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 567 TYR 0.017 0.001 TYR B 351 PHE 0.019 0.001 PHE A 157 TRP 0.031 0.001 TRP C 353 HIS 0.003 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00278 (29241) covalent geometry : angle 0.51045 (39787) SS BOND : bond 0.00221 ( 40) SS BOND : angle 0.79781 ( 80) hydrogen bonds : bond 0.03870 ( 1148) hydrogen bonds : angle 5.00079 ( 3228) link_BETA1-4 : bond 0.00275 ( 18) link_BETA1-4 : angle 0.93518 ( 54) link_NAG-ASN : bond 0.00557 ( 46) link_NAG-ASN : angle 2.59042 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 1.076 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 153 MET cc_start: 0.5363 (ptt) cc_final: 0.5038 (ppp) REVERT: A 168 PHE cc_start: 0.8254 (t80) cc_final: 0.7899 (t80) REVERT: A 170 TYR cc_start: 0.8675 (t80) cc_final: 0.8465 (t80) REVERT: A 200 TYR cc_start: 0.8540 (m-80) cc_final: 0.8286 (m-10) REVERT: A 773 GLU cc_start: 0.8831 (tt0) cc_final: 0.8503 (tt0) REVERT: A 1002 GLN cc_start: 0.9185 (tp40) cc_final: 0.8761 (tp40) REVERT: B 54 LEU cc_start: 0.9549 (mm) cc_final: 0.9031 (tp) REVERT: B 88 ASP cc_start: 0.9174 (m-30) cc_final: 0.8520 (p0) REVERT: B 153 MET cc_start: 0.6158 (ptt) cc_final: 0.5093 (pmt) REVERT: B 369 TYR cc_start: 0.8668 (t80) cc_final: 0.8329 (t80) REVERT: B 370 ASN cc_start: 0.8992 (m-40) cc_final: 0.8067 (p0) REVERT: B 425 LEU cc_start: 0.6435 (mm) cc_final: 0.6173 (mp) REVERT: B 451 TYR cc_start: 0.6336 (m-80) cc_final: 0.5954 (m-80) REVERT: C 130 VAL cc_start: 0.8452 (t) cc_final: 0.8150 (p) REVERT: C 245 HIS cc_start: 0.6599 (OUTLIER) cc_final: 0.6023 (m-70) REVERT: E 140 GLU cc_start: 0.0821 (OUTLIER) cc_final: 0.0344 (mt-10) REVERT: E 559 ARG cc_start: 0.7780 (ptm-80) cc_final: 0.7510 (ttp80) REVERT: E 579 MET cc_start: 0.6393 (tpp) cc_final: 0.5755 (tpt) REVERT: E 606 TRP cc_start: 0.2061 (p90) cc_final: 0.1639 (p90) REVERT: E 613 TYR cc_start: 0.4826 (t80) cc_final: 0.4468 (m-10) outliers start: 27 outliers final: 11 residues processed: 128 average time/residue: 0.5996 time to fit residues: 92.5947 Evaluate side-chains 117 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 195 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 319 optimal weight: 0.4980 chunk 158 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 346 optimal weight: 4.9990 chunk 124 optimal weight: 20.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.124854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.071119 restraints weight = 84600.846| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 4.60 r_work: 0.2981 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29345 Z= 0.172 Angle : 0.543 11.130 40059 Z= 0.268 Chirality : 0.043 0.268 4653 Planarity : 0.003 0.041 5070 Dihedral : 4.818 54.126 5105 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.91 % Allowed : 10.79 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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 (0.14), residues: 3465 helix: 2.30 (0.16), residues: 1026 sheet: -0.06 (0.19), residues: 690 loop : -0.34 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 452 TYR 0.025 0.001 TYR E 497 PHE 0.023 0.001 PHE A 201 TRP 0.021 0.001 TRP C 353 HIS 0.004 0.001 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00388 (29241) covalent geometry : angle 0.52027 (39787) SS BOND : bond 0.00175 ( 40) SS BOND : angle 0.72146 ( 80) hydrogen bonds : bond 0.03891 ( 1148) hydrogen bonds : angle 4.98243 ( 3228) link_BETA1-4 : bond 0.00235 ( 18) link_BETA1-4 : angle 1.04814 ( 54) link_NAG-ASN : bond 0.00584 ( 46) link_NAG-ASN : angle 2.58449 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 1.186 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 95 THR cc_start: 0.7945 (p) cc_final: 0.7736 (p) REVERT: A 153 MET cc_start: 0.5437 (ptt) cc_final: 0.5112 (ppp) REVERT: A 168 PHE cc_start: 0.8232 (t80) cc_final: 0.7889 (t80) REVERT: A 200 TYR cc_start: 0.8527 (m-80) cc_final: 0.8269 (m-10) REVERT: A 697 MET cc_start: 0.9041 (ptm) cc_final: 0.8801 (ptm) REVERT: A 773 GLU cc_start: 0.8799 (tt0) cc_final: 0.8460 (tt0) REVERT: A 1002 GLN cc_start: 0.9165 (tp40) cc_final: 0.8726 (tp40) REVERT: B 88 ASP cc_start: 0.9171 (m-30) cc_final: 0.8674 (p0) REVERT: B 153 MET cc_start: 0.5894 (ptt) cc_final: 0.5049 (pmt) REVERT: B 369 TYR cc_start: 0.8745 (t80) cc_final: 0.8390 (t80) REVERT: B 370 ASN cc_start: 0.9002 (m-40) cc_final: 0.8121 (p0) REVERT: B 425 LEU cc_start: 0.6455 (mm) cc_final: 0.6194 (mp) REVERT: B 451 TYR cc_start: 0.6244 (m-80) cc_final: 0.5966 (m-80) REVERT: C 130 VAL cc_start: 0.8363 (t) cc_final: 0.8061 (p) REVERT: C 245 HIS cc_start: 0.6725 (OUTLIER) cc_final: 0.6180 (m-70) REVERT: C 324 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8091 (pm20) REVERT: E 140 GLU cc_start: 0.1027 (OUTLIER) cc_final: 0.0562 (mt-10) REVERT: E 559 ARG cc_start: 0.7781 (ptm-80) cc_final: 0.7518 (ttp80) REVERT: E 579 MET cc_start: 0.6435 (tpp) cc_final: 0.5851 (tpt) REVERT: E 606 TRP cc_start: 0.2254 (p90) cc_final: 0.1912 (p90) REVERT: E 613 TYR cc_start: 0.4966 (t80) cc_final: 0.4606 (m-10) outliers start: 28 outliers final: 12 residues processed: 131 average time/residue: 0.5646 time to fit residues: 89.2019 Evaluate side-chains 119 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 304 optimal weight: 7.9990 chunk 213 optimal weight: 0.0070 chunk 146 optimal weight: 0.9980 chunk 188 optimal weight: 9.9990 chunk 308 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 225 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 318 optimal weight: 5.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 613 GLN ** C1010 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 = 0.4527 r_free = 0.4527 target = 0.136679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.096136 restraints weight = 103289.042| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 5.23 r_work: 0.3005 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 29345 Z= 0.104 Angle : 0.516 11.058 40059 Z= 0.254 Chirality : 0.043 0.277 4653 Planarity : 0.003 0.038 5070 Dihedral : 4.589 53.834 5105 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.68 % Allowed : 11.14 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.89 (0.14), residues: 3465 helix: 2.40 (0.16), residues: 1028 sheet: -0.04 (0.20), residues: 671 loop : -0.20 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 452 TYR 0.027 0.001 TYR A 170 PHE 0.017 0.001 PHE A 201 TRP 0.021 0.001 TRP E 594 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00228 (29241) covalent geometry : angle 0.49574 (39787) SS BOND : bond 0.00135 ( 40) SS BOND : angle 0.62302 ( 80) hydrogen bonds : bond 0.03557 ( 1148) hydrogen bonds : angle 4.80401 ( 3228) link_BETA1-4 : bond 0.00331 ( 18) link_BETA1-4 : angle 0.87214 ( 54) link_NAG-ASN : bond 0.00530 ( 46) link_NAG-ASN : angle 2.45090 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.280 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 153 MET cc_start: 0.5701 (ptt) cc_final: 0.5406 (ppp) REVERT: A 168 PHE cc_start: 0.8225 (t80) cc_final: 0.7963 (t80) REVERT: A 170 TYR cc_start: 0.8666 (t80) cc_final: 0.8464 (t80) REVERT: A 200 TYR cc_start: 0.8554 (m-80) cc_final: 0.8282 (m-10) REVERT: A 773 GLU cc_start: 0.8821 (tt0) cc_final: 0.8501 (tt0) REVERT: A 1002 GLN cc_start: 0.9160 (tp40) cc_final: 0.8719 (tp40) REVERT: B 88 ASP cc_start: 0.9184 (m-30) cc_final: 0.8642 (p0) REVERT: B 153 MET cc_start: 0.5919 (ptt) cc_final: 0.5032 (pmt) REVERT: B 369 TYR cc_start: 0.8618 (t80) cc_final: 0.8291 (t80) REVERT: B 370 ASN cc_start: 0.9011 (m-40) cc_final: 0.8076 (p0) REVERT: B 425 LEU cc_start: 0.6458 (mm) cc_final: 0.6187 (mp) REVERT: B 451 TYR cc_start: 0.6510 (m-80) cc_final: 0.6098 (m-80) REVERT: C 130 VAL cc_start: 0.8439 (t) cc_final: 0.8152 (p) REVERT: C 173 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7317 (tm-30) REVERT: C 324 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8330 (pm20) REVERT: C 353 TRP cc_start: 0.5079 (p-90) cc_final: 0.4795 (p-90) REVERT: E 376 MET cc_start: 0.2045 (mmp) cc_final: 0.1442 (mpp) REVERT: E 553 LYS cc_start: 0.7149 (mptt) cc_final: 0.6846 (ttpt) REVERT: E 559 ARG cc_start: 0.7844 (ptm-80) cc_final: 0.7552 (ttp80) REVERT: E 579 MET cc_start: 0.6472 (tpp) cc_final: 0.5853 (tpt) REVERT: E 606 TRP cc_start: 0.2237 (p90) cc_final: 0.1831 (p90) REVERT: E 613 TYR cc_start: 0.4891 (t80) cc_final: 0.4514 (m-10) outliers start: 21 outliers final: 10 residues processed: 134 average time/residue: 0.6784 time to fit residues: 108.0333 Evaluate side-chains 119 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 25 optimal weight: 0.0570 chunk 121 optimal weight: 7.9990 chunk 266 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 6 optimal weight: 4.9990 chunk 242 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 301 optimal weight: 20.0000 overall best weight: 1.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.124176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.071645 restraints weight = 86058.229| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 4.23 r_work: 0.3003 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29345 Z= 0.135 Angle : 0.532 11.117 40059 Z= 0.263 Chirality : 0.043 0.272 4653 Planarity : 0.003 0.044 5070 Dihedral : 4.574 54.604 5105 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.65 % Allowed : 11.47 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.90 (0.14), residues: 3465 helix: 2.39 (0.16), residues: 1043 sheet: 0.00 (0.19), residues: 693 loop : -0.23 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 452 TYR 0.023 0.001 TYR A 170 PHE 0.018 0.001 PHE A 106 TRP 0.038 0.001 TRP E 473 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00304 (29241) covalent geometry : angle 0.51105 (39787) SS BOND : bond 0.00136 ( 40) SS BOND : angle 0.79270 ( 80) hydrogen bonds : bond 0.03675 ( 1148) hydrogen bonds : angle 4.81362 ( 3228) link_BETA1-4 : bond 0.00233 ( 18) link_BETA1-4 : angle 1.00675 ( 54) link_NAG-ASN : bond 0.00535 ( 46) link_NAG-ASN : angle 2.46537 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 1.356 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 153 MET cc_start: 0.5615 (ptt) cc_final: 0.5350 (ppp) REVERT: A 168 PHE cc_start: 0.8210 (t80) cc_final: 0.7989 (t80) REVERT: A 200 TYR cc_start: 0.8577 (m-80) cc_final: 0.8326 (m-10) REVERT: A 773 GLU cc_start: 0.8838 (tt0) cc_final: 0.8476 (tt0) REVERT: A 1002 GLN cc_start: 0.9167 (tp40) cc_final: 0.8714 (tp40) REVERT: B 88 ASP cc_start: 0.9171 (m-30) cc_final: 0.8635 (p0) REVERT: B 153 MET cc_start: 0.6086 (ptt) cc_final: 0.5217 (pmt) REVERT: B 369 TYR cc_start: 0.8669 (t80) cc_final: 0.8334 (t80) REVERT: B 370 ASN cc_start: 0.9022 (m-40) cc_final: 0.8106 (p0) REVERT: B 425 LEU cc_start: 0.6355 (mm) cc_final: 0.6086 (mp) REVERT: B 451 TYR cc_start: 0.6405 (m-80) cc_final: 0.5976 (m-80) REVERT: C 130 VAL cc_start: 0.8320 (t) cc_final: 0.8043 (p) REVERT: C 173 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7326 (tm-30) REVERT: C 324 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8239 (pm20) REVERT: E 553 LYS cc_start: 0.7154 (mptt) cc_final: 0.6873 (ttpt) REVERT: E 559 ARG cc_start: 0.7777 (ptm-80) cc_final: 0.7531 (ttp-110) REVERT: E 579 MET cc_start: 0.6589 (tpp) cc_final: 0.6137 (tpt) REVERT: E 606 TRP cc_start: 0.2381 (p90) cc_final: 0.2060 (p90) REVERT: E 613 TYR cc_start: 0.4947 (t80) cc_final: 0.4587 (m-10) outliers start: 20 outliers final: 11 residues processed: 120 average time/residue: 0.6423 time to fit residues: 93.0307 Evaluate side-chains 115 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 320 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 196 optimal weight: 6.9990 chunk 329 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 613 GLN ** C1010 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 = 0.4494 r_free = 0.4494 target = 0.133993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.093175 restraints weight = 102204.347| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 4.88 r_work: 0.2945 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 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 : 0.006 0.054 29345 Z= 0.262 Angle : 0.624 11.413 40059 Z= 0.308 Chirality : 0.046 0.257 4653 Planarity : 0.004 0.051 5070 Dihedral : 5.072 55.604 5105 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.62 % Allowed : 11.69 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.65 (0.14), residues: 3465 helix: 2.18 (0.16), residues: 1044 sheet: -0.22 (0.19), residues: 720 loop : -0.33 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 452 TYR 0.024 0.002 TYR A 904 PHE 0.026 0.002 PHE C 106 TRP 0.032 0.002 TRP C 353 HIS 0.005 0.001 HIS E 345 Details of bonding type rmsd covalent geometry : bond 0.00591 (29241) covalent geometry : angle 0.60179 (39787) SS BOND : bond 0.00236 ( 40) SS BOND : angle 0.89912 ( 80) hydrogen bonds : bond 0.04329 ( 1148) hydrogen bonds : angle 5.11727 ( 3228) link_BETA1-4 : bond 0.00246 ( 18) link_BETA1-4 : angle 1.26802 ( 54) link_NAG-ASN : bond 0.00684 ( 46) link_NAG-ASN : angle 2.70951 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5873 (ptt) cc_final: 0.5612 (ppp) REVERT: A 168 PHE cc_start: 0.8382 (t80) cc_final: 0.8092 (t80) REVERT: A 170 TYR cc_start: 0.8735 (t80) cc_final: 0.8522 (t80) REVERT: A 200 TYR cc_start: 0.8635 (m-80) cc_final: 0.8427 (m-10) REVERT: A 773 GLU cc_start: 0.8838 (tt0) cc_final: 0.8496 (tt0) REVERT: A 1002 GLN cc_start: 0.9262 (tp40) cc_final: 0.8844 (tp40) REVERT: B 88 ASP cc_start: 0.9142 (m-30) cc_final: 0.8658 (p0) REVERT: B 153 MET cc_start: 0.6248 (ptt) cc_final: 0.5375 (pmt) REVERT: B 369 TYR cc_start: 0.8697 (t80) cc_final: 0.8375 (t80) REVERT: B 370 ASN cc_start: 0.9013 (m-40) cc_final: 0.8045 (p0) REVERT: B 425 LEU cc_start: 0.6430 (mm) cc_final: 0.6174 (mp) REVERT: B 451 TYR cc_start: 0.6260 (m-80) cc_final: 0.5879 (m-80) REVERT: C 130 VAL cc_start: 0.8411 (t) cc_final: 0.8103 (p) REVERT: C 173 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7587 (tm-30) REVERT: E 360 MET cc_start: 0.0772 (mpm) cc_final: 0.0476 (mpt) REVERT: E 376 MET cc_start: 0.1573 (mmp) cc_final: 0.0872 (mpp) REVERT: E 516 TYR cc_start: 0.4419 (OUTLIER) cc_final: 0.4177 (t80) REVERT: E 553 LYS cc_start: 0.7007 (mptt) cc_final: 0.6730 (ttpt) REVERT: E 559 ARG cc_start: 0.7953 (ptm-80) cc_final: 0.7564 (ttp-110) REVERT: E 579 MET cc_start: 0.6453 (tpp) cc_final: 0.5790 (tpt) REVERT: E 606 TRP cc_start: 0.2076 (p90) cc_final: 0.1666 (p90) REVERT: E 613 TYR cc_start: 0.4736 (t80) cc_final: 0.4372 (m-10) outliers start: 19 outliers final: 11 residues processed: 114 average time/residue: 0.6169 time to fit residues: 84.4879 Evaluate side-chains 111 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 516 TYR Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 30 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 185 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 119 optimal weight: 20.0000 chunk 164 optimal weight: 0.9980 chunk 275 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.134829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.094181 restraints weight = 102675.633| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 5.19 r_work: 0.2969 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 29345 Z= 0.165 Angle : 0.562 12.718 40059 Z= 0.277 Chirality : 0.044 0.325 4653 Planarity : 0.003 0.046 5070 Dihedral : 4.917 54.539 5105 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.45 % Allowed : 11.82 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.71 (0.14), residues: 3465 helix: 2.32 (0.16), residues: 1030 sheet: -0.35 (0.19), residues: 696 loop : -0.26 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 452 TYR 0.018 0.001 TYR A 904 PHE 0.017 0.001 PHE A 106 TRP 0.030 0.002 TRP E 473 HIS 0.004 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00373 (29241) covalent geometry : angle 0.54180 (39787) SS BOND : bond 0.00145 ( 40) SS BOND : angle 0.79166 ( 80) hydrogen bonds : bond 0.03883 ( 1148) hydrogen bonds : angle 4.94640 ( 3228) link_BETA1-4 : bond 0.00238 ( 18) link_BETA1-4 : angle 0.96883 ( 54) link_NAG-ASN : bond 0.00541 ( 46) link_NAG-ASN : angle 2.53644 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16502.28 seconds wall clock time: 280 minutes 3.72 seconds (16803.72 seconds total)