Starting phenix.real_space_refine on Fri Mar 6 10:37:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ej4_30669/03_2026/7ej4_30669.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ej4_30669/03_2026/7ej4_30669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ej4_30669/03_2026/7ej4_30669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ej4_30669/03_2026/7ej4_30669.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ej4_30669/03_2026/7ej4_30669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ej4_30669/03_2026/7ej4_30669.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.038 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 135 5.16 5 C 19057 2.51 5 N 4886 2.21 5 O 5962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30040 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 7872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7872 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 50, 'TRANS': 957} Chain breaks: 8 Chain: "B" Number of atoms: 7986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7986 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 51, 'TRANS': 970} Chain breaks: 7 Chain: "C" Number of atoms: 7906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7906 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 50, 'TRANS': 960} Chain breaks: 8 Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 828 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "I" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "M" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 828 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "J" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "N" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 828 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "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: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.81, per 1000 atoms: 0.23 Number of scatterers: 30040 At special positions: 0 Unit cell: (139.7, 170.5, 225.5, 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 135 16.00 O 5962 8.00 N 4886 7.00 C 19057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 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 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 89 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 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 d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 165 " " NAG A2004 " - " ASN A 234 " " NAG A2005 " - " ASN A 343 " " NAG A2006 " - " ASN A 603 " " NAG A2007 " - " ASN A 657 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 165 " " NAG B2004 " - " ASN B 331 " " NAG B2005 " - " ASN B 343 " " NAG B2006 " - " ASN B 603 " " NAG B2007 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 122 " " NAG C2003 " - " ASN C 165 " " NAG C2004 " - " ASN C 234 " " NAG C2005 " - " ASN C 343 " " NAG C2006 " - " ASN C 603 " " NAG C2007 " - " ASN C 657 " " NAG D 1 " - " ASN A 282 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 616 " " NAG G 1 " - " ASN A 709 " " NAG K 1 " - " ASN A 717 " " NAG O 1 " - " ASN A 801 " " NAG P 1 " - " ASN A1074 " " NAG Q 1 " - " ASN A1098 " " NAG R 1 " - " ASN A1134 " " NAG S 1 " - " ASN B 234 " " NAG T 1 " - " ASN B 282 " " NAG U 1 " - " ASN B 616 " " NAG V 1 " - " ASN B 709 " " NAG W 1 " - " ASN B 717 " " NAG X 1 " - " ASN B 801 " " NAG Y 1 " - " ASN B1074 " " NAG Z 1 " - " ASN B1098 " " NAG a 1 " - " ASN B1134 " " NAG b 1 " - " ASN C 282 " " NAG c 1 " - " ASN C 331 " " NAG d 1 " - " ASN C 616 " " NAG e 1 " - " ASN C 709 " " NAG f 1 " - " ASN C 717 " " NAG g 1 " - " ASN C 801 " " NAG h 1 " - " ASN C1074 " " NAG i 1 " - " ASN C1098 " " NAG j 1 " - " ASN C1134 " Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.1 seconds 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6946 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 57 sheets defined 21.6% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.039A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.937A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.843A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.556A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.706A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.524A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.734A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.557A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 898 through 909 removed outlier: 3.968A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.594A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.984A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.579A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.549A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.239A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.870A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.163A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.960A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.247A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 5.697A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 618 through 624 removed outlier: 4.430A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 638 removed outlier: 3.890A pdb=" N VAL B 635 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.822A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 4.667A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.602A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.638A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.584A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.602A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 910 " --> pdb=" O PHE B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.427A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 912 through 918' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.509A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.907A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.569A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.664A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.224A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 removed outlier: 4.074A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.360A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.716A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 638 removed outlier: 3.820A pdb=" N THR C 638 " --> pdb=" O ARG C 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 634 through 638' Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.981A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.781A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.861A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.556A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1034 removed outlier: 4.207A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C1034 " --> pdb=" O SER C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.924A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 65 removed outlier: 4.094A pdb=" N ALA H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.173A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.953A pdb=" N ALA L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 4.163A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 84 removed outlier: 3.540A pdb=" N ASP M 83 " --> pdb=" O GLU M 80 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA M 84 " --> pdb=" O ALA M 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 80 through 84' Processing helix chain 'N' and resid 80 through 84 removed outlier: 4.108A pdb=" N ALA N 84 " --> pdb=" O ALA N 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.778A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.496A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.726A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.649A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.183A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.857A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.561A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL A 395 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER A 514 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA A 397 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 512 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER A 399 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL A 510 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL A 401 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR A 508 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.565A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.791A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (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 713 removed outlier: 3.647A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.700A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.781A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR B 91 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.599A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.575A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.507A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.803A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.583A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.246A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 715 through 719 removed outlier: 5.959A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 715 through 719 removed outlier: 5.959A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.615A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.842A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.769A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER C 205 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.921A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.943A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.699A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.663A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.153A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.711A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.677A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1081 through 1083 Processing sheet with id=AE6, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id=AE7, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AE8, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.966A pdb=" N ASN H 59 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU H 50 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 4 through 6 removed outlier: 4.146A pdb=" N SER L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER L 68 " --> pdb=" O SER L 71 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 12 through 14 removed outlier: 6.088A pdb=" N GLU L 106 " --> pdb=" O VAL L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'L' and resid 49 through 50 Processing sheet with id=AF3, first strand: chain 'L' and resid 86 through 87 removed outlier: 3.674A pdb=" N TYR L 87 " --> pdb=" O THR L 103 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 19 through 21 Processing sheet with id=AF5, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.545A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AF7, first strand: chain 'M' and resid 12 through 14 removed outlier: 6.684A pdb=" N VAL M 13 " --> pdb=" O LYS M 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'M' and resid 54 through 55 removed outlier: 4.303A pdb=" N ILE M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 19 through 21 Processing sheet with id=AG1, first strand: chain 'J' and resid 57 through 59 removed outlier: 3.822A pdb=" N ASN J 59 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU J 50 " --> pdb=" O ASN J 59 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA J 92 " --> pdb=" O VAL J 114 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL J 114 " --> pdb=" O ALA J 92 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 5 through 6 removed outlier: 3.898A pdb=" N SER N 71 " --> pdb=" O SER N 68 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER N 68 " --> pdb=" O SER N 71 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 10 through 14 removed outlier: 6.073A pdb=" N MET N 11 " --> pdb=" O GLU N 106 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYS N 108 " --> pdb=" O MET N 11 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL N 13 " --> pdb=" O LYS N 108 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLN N 38 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU N 47 " --> pdb=" O GLN N 38 " (cutoff:3.500A) 1037 hydrogen bonds defined for protein. 2766 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.54 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9479 1.34 - 1.46: 7680 1.46 - 1.58: 13368 1.58 - 1.70: 0 1.70 - 1.82: 177 Bond restraints: 30704 Sorted by residual: bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.85e+00 bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.08e+00 bond pdb=" C1 NAG h 1 " pdb=" O5 NAG h 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.18e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.15e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.12e+00 ... (remaining 30699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 40360 1.54 - 3.08: 1211 3.08 - 4.61: 147 4.61 - 6.15: 33 6.15 - 7.69: 11 Bond angle restraints: 41762 Sorted by residual: angle pdb=" C PHE C 486 " pdb=" N ASN C 487 " pdb=" CA ASN C 487 " ideal model delta sigma weight residual 122.61 128.22 -5.61 1.56e+00 4.11e-01 1.29e+01 angle pdb=" C PHE B 486 " pdb=" N ASN B 487 " pdb=" CA ASN B 487 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C ASN C 234 " pdb=" N ILE C 235 " pdb=" CA ILE C 235 " ideal model delta sigma weight residual 121.97 128.18 -6.21 1.80e+00 3.09e-01 1.19e+01 angle pdb=" N GLY A 593 " pdb=" CA GLY A 593 " pdb=" C GLY A 593 " ideal model delta sigma weight residual 110.63 115.32 -4.69 1.45e+00 4.76e-01 1.05e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.64 -3.94 1.22e+00 6.72e-01 1.05e+01 ... (remaining 41757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.01: 17639 20.01 - 40.02: 1261 40.02 - 60.03: 243 60.03 - 80.05: 38 80.05 - 100.06: 15 Dihedral angle restraints: 19196 sinusoidal: 8374 harmonic: 10822 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 14.84 78.16 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -164.06 78.06 1 1.00e+01 1.00e-02 7.61e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 17.74 75.26 1 1.00e+01 1.00e-02 7.16e+01 ... (remaining 19193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 4900 0.140 - 0.280: 33 0.280 - 0.419: 0 0.419 - 0.559: 2 0.559 - 0.699: 1 Chirality restraints: 4936 Sorted by residual: chirality pdb=" C1 NAG j 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG j 1 " pdb=" O5 NAG j 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" C1 NAG A2007 " pdb=" ND2 ASN A 657 " pdb=" C2 NAG A2007 " pdb=" O5 NAG A2007 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 4933 not shown) Planarity restraints: 5326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " 0.024 2.00e-02 2.50e+03 2.24e-02 6.30e+00 pdb=" CG ASN B 234 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " -0.022 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.62e+00 pdb=" N PRO A 521 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.59e+00 pdb=" N PRO C 986 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " 0.026 5.00e-02 4.00e+02 ... (remaining 5323 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 773 2.69 - 3.24: 29027 3.24 - 3.79: 45150 3.79 - 4.35: 56687 4.35 - 4.90: 94410 Nonbonded interactions: 226047 Sorted by model distance: nonbonded pdb=" OG1 THR H 33 " pdb=" O PHE H 99 " model vdw 2.132 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.150 3.040 nonbonded pdb=" OH TYR C 453 " pdb=" OG SER N 31 " model vdw 2.171 3.040 nonbonded pdb=" OG1 THR B 716 " pdb=" O GLN B1071 " model vdw 2.171 3.040 nonbonded pdb=" O PHE I 29 " pdb=" OG SER I 53 " model vdw 2.174 3.040 ... (remaining 226042 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 27 through 622 or resid 636 through 827 or resid 855 throu \ gh 2007)) selection = (chain 'C' and (resid 27 through 621 or resid 635 through 827 or resid 855 throu \ gh 2007)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'K' 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' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 5.110 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: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 27.790 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 : 0.003 0.044 30821 Z= 0.171 Angle : 0.651 16.735 42070 Z= 0.320 Chirality : 0.048 0.699 4936 Planarity : 0.004 0.048 5279 Dihedral : 13.823 100.058 12121 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.93 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -1.14 (0.14), residues: 3661 helix: 1.71 (0.22), residues: 649 sheet: -0.51 (0.17), residues: 914 loop : -1.75 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 815 TYR 0.018 0.001 TYR I 95 PHE 0.019 0.001 PHE B 906 TRP 0.022 0.001 TRP M 48 HIS 0.002 0.000 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00347 (30704) covalent geometry : angle 0.61720 (41762) SS BOND : bond 0.00410 ( 43) SS BOND : angle 1.23502 ( 86) hydrogen bonds : bond 0.14749 ( 1033) hydrogen bonds : angle 6.40924 ( 2766) link_BETA1-4 : bond 0.00526 ( 27) link_BETA1-4 : angle 3.17071 ( 81) link_NAG-ASN : bond 0.00353 ( 47) link_NAG-ASN : angle 2.59933 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8717 (t80) cc_final: 0.7999 (t80) REVERT: A 902 MET cc_start: 0.8566 (mmm) cc_final: 0.8307 (mmt) REVERT: B 759 PHE cc_start: 0.7058 (p90) cc_final: 0.6806 (p90) REVERT: B 869 MET cc_start: 0.8448 (mpp) cc_final: 0.8024 (mpp) REVERT: B 1031 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8234 (tm-30) REVERT: C 452 LEU cc_start: 0.8476 (mm) cc_final: 0.8243 (tp) REVERT: C 740 MET cc_start: 0.8097 (tpt) cc_final: 0.7857 (mmm) REVERT: H 80 TYR cc_start: 0.9103 (m-80) cc_final: 0.8668 (m-80) REVERT: N 21 MET cc_start: 0.7488 (tmm) cc_final: 0.7256 (tmm) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1801 time to fit residues: 49.1934 Evaluate side-chains 120 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A1106 GLN C 196 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.098428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.062602 restraints weight = 133507.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.064303 restraints weight = 67856.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.065462 restraints weight = 46285.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.066153 restraints weight = 36589.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.066542 restraints weight = 31911.784| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 30821 Z= 0.159 Angle : 0.624 11.781 42070 Z= 0.313 Chirality : 0.046 0.489 4936 Planarity : 0.004 0.048 5279 Dihedral : 8.185 74.519 5576 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.95 % Favored : 93.99 % Rotamer: Outliers : 0.40 % Allowed : 6.72 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -1.11 (0.14), residues: 3661 helix: 1.58 (0.22), residues: 666 sheet: -0.45 (0.17), residues: 928 loop : -1.73 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 67 TYR 0.017 0.001 TYR C 91 PHE 0.015 0.001 PHE A 456 TRP 0.016 0.001 TRP M 48 HIS 0.004 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00359 (30704) covalent geometry : angle 0.60079 (41762) SS BOND : bond 0.00352 ( 43) SS BOND : angle 1.04889 ( 86) hydrogen bonds : bond 0.05507 ( 1033) hydrogen bonds : angle 5.44259 ( 2766) link_BETA1-4 : bond 0.00475 ( 27) link_BETA1-4 : angle 2.37514 ( 81) link_NAG-ASN : bond 0.00243 ( 47) link_NAG-ASN : angle 2.35168 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 869 MET cc_start: 0.8404 (mpp) cc_final: 0.7968 (mpp) REVERT: C 740 MET cc_start: 0.8074 (tpt) cc_final: 0.7838 (mmm) REVERT: H 80 TYR cc_start: 0.9335 (m-80) cc_final: 0.9126 (m-80) REVERT: L 21 MET cc_start: 0.4910 (ttp) cc_final: 0.4638 (mpp) REVERT: J 34 MET cc_start: 0.5512 (tpt) cc_final: 0.5198 (tpt) outliers start: 13 outliers final: 10 residues processed: 141 average time/residue: 0.1669 time to fit residues: 40.0215 Evaluate side-chains 127 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain M residue 35 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 179 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 256 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 349 optimal weight: 9.9990 chunk 192 optimal weight: 0.6980 chunk 115 optimal weight: 0.3980 chunk 203 optimal weight: 0.7980 chunk 127 optimal weight: 5.9990 chunk 317 optimal weight: 8.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN C 919 ASN L 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.100228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.064162 restraints weight = 118830.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.067807 restraints weight = 67641.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.067391 restraints weight = 37999.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.067783 restraints weight = 37302.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.067986 restraints weight = 34514.715| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30821 Z= 0.117 Angle : 0.580 11.808 42070 Z= 0.286 Chirality : 0.045 0.478 4936 Planarity : 0.004 0.046 5279 Dihedral : 7.512 67.439 5576 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.16 % Favored : 94.78 % Rotamer: Outliers : 0.62 % Allowed : 9.97 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -1.00 (0.14), residues: 3661 helix: 1.65 (0.22), residues: 666 sheet: -0.31 (0.17), residues: 926 loop : -1.69 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1107 TYR 0.029 0.001 TYR N 37 PHE 0.015 0.001 PHE B 759 TRP 0.014 0.001 TRP N 48 HIS 0.005 0.001 HIS N 35 Details of bonding type rmsd covalent geometry : bond 0.00259 (30704) covalent geometry : angle 0.55477 (41762) SS BOND : bond 0.00268 ( 43) SS BOND : angle 0.93538 ( 86) hydrogen bonds : bond 0.05000 ( 1033) hydrogen bonds : angle 5.08018 ( 2766) link_BETA1-4 : bond 0.00507 ( 27) link_BETA1-4 : angle 2.39317 ( 81) link_NAG-ASN : bond 0.00278 ( 47) link_NAG-ASN : angle 2.32459 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: B 869 MET cc_start: 0.8486 (mpp) cc_final: 0.8015 (mpp) REVERT: C 740 MET cc_start: 0.8096 (tpt) cc_final: 0.7864 (mmm) REVERT: H 80 TYR cc_start: 0.9235 (m-80) cc_final: 0.8838 (m-80) REVERT: L 21 MET cc_start: 0.4782 (ttp) cc_final: 0.4247 (mpp) REVERT: M 29 VAL cc_start: 0.5596 (OUTLIER) cc_final: 0.5139 (m) REVERT: J 34 MET cc_start: 0.7211 (tpt) cc_final: 0.6466 (tpt) outliers start: 20 outliers final: 14 residues processed: 145 average time/residue: 0.1722 time to fit residues: 42.4376 Evaluate side-chains 134 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain N residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 265 optimal weight: 0.0770 chunk 189 optimal weight: 0.9990 chunk 133 optimal weight: 40.0000 chunk 299 optimal weight: 0.0670 chunk 58 optimal weight: 5.9990 chunk 236 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 chunk 283 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 overall best weight: 2.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.097541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.061314 restraints weight = 122130.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.063464 restraints weight = 61923.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.064806 restraints weight = 42234.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.065630 restraints weight = 33670.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.066172 restraints weight = 29286.424| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30821 Z= 0.158 Angle : 0.600 12.580 42070 Z= 0.297 Chirality : 0.045 0.496 4936 Planarity : 0.004 0.048 5279 Dihedral : 7.170 62.547 5576 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.15 % Favored : 93.80 % Rotamer: Outliers : 1.11 % Allowed : 12.26 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -0.98 (0.14), residues: 3661 helix: 1.77 (0.21), residues: 659 sheet: -0.28 (0.17), residues: 899 loop : -1.69 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1107 TYR 0.018 0.001 TYR C 91 PHE 0.013 0.001 PHE A 92 TRP 0.012 0.001 TRP I 36 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00361 (30704) covalent geometry : angle 0.57518 (41762) SS BOND : bond 0.00279 ( 43) SS BOND : angle 1.00216 ( 86) hydrogen bonds : bond 0.05355 ( 1033) hydrogen bonds : angle 5.11402 ( 2766) link_BETA1-4 : bond 0.00400 ( 27) link_BETA1-4 : angle 2.34930 ( 81) link_NAG-ASN : bond 0.00249 ( 47) link_NAG-ASN : angle 2.40586 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 869 MET cc_start: 0.8517 (mpp) cc_final: 0.8070 (mpp) REVERT: C 740 MET cc_start: 0.8139 (tpt) cc_final: 0.7894 (mmm) REVERT: H 67 ARG cc_start: 0.6732 (ptm-80) cc_final: 0.6009 (ptm-80) REVERT: H 80 TYR cc_start: 0.9137 (m-80) cc_final: 0.8758 (m-80) REVERT: L 11 MET cc_start: 0.6844 (mpp) cc_final: 0.6091 (pmm) REVERT: L 21 MET cc_start: 0.4890 (ttp) cc_final: 0.4132 (mpp) REVERT: L 33 TYR cc_start: 0.7068 (OUTLIER) cc_final: 0.6672 (m-10) REVERT: L 48 TRP cc_start: 0.4727 (OUTLIER) cc_final: 0.4397 (m-10) REVERT: J 34 MET cc_start: 0.7201 (tpt) cc_final: 0.6424 (tpt) REVERT: N 35 HIS cc_start: 0.6493 (OUTLIER) cc_final: 0.6269 (p90) REVERT: N 52 THR cc_start: 0.6508 (OUTLIER) cc_final: 0.6291 (p) outliers start: 36 outliers final: 19 residues processed: 152 average time/residue: 0.1724 time to fit residues: 44.8887 Evaluate side-chains 138 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain N residue 35 HIS Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 188 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 278 optimal weight: 0.9980 chunk 244 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 362 optimal weight: 50.0000 chunk 37 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 156 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.098420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.062371 restraints weight = 121850.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.064571 restraints weight = 61456.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.065928 restraints weight = 41784.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.066787 restraints weight = 33242.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.067240 restraints weight = 28874.509| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30821 Z= 0.113 Angle : 0.571 12.628 42070 Z= 0.280 Chirality : 0.045 0.493 4936 Planarity : 0.004 0.048 5279 Dihedral : 6.872 60.832 5576 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.57 % Favored : 94.37 % Rotamer: Outliers : 1.05 % Allowed : 13.65 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.14), residues: 3661 helix: 1.84 (0.22), residues: 649 sheet: -0.23 (0.17), residues: 902 loop : -1.64 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 67 TYR 0.015 0.001 TYR N 37 PHE 0.011 0.001 PHE B 392 TRP 0.014 0.001 TRP H 36 HIS 0.008 0.001 HIS N 35 Details of bonding type rmsd covalent geometry : bond 0.00251 (30704) covalent geometry : angle 0.54539 (41762) SS BOND : bond 0.00286 ( 43) SS BOND : angle 1.02942 ( 86) hydrogen bonds : bond 0.04871 ( 1033) hydrogen bonds : angle 4.95138 ( 2766) link_BETA1-4 : bond 0.00468 ( 27) link_BETA1-4 : angle 2.34093 ( 81) link_NAG-ASN : bond 0.00262 ( 47) link_NAG-ASN : angle 2.34697 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 869 MET cc_start: 0.8472 (mpp) cc_final: 0.8006 (mpp) REVERT: C 740 MET cc_start: 0.8057 (tpt) cc_final: 0.7827 (mmm) REVERT: L 11 MET cc_start: 0.6895 (mpp) cc_final: 0.6164 (pmm) REVERT: L 21 MET cc_start: 0.4868 (ttp) cc_final: 0.4119 (mpp) REVERT: L 48 TRP cc_start: 0.4632 (OUTLIER) cc_final: 0.4248 (m-10) outliers start: 34 outliers final: 19 residues processed: 153 average time/residue: 0.1743 time to fit residues: 45.1978 Evaluate side-chains 136 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain N residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 108 optimal weight: 7.9990 chunk 147 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 284 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 309 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 364 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN ** M 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.098353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.060238 restraints weight = 125502.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.062372 restraints weight = 63620.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.063726 restraints weight = 43693.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.064518 restraints weight = 34855.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.065094 restraints weight = 30354.938| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 30821 Z= 0.234 Angle : 0.659 13.432 42070 Z= 0.327 Chirality : 0.046 0.508 4936 Planarity : 0.004 0.050 5279 Dihedral : 7.008 59.076 5576 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.02 % Favored : 92.90 % Rotamer: Outliers : 1.45 % Allowed : 14.14 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -1.14 (0.14), residues: 3661 helix: 1.41 (0.21), residues: 671 sheet: -0.38 (0.17), residues: 918 loop : -1.74 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 34 TYR 0.027 0.001 TYR C 91 PHE 0.019 0.002 PHE C 275 TRP 0.013 0.001 TRP M 48 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00538 (30704) covalent geometry : angle 0.63343 (41762) SS BOND : bond 0.00365 ( 43) SS BOND : angle 1.16679 ( 86) hydrogen bonds : bond 0.06228 ( 1033) hydrogen bonds : angle 5.32285 ( 2766) link_BETA1-4 : bond 0.00381 ( 27) link_BETA1-4 : angle 2.37182 ( 81) link_NAG-ASN : bond 0.00368 ( 47) link_NAG-ASN : angle 2.55403 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 118 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 869 MET cc_start: 0.8590 (mpp) cc_final: 0.8128 (mpp) REVERT: C 740 MET cc_start: 0.8171 (tpt) cc_final: 0.7948 (mmm) REVERT: L 48 TRP cc_start: 0.4911 (OUTLIER) cc_final: 0.4435 (m-10) REVERT: I 1 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6554 (pp20) REVERT: J 1 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7322 (pp20) REVERT: N 33 TYR cc_start: 0.1859 (OUTLIER) cc_final: 0.1608 (m-80) REVERT: N 52 THR cc_start: 0.6495 (OUTLIER) cc_final: 0.6286 (p) outliers start: 47 outliers final: 29 residues processed: 156 average time/residue: 0.1549 time to fit residues: 42.5682 Evaluate side-chains 145 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain J residue 1 GLU Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain N residue 33 TYR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 355 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 218 optimal weight: 0.8980 chunk 225 optimal weight: 0.9980 chunk 133 optimal weight: 0.3980 chunk 306 optimal weight: 20.0000 chunk 207 optimal weight: 0.4980 chunk 82 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.099395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.062451 restraints weight = 123574.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.064711 restraints weight = 60570.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.066144 restraints weight = 40724.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.067003 restraints weight = 32084.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.067581 restraints weight = 27806.455| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30821 Z= 0.104 Angle : 0.578 12.984 42070 Z= 0.283 Chirality : 0.045 0.502 4936 Planarity : 0.004 0.049 5279 Dihedral : 6.621 59.009 5576 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.27 % Favored : 94.67 % Rotamer: Outliers : 1.55 % Allowed : 14.55 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: 3661 helix: 1.88 (0.22), residues: 653 sheet: -0.07 (0.17), residues: 872 loop : -1.68 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1107 TYR 0.014 0.001 TYR C 91 PHE 0.011 0.001 PHE B 338 TRP 0.019 0.001 TRP N 48 HIS 0.003 0.001 HIS N 35 Details of bonding type rmsd covalent geometry : bond 0.00223 (30704) covalent geometry : angle 0.55250 (41762) SS BOND : bond 0.00325 ( 43) SS BOND : angle 0.93109 ( 86) hydrogen bonds : bond 0.04862 ( 1033) hydrogen bonds : angle 4.90928 ( 2766) link_BETA1-4 : bond 0.00523 ( 27) link_BETA1-4 : angle 2.34601 ( 81) link_NAG-ASN : bond 0.00305 ( 47) link_NAG-ASN : angle 2.36025 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 130 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 985 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8112 (t0) REVERT: B 869 MET cc_start: 0.8494 (mpp) cc_final: 0.8025 (mpp) REVERT: C 740 MET cc_start: 0.8030 (tpt) cc_final: 0.7827 (mmm) REVERT: H 80 TYR cc_start: 0.9124 (m-80) cc_final: 0.8622 (m-80) REVERT: L 11 MET cc_start: 0.6429 (mpp) cc_final: 0.5984 (pmm) REVERT: L 48 TRP cc_start: 0.4992 (OUTLIER) cc_final: 0.4459 (m-10) REVERT: I 1 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6336 (pp20) REVERT: I 50 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7910 (tp30) REVERT: J 1 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7231 (pp20) REVERT: N 52 THR cc_start: 0.6489 (OUTLIER) cc_final: 0.6286 (p) outliers start: 50 outliers final: 26 residues processed: 167 average time/residue: 0.1555 time to fit residues: 45.0853 Evaluate side-chains 157 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain J residue 1 GLU Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain N residue 35 HIS Chi-restraints excluded: chain N residue 52 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 32 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 83 optimal weight: 0.0770 chunk 24 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 323 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 288 optimal weight: 4.9990 chunk 246 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 overall best weight: 3.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.096572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.060112 restraints weight = 122881.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.062221 restraints weight = 63006.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.063548 restraints weight = 43326.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.064373 restraints weight = 34582.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.064845 restraints weight = 30152.127| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 30821 Z= 0.219 Angle : 0.650 13.695 42070 Z= 0.321 Chirality : 0.046 0.506 4936 Planarity : 0.004 0.049 5279 Dihedral : 6.759 59.227 5576 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.66 % Favored : 93.25 % Rotamer: Outliers : 1.33 % Allowed : 15.26 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -1.08 (0.14), residues: 3661 helix: 1.53 (0.21), residues: 672 sheet: -0.14 (0.17), residues: 859 loop : -1.80 (0.12), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.026 0.001 TYR C 91 PHE 0.016 0.002 PHE C 43 TRP 0.015 0.001 TRP N 48 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00503 (30704) covalent geometry : angle 0.62423 (41762) SS BOND : bond 0.00382 ( 43) SS BOND : angle 1.13795 ( 86) hydrogen bonds : bond 0.05937 ( 1033) hydrogen bonds : angle 5.22784 ( 2766) link_BETA1-4 : bond 0.00403 ( 27) link_BETA1-4 : angle 2.36754 ( 81) link_NAG-ASN : bond 0.00323 ( 47) link_NAG-ASN : angle 2.54213 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 126 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: B 581 THR cc_start: 0.9338 (OUTLIER) cc_final: 0.9120 (p) REVERT: B 869 MET cc_start: 0.8579 (mpp) cc_final: 0.8094 (mpp) REVERT: C 740 MET cc_start: 0.8162 (tpt) cc_final: 0.7918 (mmm) REVERT: L 11 MET cc_start: 0.6512 (mpp) cc_final: 0.6077 (pmm) REVERT: L 48 TRP cc_start: 0.5430 (OUTLIER) cc_final: 0.4779 (m-10) REVERT: I 1 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6230 (pp20) REVERT: I 50 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7925 (tp30) REVERT: M 11 MET cc_start: 0.6960 (mmp) cc_final: 0.6414 (mpp) REVERT: J 1 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7375 (pp20) REVERT: J 34 MET cc_start: 0.6675 (tpt) cc_final: 0.6273 (tpt) outliers start: 43 outliers final: 33 residues processed: 161 average time/residue: 0.1528 time to fit residues: 43.1818 Evaluate side-chains 154 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain J residue 1 GLU Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain N residue 35 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 320 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 237 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 83 optimal weight: 0.0980 chunk 356 optimal weight: 9.9990 chunk 344 optimal weight: 20.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.097384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.060983 restraints weight = 120982.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.063035 restraints weight = 62674.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.064317 restraints weight = 43387.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.065127 restraints weight = 34829.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.065616 restraints weight = 30415.621| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 30821 Z= 0.201 Angle : 0.640 13.731 42070 Z= 0.316 Chirality : 0.046 0.519 4936 Planarity : 0.004 0.049 5279 Dihedral : 6.764 59.599 5576 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.42 % Favored : 93.50 % Rotamer: Outliers : 1.39 % Allowed : 15.82 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -1.15 (0.14), residues: 3661 helix: 1.56 (0.21), residues: 660 sheet: -0.33 (0.17), residues: 895 loop : -1.82 (0.12), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 34 TYR 0.026 0.001 TYR C 91 PHE 0.014 0.001 PHE B 238 TRP 0.015 0.001 TRP N 48 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00461 (30704) covalent geometry : angle 0.61453 (41762) SS BOND : bond 0.00301 ( 43) SS BOND : angle 1.17042 ( 86) hydrogen bonds : bond 0.05892 ( 1033) hydrogen bonds : angle 5.20251 ( 2766) link_BETA1-4 : bond 0.00423 ( 27) link_BETA1-4 : angle 2.36735 ( 81) link_NAG-ASN : bond 0.00281 ( 47) link_NAG-ASN : angle 2.52506 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 120 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: A 985 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8237 (t0) REVERT: B 581 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.9111 (p) REVERT: B 869 MET cc_start: 0.8577 (mpp) cc_final: 0.8113 (mpp) REVERT: C 740 MET cc_start: 0.8131 (tpt) cc_final: 0.7897 (mmm) REVERT: H 13 LYS cc_start: 0.8201 (pttm) cc_final: 0.7870 (ttmm) REVERT: L 11 MET cc_start: 0.6561 (mpp) cc_final: 0.6195 (pmm) REVERT: L 48 TRP cc_start: 0.5403 (OUTLIER) cc_final: 0.4810 (m100) REVERT: I 1 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6165 (pp20) REVERT: I 50 GLU cc_start: 0.8390 (tm-30) cc_final: 0.7976 (tp30) REVERT: M 11 MET cc_start: 0.7157 (mmp) cc_final: 0.6669 (mpp) REVERT: J 1 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7387 (pp20) REVERT: J 34 MET cc_start: 0.6921 (tpt) cc_final: 0.6483 (tpt) REVERT: N 21 MET cc_start: 0.7678 (tmm) cc_final: 0.7462 (tmm) REVERT: N 63 PHE cc_start: 0.4925 (OUTLIER) cc_final: 0.4328 (m-80) REVERT: N 72 TYR cc_start: 0.7252 (m-10) cc_final: 0.7031 (m-80) outliers start: 45 outliers final: 37 residues processed: 158 average time/residue: 0.1655 time to fit residues: 44.9962 Evaluate side-chains 159 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 116 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain J residue 1 GLU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain N residue 35 HIS Chi-restraints excluded: chain N residue 63 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 181 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 192 optimal weight: 0.7980 chunk 317 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 318 optimal weight: 0.9990 chunk 278 optimal weight: 0.9980 chunk 220 optimal weight: 2.9990 chunk 306 optimal weight: 20.0000 chunk 136 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.097970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.062988 restraints weight = 132406.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.065546 restraints weight = 72486.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.065913 restraints weight = 48173.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.066247 restraints weight = 35679.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.066335 restraints weight = 31881.433| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30821 Z= 0.124 Angle : 0.598 13.435 42070 Z= 0.293 Chirality : 0.045 0.514 4936 Planarity : 0.004 0.049 5279 Dihedral : 6.578 59.693 5576 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.79 % Favored : 94.13 % Rotamer: Outliers : 1.36 % Allowed : 15.82 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -0.99 (0.14), residues: 3661 helix: 1.83 (0.21), residues: 654 sheet: -0.20 (0.17), residues: 888 loop : -1.76 (0.13), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1107 TYR 0.016 0.001 TYR C 91 PHE 0.010 0.001 PHE B 759 TRP 0.017 0.001 TRP N 48 HIS 0.016 0.001 HIS N 35 Details of bonding type rmsd covalent geometry : bond 0.00278 (30704) covalent geometry : angle 0.57219 (41762) SS BOND : bond 0.00283 ( 43) SS BOND : angle 1.03252 ( 86) hydrogen bonds : bond 0.05226 ( 1033) hydrogen bonds : angle 4.94555 ( 2766) link_BETA1-4 : bond 0.00474 ( 27) link_BETA1-4 : angle 2.35217 ( 81) link_NAG-ASN : bond 0.00253 ( 47) link_NAG-ASN : angle 2.43791 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 985 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8211 (t0) REVERT: B 581 THR cc_start: 0.9340 (OUTLIER) cc_final: 0.9124 (p) REVERT: B 869 MET cc_start: 0.8563 (mpp) cc_final: 0.8031 (mpp) REVERT: C 740 MET cc_start: 0.8083 (tpt) cc_final: 0.7829 (mmm) REVERT: H 13 LYS cc_start: 0.8384 (pttm) cc_final: 0.8163 (ttmm) REVERT: L 11 MET cc_start: 0.7505 (mpp) cc_final: 0.6803 (pmm) REVERT: L 48 TRP cc_start: 0.6174 (OUTLIER) cc_final: 0.5474 (m-10) REVERT: I 1 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6880 (pp20) REVERT: I 50 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7685 (tp30) REVERT: M 11 MET cc_start: 0.7556 (mmp) cc_final: 0.6924 (mtm) REVERT: N 63 PHE cc_start: 0.4852 (OUTLIER) cc_final: 0.4265 (m-80) outliers start: 44 outliers final: 35 residues processed: 157 average time/residue: 0.1564 time to fit residues: 42.7201 Evaluate side-chains 162 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 122 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain N residue 63 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 39 optimal weight: 0.0470 chunk 100 optimal weight: 10.0000 chunk 303 optimal weight: 30.0000 chunk 306 optimal weight: 9.9990 chunk 171 optimal weight: 0.9990 chunk 338 optimal weight: 40.0000 chunk 189 optimal weight: 3.9990 chunk 226 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 334 optimal weight: 5.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.097967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.061502 restraints weight = 119789.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.063574 restraints weight = 62587.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.064858 restraints weight = 43589.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.065667 restraints weight = 35164.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.066136 restraints weight = 30840.646| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 30821 Z= 0.205 Angle : 0.648 13.797 42070 Z= 0.319 Chirality : 0.046 0.522 4936 Planarity : 0.004 0.050 5279 Dihedral : 6.707 59.632 5576 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.99 % Favored : 92.93 % Rotamer: Outliers : 1.27 % Allowed : 16.09 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -1.13 (0.14), residues: 3661 helix: 1.59 (0.21), residues: 660 sheet: -0.29 (0.17), residues: 895 loop : -1.82 (0.12), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.025 0.001 TYR C 91 PHE 0.014 0.001 PHE C 43 TRP 0.015 0.001 TRP N 48 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00470 (30704) covalent geometry : angle 0.62235 (41762) SS BOND : bond 0.00319 ( 43) SS BOND : angle 1.17226 ( 86) hydrogen bonds : bond 0.05914 ( 1033) hydrogen bonds : angle 5.15824 ( 2766) link_BETA1-4 : bond 0.00390 ( 27) link_BETA1-4 : angle 2.38776 ( 81) link_NAG-ASN : bond 0.00307 ( 47) link_NAG-ASN : angle 2.55165 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6512.39 seconds wall clock time: 112 minutes 34.62 seconds (6754.62 seconds total)