Starting phenix.real_space_refine on Fri Feb 6 20:09:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d0d_30531/02_2026/7d0d_30531.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d0d_30531/02_2026/7d0d_30531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d0d_30531/02_2026/7d0d_30531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d0d_30531/02_2026/7d0d_30531.map" model { file = "/net/cci-nas-00/data/ceres_data/7d0d_30531/02_2026/7d0d_30531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d0d_30531/02_2026/7d0d_30531.cif" } resolution = 3.8 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= 0.000 sd= 0.004 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 121 5.16 5 C 17873 2.51 5 N 4562 2.21 5 O 5540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 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: 28096 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 8 Chain: "C" Number of atoms: 7696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7696 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 47, 'TRANS': 934} Chain breaks: 11 Chain: "H" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "L" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 880 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "G" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "F" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 880 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "B" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "Z" 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: 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.28, per 1000 atoms: 0.22 Number of scatterers: 28096 At special positions: 0 Unit cell: (136.962, 169.572, 221.748, 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 121 16.00 O 5540 8.00 N 4562 7.00 C 17873 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.64 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.17 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 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=1.98 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.78 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B 709 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 343 " " NAG C1407 " - " ASN C 603 " " NAG C1408 " - " ASN C 616 " " NAG C1409 " - " ASN C 657 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG I 1 " - " ASN A 709 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1074 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN C 331 " " NAG Q 1 " - " ASN C 709 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " " NAG V 1 " - " ASN B 331 " " NAG W 1 " - " ASN B 343 " " NAG X 1 " - " ASN B 717 " " NAG Y 1 " - " ASN B 801 " " NAG Z 1 " - " ASN B1074 " " NAG a 1 " - " ASN B1098 " " NAG b 1 " - " ASN B1134 " " NAG c 1 " - " ASN C1074 " Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.2 seconds 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6500 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 60 sheets defined 21.0% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.256A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.625A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.582A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.717A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) 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: 3.561A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.604A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.590A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.355A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (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 977 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.220A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.641A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.965A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.010A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.372A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'H' and resid 103 through 106 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 103 through 106 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.625A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.631A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.771A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.634A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.647A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.574A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.995A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.626A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.878A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.632A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.151A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 10.527A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.757A pdb=" N THR A 274 " --> pdb=" O CYS A 291 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS A 291 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.248A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.666A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 543 Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.878A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.231A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 removed outlier: 6.914A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.568A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.810A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.539A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.074A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.444A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.649A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.780A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.572A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.673A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AC8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.219A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.578A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 788 through 790 removed outlier: 5.732A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AD6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AD7, first strand: chain 'H' and resid 59 through 61 removed outlier: 6.307A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU H 52 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL H 36 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR H 54 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL H 34 " --> pdb=" O TYR H 54 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 69 through 74 Processing sheet with id=AD9, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AE1, first strand: chain 'L' and resid 11 through 14 removed outlier: 5.718A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LYS L 113 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL L 13 " --> pdb=" O LYS L 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'L' and resid 19 through 20 removed outlier: 3.881A pdb=" N ILE L 81 " --> pdb=" O ALA L 19 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 59 through 60 removed outlier: 6.595A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 5 through 7 Processing sheet with id=AE5, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AE6, first strand: chain 'G' and resid 59 through 61 removed outlier: 6.307A pdb=" N TRP G 38 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU G 52 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL G 36 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR G 54 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL G 34 " --> pdb=" O TYR G 54 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 69 through 74 Processing sheet with id=AE8, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AE9, first strand: chain 'F' and resid 11 through 14 removed outlier: 5.718A pdb=" N LEU F 11 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LYS F 113 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL F 13 " --> pdb=" O LYS F 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.881A pdb=" N ILE F 81 " --> pdb=" O ALA F 19 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 59 through 60 removed outlier: 6.596A pdb=" N TRP F 41 " --> pdb=" O LEU F 53 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.569A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AF6, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.732A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 309 through 319 removed outlier: 6.678A pdb=" N GLU B 309 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY B 601 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.542A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AG2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.256A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) 994 hydrogen bonds defined for protein. 2688 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: 6.09 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8661 1.34 - 1.46: 7456 1.46 - 1.59: 12440 1.59 - 1.72: 0 1.72 - 1.84: 154 Bond restraints: 28711 Sorted by residual: bond pdb=" C THR A 588 " pdb=" N PRO A 589 " ideal model delta sigma weight residual 1.332 1.389 -0.057 1.34e-02 5.57e+03 1.80e+01 bond pdb=" C HIS C1088 " pdb=" N PHE C1089 " ideal model delta sigma weight residual 1.331 1.265 0.067 1.59e-02 3.96e+03 1.75e+01 bond pdb=" N PRO A 589 " pdb=" CD PRO A 589 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.65e+01 bond pdb=" N PRO F 101 " pdb=" CD PRO F 101 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" N PRO L 101 " pdb=" CD PRO L 101 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.63e+01 ... (remaining 28706 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 38115 2.76 - 5.53: 869 5.53 - 8.29: 64 8.29 - 11.05: 8 11.05 - 13.82: 4 Bond angle restraints: 39060 Sorted by residual: angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.84 -11.30 1.91e+00 2.74e-01 3.50e+01 angle pdb=" N GLU A 156 " pdb=" CA GLU A 156 " pdb=" C GLU A 156 " ideal model delta sigma weight residual 108.45 115.82 -7.37 1.26e+00 6.30e-01 3.42e+01 angle pdb=" C THR A 588 " pdb=" N PRO A 589 " pdb=" CA PRO A 589 " ideal model delta sigma weight residual 119.78 114.06 5.72 1.03e+00 9.43e-01 3.08e+01 angle pdb=" C LEU C 212 " pdb=" N VAL C 213 " pdb=" CA VAL C 213 " ideal model delta sigma weight residual 123.08 117.61 5.47 1.01e+00 9.80e-01 2.93e+01 angle pdb=" C SER B 31 " pdb=" N PHE B 32 " pdb=" CA PHE B 32 " ideal model delta sigma weight residual 122.56 115.26 7.30 1.50e+00 4.44e-01 2.37e+01 ... (remaining 39055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 15482 17.91 - 35.82: 1760 35.82 - 53.73: 529 53.73 - 71.64: 173 71.64 - 89.55: 56 Dihedral angle restraints: 18000 sinusoidal: 7907 harmonic: 10093 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual 93.00 12.13 80.87 1 1.00e+01 1.00e-02 8.08e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 19.60 73.40 1 1.00e+01 1.00e-02 6.86e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.09 71.91 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 17997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 4641 0.328 - 0.656: 3 0.656 - 0.984: 4 0.984 - 1.312: 0 1.312 - 1.640: 1 Chirality restraints: 4649 Sorted by residual: chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-01 2.50e+01 6.73e+01 chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 1.98e+01 ... (remaining 4646 not shown) Planarity restraints: 4980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.133 2.00e-02 2.50e+03 1.86e-01 4.33e+02 pdb=" CG ASN A 331 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.327 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.209 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " -0.060 5.00e-02 4.00e+02 9.15e-02 1.34e+01 pdb=" N PRO A 527 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1134 " 0.022 2.00e-02 2.50e+03 3.15e-02 1.24e+01 pdb=" CG ASN A1134 " -0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN A1134 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A1134 " -0.056 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.034 2.00e-02 2.50e+03 ... (remaining 4977 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 343 2.57 - 3.15: 22049 3.15 - 3.73: 41810 3.73 - 4.32: 61132 4.32 - 4.90: 100994 Nonbonded interactions: 226328 Sorted by model distance: nonbonded pdb=" NH1 ARG B 346 " pdb=" O PHE B 347 " model vdw 1.982 3.120 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.982 3.120 nonbonded pdb=" O SER H 110 " pdb=" CD1 TRP H 111 " model vdw 2.020 3.260 nonbonded pdb=" O SER G 110 " pdb=" CD1 TRP G 111 " model vdw 2.020 3.260 nonbonded pdb=" O SER G 110 " pdb=" CG TRP G 111 " model vdw 2.033 3.260 ... (remaining 226323 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 826 or resid 855 through 1408)) selection = (chain 'B' and (resid 27 through 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 620 or resid 641 through 939 or resid 944 through 14 \ 08)) selection = (chain 'C' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.570 Find NCS groups from input model: 0.810 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 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 : 0.012 0.747 28823 Z= 0.565 Angle : 1.227 48.978 39354 Z= 0.643 Chirality : 0.071 1.640 4649 Planarity : 0.007 0.091 4932 Dihedral : 17.646 89.551 11374 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 1.12 % Allowed : 9.59 % Favored : 89.29 % Rotamer: Outliers : 11.01 % Allowed : 18.07 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.87 (0.12), residues: 3400 helix: -2.12 (0.17), residues: 647 sheet: -2.15 (0.16), residues: 847 loop : -3.02 (0.12), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1039 TYR 0.026 0.003 TYR C1067 PHE 0.035 0.003 PHE G 24 TRP 0.025 0.003 TRP B 104 HIS 0.009 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.01098 (28711) covalent geometry : angle 1.03047 (39060) SS BOND : bond 0.15077 ( 42) SS BOND : angle 9.59153 ( 84) hydrogen bonds : bond 0.20428 ( 956) hydrogen bonds : angle 8.12601 ( 2688) link_BETA1-4 : bond 0.04167 ( 22) link_BETA1-4 : angle 4.32547 ( 66) link_NAG-ASN : bond 0.02929 ( 48) link_NAG-ASN : angle 7.81963 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 335 poor density : 486 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 SER cc_start: 0.7524 (OUTLIER) cc_final: 0.6088 (p) REVERT: A 587 ILE cc_start: 0.9124 (mt) cc_final: 0.8881 (mt) REVERT: A 975 SER cc_start: 0.8796 (OUTLIER) cc_final: 0.8465 (p) REVERT: C 52 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8015 (tm-30) REVERT: C 317 ASN cc_start: 0.8275 (m110) cc_final: 0.7944 (t0) REVERT: C 409 GLN cc_start: 0.5335 (OUTLIER) cc_final: 0.4898 (tp40) REVERT: C 869 MET cc_start: 0.7832 (mtt) cc_final: 0.7571 (mtt) REVERT: C 1050 MET cc_start: 0.8145 (ptm) cc_final: 0.7906 (ptm) REVERT: L 66 ASP cc_start: 0.6990 (m-30) cc_final: 0.6588 (p0) REVERT: F 97 TYR cc_start: 0.0242 (t80) cc_final: -0.0189 (t80) REVERT: B 81 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.7987 (m110) REVERT: B 459 SER cc_start: 0.1990 (OUTLIER) cc_final: 0.1642 (p) REVERT: B 692 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8202 (mm) REVERT: B 1051 SER cc_start: 0.9365 (m) cc_final: 0.8869 (p) REVERT: B 1077 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8863 (m) outliers start: 335 outliers final: 70 residues processed: 753 average time/residue: 0.1783 time to fit residues: 213.5477 Evaluate side-chains 261 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 183 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 66 HIS ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN A 188 ASN A 207 HIS A 211 ASN A 280 ASN A 321 GLN A 394 ASN A 422 ASN A 450 ASN A 606 ASN A 641 ASN A 690 GLN A 703 ASN A 751 ASN A 901 GLN A 914 ASN A 926 GLN A 992 GLN A1071 GLN A1101 HIS A1135 ASN C 66 HIS C 115 GLN C 188 ASN C 422 ASN C 487 ASN C 540 ASN C 563 GLN ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 914 ASN C 919 ASN C 920 GLN C 954 GLN C 992 GLN C1054 GLN L 6 GLN L 95 GLN ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 HIS ** G 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN F 95 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 115 GLN B 134 GLN B 137 ASN B 239 GLN B 422 ASN B 437 ASN B 440 ASN B 498 GLN B 644 GLN B 658 ASN B 690 GLN B 703 ASN B 764 ASN B 856 ASN B 901 GLN B 907 ASN B 914 ASN B 919 ASN B 955 ASN B 969 ASN B 992 GLN B1011 GLN Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.110199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.072191 restraints weight = 87888.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.073157 restraints weight = 63011.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.073456 restraints weight = 38880.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.073890 restraints weight = 34662.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.074004 restraints weight = 32019.817| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 28823 Z= 0.236 Angle : 0.866 14.419 39354 Z= 0.427 Chirality : 0.053 0.802 4649 Planarity : 0.006 0.061 4932 Dihedral : 9.691 86.499 5302 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.62 % Favored : 92.18 % Rotamer: Outliers : 5.39 % Allowed : 20.89 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.61 (0.13), residues: 3400 helix: -0.01 (0.20), residues: 649 sheet: -1.57 (0.16), residues: 833 loop : -2.52 (0.12), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 995 TYR 0.023 0.002 TYR B 453 PHE 0.029 0.002 PHE H 114 TRP 0.023 0.002 TRP G 117 HIS 0.006 0.001 HIS L 102 Details of bonding type rmsd covalent geometry : bond 0.00543 (28711) covalent geometry : angle 0.82913 (39060) SS BOND : bond 0.01060 ( 42) SS BOND : angle 2.73748 ( 84) hydrogen bonds : bond 0.05159 ( 956) hydrogen bonds : angle 6.26679 ( 2688) link_BETA1-4 : bond 0.00542 ( 22) link_BETA1-4 : angle 2.38343 ( 66) link_NAG-ASN : bond 0.00405 ( 48) link_NAG-ASN : angle 3.41079 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 192 time to evaluate : 1.048 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 221 SER cc_start: 0.9031 (OUTLIER) cc_final: 0.8723 (p) REVERT: A 353 TRP cc_start: 0.5599 (OUTLIER) cc_final: 0.4589 (p-90) REVERT: A 464 PHE cc_start: 0.7562 (m-80) cc_final: 0.7157 (m-80) REVERT: A 587 ILE cc_start: 0.9230 (mt) cc_final: 0.8745 (mt) REVERT: A 1005 GLN cc_start: 0.8696 (tp40) cc_final: 0.8472 (mm110) REVERT: C 104 TRP cc_start: 0.6666 (m-90) cc_final: 0.6187 (m-90) REVERT: C 467 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6884 (m-30) REVERT: C 740 MET cc_start: 0.7979 (mmm) cc_final: 0.7778 (mmm) REVERT: C 784 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7844 (mm-40) REVERT: C 1050 MET cc_start: 0.7700 (ptm) cc_final: 0.7332 (ptm) REVERT: H 72 THR cc_start: 0.2621 (OUTLIER) cc_final: 0.2151 (m) REVERT: H 87 MET cc_start: 0.0194 (ttm) cc_final: -0.0476 (mtt) REVERT: H 100 SER cc_start: -0.1026 (OUTLIER) cc_final: -0.1731 (t) REVERT: H 114 PHE cc_start: 0.1985 (m-10) cc_final: 0.1693 (m-10) REVERT: L 66 ASP cc_start: 0.6838 (m-30) cc_final: 0.6419 (p0) REVERT: B 90 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8276 (p) REVERT: B 101 ILE cc_start: 0.8437 (mm) cc_final: 0.8172 (mp) REVERT: B 153 MET cc_start: 0.0629 (mpp) cc_final: 0.0410 (mpp) REVERT: B 398 ASP cc_start: 0.3005 (OUTLIER) cc_final: 0.2035 (m-30) REVERT: B 546 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7303 (tp) REVERT: B 979 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7917 (t0) outliers start: 164 outliers final: 86 residues processed: 340 average time/residue: 0.1549 time to fit residues: 89.2831 Evaluate side-chains 239 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 144 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1114 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 286 optimal weight: 7.9990 chunk 223 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 340 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 302 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 190 optimal weight: 0.5980 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 498 GLN C 66 HIS C 703 ASN C 804 GLN C 913 GLN C 935 GLN C1135 ASN L 37 ASN L 95 GLN ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 824 ASN B1135 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.107245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.068752 restraints weight = 87826.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.071000 restraints weight = 53196.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.070992 restraints weight = 31484.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.071466 restraints weight = 29462.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.071500 restraints weight = 27693.412| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 28823 Z= 0.224 Angle : 0.783 13.389 39354 Z= 0.383 Chirality : 0.051 0.770 4649 Planarity : 0.005 0.057 4932 Dihedral : 8.530 75.669 5234 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.41 % Favored : 92.41 % Rotamer: Outliers : 5.29 % Allowed : 21.19 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.04 (0.13), residues: 3400 helix: 0.71 (0.21), residues: 658 sheet: -1.38 (0.16), residues: 830 loop : -2.17 (0.12), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 40 TYR 0.027 0.002 TYR C 200 PHE 0.026 0.002 PHE H 114 TRP 0.042 0.002 TRP H 111 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00529 (28711) covalent geometry : angle 0.74870 (39060) SS BOND : bond 0.01028 ( 42) SS BOND : angle 2.55245 ( 84) hydrogen bonds : bond 0.04874 ( 956) hydrogen bonds : angle 5.84032 ( 2688) link_BETA1-4 : bond 0.00515 ( 22) link_BETA1-4 : angle 2.39569 ( 66) link_NAG-ASN : bond 0.00401 ( 48) link_NAG-ASN : angle 3.00201 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 160 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8290 (m-30) REVERT: A 301 CYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6911 (m) REVERT: A 429 PHE cc_start: 0.8222 (t80) cc_final: 0.7856 (t80) REVERT: A 464 PHE cc_start: 0.7461 (m-80) cc_final: 0.7003 (m-80) REVERT: A 505 TYR cc_start: 0.7290 (t80) cc_final: 0.6682 (t80) REVERT: A 1005 GLN cc_start: 0.8716 (tp40) cc_final: 0.8464 (mm110) REVERT: C 82 PRO cc_start: 0.7801 (Cg_exo) cc_final: 0.7565 (Cg_endo) REVERT: C 104 TRP cc_start: 0.6929 (m-90) cc_final: 0.6442 (m-90) REVERT: C 214 ARG cc_start: 0.1171 (OUTLIER) cc_final: -0.0166 (mtt180) REVERT: C 461 LEU cc_start: 0.7835 (tp) cc_final: 0.7308 (mp) REVERT: C 642 VAL cc_start: 0.9239 (OUTLIER) cc_final: 0.8881 (p) REVERT: C 740 MET cc_start: 0.8024 (mmm) cc_final: 0.7802 (tpt) REVERT: C 784 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8046 (mm-40) REVERT: C 1050 MET cc_start: 0.7635 (ptm) cc_final: 0.7369 (ptm) REVERT: H 39 ILE cc_start: 0.3889 (OUTLIER) cc_final: 0.3337 (mt) REVERT: L 37 ASN cc_start: 0.5642 (m-40) cc_final: 0.5402 (m110) REVERT: L 66 ASP cc_start: 0.6719 (m-30) cc_final: 0.6406 (p0) REVERT: L 97 TYR cc_start: 0.2179 (t80) cc_final: 0.1428 (t80) REVERT: B 153 MET cc_start: 0.1322 (mpp) cc_final: 0.0889 (mpp) REVERT: B 523 THR cc_start: 0.1550 (OUTLIER) cc_final: 0.1105 (m) REVERT: B 525 CYS cc_start: 0.6680 (OUTLIER) cc_final: 0.6002 (m) REVERT: B 584 ILE cc_start: 0.8494 (mm) cc_final: 0.8209 (mm) outliers start: 161 outliers final: 83 residues processed: 310 average time/residue: 0.1543 time to fit residues: 80.9087 Evaluate side-chains 216 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 126 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 10 optimal weight: 0.3980 chunk 121 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 201 optimal weight: 9.9990 chunk 186 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 38 optimal weight: 20.0000 chunk 145 optimal weight: 4.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 394 ASN A 414 GLN A 493 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 81 ASN B 450 ASN B1106 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.106277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.068444 restraints weight = 87741.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.070801 restraints weight = 53278.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.070354 restraints weight = 30579.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.070747 restraints weight = 28650.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.070735 restraints weight = 28089.740| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 28823 Z= 0.204 Angle : 0.742 11.861 39354 Z= 0.360 Chirality : 0.051 0.893 4649 Planarity : 0.004 0.057 4932 Dihedral : 8.003 59.402 5218 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.15 % Favored : 92.68 % Rotamer: Outliers : 4.93 % Allowed : 21.48 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.14), residues: 3400 helix: 0.96 (0.21), residues: 672 sheet: -1.12 (0.17), residues: 822 loop : -2.09 (0.13), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 509 TYR 0.019 0.001 TYR B1067 PHE 0.025 0.002 PHE A 456 TRP 0.047 0.002 TRP H 111 HIS 0.005 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00475 (28711) covalent geometry : angle 0.71217 (39060) SS BOND : bond 0.00778 ( 42) SS BOND : angle 1.95836 ( 84) hydrogen bonds : bond 0.04366 ( 956) hydrogen bonds : angle 5.66082 ( 2688) link_BETA1-4 : bond 0.00535 ( 22) link_BETA1-4 : angle 2.30036 ( 66) link_NAG-ASN : bond 0.00328 ( 48) link_NAG-ASN : angle 2.87988 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 136 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7956 (mttm) REVERT: A 287 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8286 (m-30) REVERT: A 301 CYS cc_start: 0.7302 (OUTLIER) cc_final: 0.7024 (m) REVERT: A 394 ASN cc_start: 0.7644 (OUTLIER) cc_final: 0.7374 (t0) REVERT: A 464 PHE cc_start: 0.7621 (m-80) cc_final: 0.7249 (m-80) REVERT: A 505 TYR cc_start: 0.7292 (t80) cc_final: 0.6438 (t80) REVERT: A 1005 GLN cc_start: 0.8654 (tp40) cc_final: 0.8368 (mm110) REVERT: C 104 TRP cc_start: 0.7093 (m-90) cc_final: 0.6748 (m-90) REVERT: C 214 ARG cc_start: 0.0971 (OUTLIER) cc_final: -0.0429 (mtt180) REVERT: C 461 LEU cc_start: 0.7990 (tp) cc_final: 0.7546 (mp) REVERT: C 740 MET cc_start: 0.8043 (mmm) cc_final: 0.7838 (tpt) REVERT: C 784 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8171 (mm-40) REVERT: C 912 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8851 (p) REVERT: C 1050 MET cc_start: 0.7588 (ptm) cc_final: 0.7348 (ptm) REVERT: H 100 SER cc_start: -0.0830 (OUTLIER) cc_final: -0.1230 (t) REVERT: H 114 PHE cc_start: 0.1342 (m-10) cc_final: 0.1016 (m-10) REVERT: L 21 ILE cc_start: -0.0049 (OUTLIER) cc_final: -0.0254 (tp) REVERT: L 58 SER cc_start: 0.2969 (OUTLIER) cc_final: 0.2621 (t) REVERT: L 66 ASP cc_start: 0.6605 (OUTLIER) cc_final: 0.6366 (p0) REVERT: B 153 MET cc_start: 0.1636 (mpp) cc_final: 0.1047 (mpp) REVERT: B 584 ILE cc_start: 0.8634 (mm) cc_final: 0.8307 (mm) outliers start: 150 outliers final: 100 residues processed: 277 average time/residue: 0.1594 time to fit residues: 76.2351 Evaluate side-chains 229 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 119 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1077 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 324 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 173 optimal weight: 0.6980 chunk 135 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 154 optimal weight: 5.9990 chunk 303 optimal weight: 2.9990 chunk 236 optimal weight: 8.9990 chunk 326 optimal weight: 0.9990 chunk 227 optimal weight: 50.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 ASN ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 81 ASN B 218 GLN B1088 HIS B1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.106347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.066637 restraints weight = 87202.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.068325 restraints weight = 46801.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.069382 restraints weight = 31440.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.070007 restraints weight = 24729.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.070337 restraints weight = 21315.736| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 28823 Z= 0.167 Angle : 0.699 11.720 39354 Z= 0.338 Chirality : 0.049 0.717 4649 Planarity : 0.004 0.056 4932 Dihedral : 7.764 59.021 5217 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.29 % Favored : 93.56 % Rotamer: Outliers : 4.53 % Allowed : 21.81 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.14), residues: 3400 helix: 1.23 (0.21), residues: 666 sheet: -0.96 (0.17), residues: 827 loop : -1.96 (0.13), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 408 TYR 0.020 0.001 TYR F 97 PHE 0.029 0.002 PHE A 456 TRP 0.045 0.002 TRP H 111 HIS 0.004 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00389 (28711) covalent geometry : angle 0.67093 (39060) SS BOND : bond 0.00526 ( 42) SS BOND : angle 1.78458 ( 84) hydrogen bonds : bond 0.04128 ( 956) hydrogen bonds : angle 5.51210 ( 2688) link_BETA1-4 : bond 0.00488 ( 22) link_BETA1-4 : angle 2.25183 ( 66) link_NAG-ASN : bond 0.00428 ( 48) link_NAG-ASN : angle 2.67712 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 128 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8026 (mmtt) REVERT: A 120 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8518 (m) REVERT: A 287 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8225 (m-30) REVERT: A 429 PHE cc_start: 0.8231 (t80) cc_final: 0.7806 (m-80) REVERT: A 464 PHE cc_start: 0.7502 (m-80) cc_final: 0.7083 (m-80) REVERT: A 505 TYR cc_start: 0.6973 (t80) cc_final: 0.6216 (t80) REVERT: A 1005 GLN cc_start: 0.8713 (tp40) cc_final: 0.8400 (mm110) REVERT: A 1037 SER cc_start: 0.9222 (t) cc_final: 0.9021 (p) REVERT: C 104 TRP cc_start: 0.7044 (m-90) cc_final: 0.6768 (m-90) REVERT: C 214 ARG cc_start: 0.0847 (OUTLIER) cc_final: -0.0526 (mtt180) REVERT: C 301 CYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6987 (m) REVERT: C 461 LEU cc_start: 0.7946 (tp) cc_final: 0.7615 (mp) REVERT: C 784 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8200 (mm-40) REVERT: C 912 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8917 (p) REVERT: C 1050 MET cc_start: 0.7685 (ptm) cc_final: 0.7464 (ptm) REVERT: H 100 SER cc_start: -0.0970 (OUTLIER) cc_final: -0.1330 (t) REVERT: H 114 PHE cc_start: 0.1525 (m-10) cc_final: 0.1185 (m-10) REVERT: L 66 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6701 (p0) REVERT: B 153 MET cc_start: 0.1902 (mpp) cc_final: 0.1225 (mpp) REVERT: B 523 THR cc_start: 0.1105 (OUTLIER) cc_final: 0.0493 (m) REVERT: B 525 CYS cc_start: 0.6446 (OUTLIER) cc_final: 0.6199 (m) REVERT: B 584 ILE cc_start: 0.8723 (mm) cc_final: 0.8399 (mm) outliers start: 138 outliers final: 102 residues processed: 258 average time/residue: 0.1438 time to fit residues: 64.5426 Evaluate side-chains 229 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 117 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 117 optimal weight: 9.9990 chunk 323 optimal weight: 2.9990 chunk 227 optimal weight: 50.0000 chunk 20 optimal weight: 5.9990 chunk 199 optimal weight: 30.0000 chunk 210 optimal weight: 8.9990 chunk 326 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 751 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.105770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.066296 restraints weight = 86846.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.067905 restraints weight = 46895.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.068926 restraints weight = 31641.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.069523 restraints weight = 24832.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.069989 restraints weight = 21429.445| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.5374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28823 Z= 0.174 Angle : 0.690 11.914 39354 Z= 0.332 Chirality : 0.049 0.678 4649 Planarity : 0.004 0.055 4932 Dihedral : 7.558 58.462 5213 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.59 % Favored : 93.29 % Rotamer: Outliers : 4.73 % Allowed : 22.17 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.14), residues: 3400 helix: 1.28 (0.21), residues: 672 sheet: -0.85 (0.17), residues: 831 loop : -1.90 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 408 TYR 0.019 0.001 TYR A1067 PHE 0.023 0.002 PHE B 342 TRP 0.045 0.002 TRP H 111 HIS 0.004 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00406 (28711) covalent geometry : angle 0.66292 (39060) SS BOND : bond 0.00508 ( 42) SS BOND : angle 1.72286 ( 84) hydrogen bonds : bond 0.04064 ( 956) hydrogen bonds : angle 5.37813 ( 2688) link_BETA1-4 : bond 0.00449 ( 22) link_BETA1-4 : angle 2.25330 ( 66) link_NAG-ASN : bond 0.00404 ( 48) link_NAG-ASN : angle 2.62812 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 129 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8185 (mmtt) REVERT: A 117 LEU cc_start: 0.8857 (pt) cc_final: 0.8434 (tp) REVERT: A 120 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8527 (m) REVERT: A 287 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8216 (m-30) REVERT: A 464 PHE cc_start: 0.7500 (m-80) cc_final: 0.7139 (m-80) REVERT: A 505 TYR cc_start: 0.6892 (t80) cc_final: 0.6150 (t80) REVERT: A 1005 GLN cc_start: 0.8642 (tp40) cc_final: 0.8344 (mm110) REVERT: C 301 CYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6952 (m) REVERT: C 461 LEU cc_start: 0.8003 (tp) cc_final: 0.7713 (mp) REVERT: C 784 GLN cc_start: 0.8308 (mm-40) cc_final: 0.8028 (mm-40) REVERT: L 66 ASP cc_start: 0.6975 (OUTLIER) cc_final: 0.6685 (p0) REVERT: L 97 TYR cc_start: 0.1283 (t80) cc_final: 0.0976 (t80) REVERT: B 153 MET cc_start: 0.2175 (mpp) cc_final: 0.1315 (mpp) REVERT: B 517 LEU cc_start: 0.4907 (OUTLIER) cc_final: 0.4190 (mt) REVERT: B 523 THR cc_start: 0.1542 (OUTLIER) cc_final: 0.1163 (m) REVERT: B 525 CYS cc_start: 0.6568 (OUTLIER) cc_final: 0.6088 (m) REVERT: B 584 ILE cc_start: 0.8804 (mm) cc_final: 0.8582 (mm) outliers start: 144 outliers final: 105 residues processed: 264 average time/residue: 0.1570 time to fit residues: 71.5615 Evaluate side-chains 231 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 118 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 210 optimal weight: 7.9990 chunk 208 optimal weight: 20.0000 chunk 59 optimal weight: 0.5980 chunk 343 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 308 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 307 optimal weight: 2.9990 chunk 300 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A1088 HIS C 30 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 501 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.104266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.066368 restraints weight = 87375.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.068619 restraints weight = 52920.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.068600 restraints weight = 31463.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.068606 restraints weight = 25732.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.068786 restraints weight = 28082.856| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.5687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 28823 Z= 0.218 Angle : 0.720 11.647 39354 Z= 0.348 Chirality : 0.049 0.681 4649 Planarity : 0.004 0.056 4932 Dihedral : 7.623 59.288 5209 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.50 % Favored : 92.38 % Rotamer: Outliers : 4.86 % Allowed : 22.14 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.14), residues: 3400 helix: 1.26 (0.21), residues: 671 sheet: -0.81 (0.17), residues: 824 loop : -1.89 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 408 TYR 0.032 0.002 TYR B 495 PHE 0.023 0.002 PHE H 114 TRP 0.044 0.002 TRP H 111 HIS 0.004 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00514 (28711) covalent geometry : angle 0.69380 (39060) SS BOND : bond 0.00523 ( 42) SS BOND : angle 1.71556 ( 84) hydrogen bonds : bond 0.04353 ( 956) hydrogen bonds : angle 5.38923 ( 2688) link_BETA1-4 : bond 0.00382 ( 22) link_BETA1-4 : angle 2.29571 ( 66) link_NAG-ASN : bond 0.00393 ( 48) link_NAG-ASN : angle 2.60560 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 124 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8433 (m) REVERT: A 287 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8439 (m-30) REVERT: A 429 PHE cc_start: 0.8427 (t80) cc_final: 0.7793 (m-80) REVERT: A 464 PHE cc_start: 0.7555 (m-80) cc_final: 0.7199 (m-80) REVERT: C 301 CYS cc_start: 0.7316 (OUTLIER) cc_final: 0.6896 (m) REVERT: C 461 LEU cc_start: 0.8051 (tp) cc_final: 0.7684 (mp) REVERT: C 784 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8163 (mm-40) REVERT: L 97 TYR cc_start: 0.1195 (t80) cc_final: 0.0888 (t80) REVERT: F 41 TRP cc_start: 0.3295 (m100) cc_final: 0.2490 (m100) outliers start: 148 outliers final: 115 residues processed: 263 average time/residue: 0.1553 time to fit residues: 70.6496 Evaluate side-chains 233 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 115 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 93 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 308 optimal weight: 5.9990 chunk 145 optimal weight: 0.0060 chunk 138 optimal weight: 9.9990 chunk 320 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 212 optimal weight: 40.0000 chunk 305 optimal weight: 3.9990 chunk 295 optimal weight: 5.9990 overall best weight: 1.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 755 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.105248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.067531 restraints weight = 87449.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.069317 restraints weight = 52919.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.069793 restraints weight = 32427.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.070013 restraints weight = 26125.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.070201 restraints weight = 26093.907| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28823 Z= 0.137 Angle : 0.671 11.551 39354 Z= 0.322 Chirality : 0.048 0.625 4649 Planarity : 0.004 0.059 4932 Dihedral : 7.389 59.754 5209 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.47 % Favored : 93.41 % Rotamer: Outliers : 3.81 % Allowed : 23.42 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.14), residues: 3400 helix: 1.43 (0.21), residues: 672 sheet: -0.62 (0.17), residues: 817 loop : -1.80 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 408 TYR 0.030 0.001 TYR B 495 PHE 0.035 0.001 PHE C 168 TRP 0.046 0.002 TRP H 111 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00316 (28711) covalent geometry : angle 0.64447 (39060) SS BOND : bond 0.00468 ( 42) SS BOND : angle 1.53574 ( 84) hydrogen bonds : bond 0.03892 ( 956) hydrogen bonds : angle 5.22175 ( 2688) link_BETA1-4 : bond 0.00470 ( 22) link_BETA1-4 : angle 2.28437 ( 66) link_NAG-ASN : bond 0.00411 ( 48) link_NAG-ASN : angle 2.59385 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 126 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8542 (pt) cc_final: 0.8047 (tp) REVERT: A 120 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8367 (m) REVERT: A 408 ARG cc_start: 0.7578 (mmm160) cc_final: 0.7191 (mtm-85) REVERT: A 429 PHE cc_start: 0.8437 (t80) cc_final: 0.7766 (m-80) REVERT: A 464 PHE cc_start: 0.7590 (m-80) cc_final: 0.7172 (m-80) REVERT: C 214 ARG cc_start: 0.1146 (OUTLIER) cc_final: -0.0835 (mmm160) REVERT: C 301 CYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6962 (m) REVERT: C 340 GLU cc_start: 0.8868 (pm20) cc_final: 0.8597 (pm20) REVERT: C 461 LEU cc_start: 0.8007 (tp) cc_final: 0.7672 (mp) REVERT: C 784 GLN cc_start: 0.8368 (mm-40) cc_final: 0.8143 (mm-40) REVERT: H 87 MET cc_start: 0.2167 (OUTLIER) cc_final: 0.1647 (ppp) REVERT: H 100 SER cc_start: -0.1589 (OUTLIER) cc_final: -0.1867 (t) REVERT: L 97 TYR cc_start: 0.1050 (t80) cc_final: 0.0797 (t80) REVERT: F 41 TRP cc_start: 0.3325 (m100) cc_final: 0.2569 (m100) REVERT: F 97 TYR cc_start: -0.0021 (t80) cc_final: -0.0240 (t80) REVERT: B 525 CYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6199 (m) REVERT: B 1051 SER cc_start: 0.9472 (m) cc_final: 0.9052 (p) outliers start: 116 outliers final: 88 residues processed: 236 average time/residue: 0.1553 time to fit residues: 62.1704 Evaluate side-chains 212 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 118 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 98 optimal weight: 8.9990 chunk 196 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 338 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 169 optimal weight: 9.9990 chunk 267 optimal weight: 7.9990 chunk 278 optimal weight: 3.9990 chunk 219 optimal weight: 30.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 501 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.104040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.066361 restraints weight = 88039.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.068273 restraints weight = 52767.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.068225 restraints weight = 36614.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.068779 restraints weight = 27988.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.068856 restraints weight = 27339.258| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.6010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28823 Z= 0.205 Angle : 0.712 11.631 39354 Z= 0.343 Chirality : 0.049 0.653 4649 Planarity : 0.004 0.059 4932 Dihedral : 7.485 59.648 5207 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.71 % Favored : 92.18 % Rotamer: Outliers : 3.91 % Allowed : 23.55 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.14), residues: 3400 helix: 1.35 (0.21), residues: 671 sheet: -0.61 (0.17), residues: 829 loop : -1.80 (0.13), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 408 TYR 0.031 0.001 TYR B 495 PHE 0.019 0.002 PHE C 133 TRP 0.056 0.002 TRP H 111 HIS 0.004 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00482 (28711) covalent geometry : angle 0.68537 (39060) SS BOND : bond 0.00497 ( 42) SS BOND : angle 1.65586 ( 84) hydrogen bonds : bond 0.04244 ( 956) hydrogen bonds : angle 5.29659 ( 2688) link_BETA1-4 : bond 0.00407 ( 22) link_BETA1-4 : angle 2.34123 ( 66) link_NAG-ASN : bond 0.00379 ( 48) link_NAG-ASN : angle 2.64886 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 123 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8421 (m) REVERT: A 233 ILE cc_start: 0.8152 (mm) cc_final: 0.7895 (mm) REVERT: A 408 ARG cc_start: 0.7624 (mmm160) cc_final: 0.7230 (mtm-85) REVERT: A 429 PHE cc_start: 0.8442 (t80) cc_final: 0.7623 (m-80) REVERT: A 464 PHE cc_start: 0.7538 (m-80) cc_final: 0.7272 (m-80) REVERT: C 214 ARG cc_start: 0.1209 (OUTLIER) cc_final: -0.0895 (mmm160) REVERT: C 301 CYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6952 (m) REVERT: C 461 LEU cc_start: 0.8096 (tp) cc_final: 0.7732 (mp) REVERT: C 784 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8184 (mm-40) REVERT: H 87 MET cc_start: 0.1749 (OUTLIER) cc_final: 0.1428 (ppp) REVERT: H 100 SER cc_start: -0.1594 (OUTLIER) cc_final: -0.2161 (t) REVERT: H 114 PHE cc_start: 0.0683 (m-10) cc_final: 0.0215 (m-10) REVERT: F 41 TRP cc_start: 0.3463 (m100) cc_final: 0.2710 (m100) REVERT: B 425 LEU cc_start: 0.5968 (mm) cc_final: 0.5759 (tp) REVERT: B 495 TYR cc_start: 0.5355 (m-80) cc_final: 0.4908 (m-80) REVERT: B 517 LEU cc_start: 0.4968 (OUTLIER) cc_final: 0.4496 (mt) outliers start: 119 outliers final: 99 residues processed: 236 average time/residue: 0.1599 time to fit residues: 64.6427 Evaluate side-chains 224 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 119 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 46 optimal weight: 3.9990 chunk 267 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 292 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 257 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.105299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.067698 restraints weight = 87292.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.069745 restraints weight = 51375.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.070051 restraints weight = 30331.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.070221 restraints weight = 25609.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.070401 restraints weight = 26664.052| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.6092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28823 Z= 0.125 Angle : 0.655 11.516 39354 Z= 0.314 Chirality : 0.048 0.588 4649 Planarity : 0.004 0.066 4932 Dihedral : 7.164 58.603 5207 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.09 % Favored : 93.79 % Rotamer: Outliers : 3.02 % Allowed : 24.34 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.14), residues: 3400 helix: 1.51 (0.21), residues: 672 sheet: -0.44 (0.17), residues: 829 loop : -1.73 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 408 TYR 0.025 0.001 TYR B 495 PHE 0.016 0.001 PHE C 135 TRP 0.063 0.002 TRP H 111 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00285 (28711) covalent geometry : angle 0.63034 (39060) SS BOND : bond 0.00447 ( 42) SS BOND : angle 1.47411 ( 84) hydrogen bonds : bond 0.03642 ( 956) hydrogen bonds : angle 5.08021 ( 2688) link_BETA1-4 : bond 0.00503 ( 22) link_BETA1-4 : angle 2.29180 ( 66) link_NAG-ASN : bond 0.00339 ( 48) link_NAG-ASN : angle 2.41102 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 130 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8385 (m) REVERT: A 408 ARG cc_start: 0.7635 (mmm160) cc_final: 0.7306 (mtm-85) REVERT: A 429 PHE cc_start: 0.8347 (t80) cc_final: 0.7714 (m-80) REVERT: C 231 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.8976 (mm) REVERT: C 301 CYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7008 (m) REVERT: C 461 LEU cc_start: 0.8015 (tp) cc_final: 0.7738 (mp) REVERT: H 87 MET cc_start: 0.2092 (OUTLIER) cc_final: 0.1777 (ppp) REVERT: H 97 CYS cc_start: 0.0483 (OUTLIER) cc_final: -0.0130 (p) REVERT: H 100 SER cc_start: -0.1458 (OUTLIER) cc_final: -0.1709 (t) REVERT: F 41 TRP cc_start: 0.3414 (m100) cc_final: 0.2668 (m100) REVERT: B 495 TYR cc_start: 0.5232 (m-80) cc_final: 0.5014 (m-80) REVERT: B 517 LEU cc_start: 0.4988 (OUTLIER) cc_final: 0.4537 (mt) REVERT: B 1051 SER cc_start: 0.9437 (m) cc_final: 0.9009 (p) outliers start: 92 outliers final: 74 residues processed: 216 average time/residue: 0.1558 time to fit residues: 57.8043 Evaluate side-chains 199 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 118 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 97 CYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 297 optimal weight: 9.9990 chunk 309 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 51 optimal weight: 0.0170 chunk 197 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 332 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.106420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.067089 restraints weight = 87165.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.068678 restraints weight = 46887.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.069730 restraints weight = 31667.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.070352 restraints weight = 24702.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.070758 restraints weight = 21256.764| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28823 Z= 0.106 Angle : 0.637 11.393 39354 Z= 0.305 Chirality : 0.047 0.555 4649 Planarity : 0.004 0.058 4932 Dihedral : 6.786 58.441 5204 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.79 % Favored : 94.12 % Rotamer: Outliers : 2.37 % Allowed : 25.10 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3400 helix: 1.64 (0.21), residues: 674 sheet: -0.24 (0.17), residues: 856 loop : -1.65 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 765 TYR 0.024 0.001 TYR H 61 PHE 0.023 0.001 PHE A 464 TRP 0.058 0.002 TRP H 111 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00231 (28711) covalent geometry : angle 0.61481 (39060) SS BOND : bond 0.00438 ( 42) SS BOND : angle 1.33916 ( 84) hydrogen bonds : bond 0.03269 ( 956) hydrogen bonds : angle 4.91557 ( 2688) link_BETA1-4 : bond 0.00506 ( 22) link_BETA1-4 : angle 2.23790 ( 66) link_NAG-ASN : bond 0.00354 ( 48) link_NAG-ASN : angle 2.20815 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4939.51 seconds wall clock time: 86 minutes 11.75 seconds (5171.75 seconds total)