Starting phenix.real_space_refine on Thu Mar 5 20:14:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eb3_31050/03_2026/7eb3_31050.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eb3_31050/03_2026/7eb3_31050.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/7eb3_31050/03_2026/7eb3_31050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eb3_31050/03_2026/7eb3_31050.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7eb3_31050/03_2026/7eb3_31050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eb3_31050/03_2026/7eb3_31050.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= -0.001 sd= 0.042 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 105 5.16 5 C 15799 2.51 5 N 4023 2.21 5 O 4917 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24844 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 7879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1010, 7879 Classifications: {'peptide': 1010} Link IDs: {'PTRANS': 50, 'TRANS': 959} Chain breaks: 7 Chain: "B" Number of atoms: 7935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 7935 Classifications: {'peptide': 1016} Link IDs: {'PTRANS': 51, 'TRANS': 964} Chain breaks: 7 Chain: "C" Number of atoms: 7927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7927 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 51, 'TRANS': 963} Chain breaks: 7 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.31, per 1000 atoms: 0.21 Number of scatterers: 24844 At special positions: 0 Unit cell: (137.5, 141.9, 200.2, 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 105 16.00 O 4917 8.00 N 4023 7.00 C 15799 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, 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 538 " - pdb=" SG CYS A 590 " 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=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 D 2 " - " BMA D 3 " " 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 K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG 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-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 165 " " NAG A2004 " - " ASN A 603 " " NAG A2005 " - " ASN A 657 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 165 " " NAG B2004 " - " ASN B 234 " " NAG B2005 " - " ASN B 331 " " 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 331 " " NAG C2005 " - " ASN C 603 " " NAG C2006 " - " ASN C 657 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 343 " " NAG H 1 " - " ASN A 616 " " NAG I 1 " - " ASN A 709 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 282 " " NAG P 1 " - " ASN B 343 " " NAG Q 1 " - " ASN B 616 " " NAG R 1 " - " ASN B 709 " " NAG S 1 " - " ASN B 717 " " NAG T 1 " - " ASN B 801 " " NAG U 1 " - " ASN B1074 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 234 " " NAG Y 1 " - " ASN C 282 " " NAG Z 1 " - " ASN C 343 " " NAG a 1 " - " ASN C 616 " " NAG b 1 " - " ASN C 709 " " NAG c 1 " - " ASN C 717 " " NAG d 1 " - " ASN C 801 " " NAG e 1 " - " ASN C1074 " " NAG f 1 " - " ASN C1098 " " NAG g 1 " - " ASN C1134 " Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 990.0 milliseconds 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5692 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 47 sheets defined 25.1% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.606A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.504A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.885A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.683A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.908A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.671A 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: 3.700A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.623A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.561A 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: 3.584A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.629A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.593A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.591A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.789A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.640A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.585A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.503A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 908 removed outlier: 3.844A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.608A 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 982 removed outlier: 3.818A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.578A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.940A 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 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.230A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 633 through 638 removed outlier: 3.603A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.688A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.881A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 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 909 removed outlier: 3.786A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.696A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.558A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.565A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.610A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.323A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.778A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASN C 540 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.620A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.805A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 313 removed outlier: 4.937A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.774A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 573 through 576 removed outlier: 4.217A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.354A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS A 671 " --> pdb=" O TYR A 695 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.636A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 1076 through 1077 removed outlier: 3.501A pdb=" N VAL A1104 " --> pdb=" O GLN A1113 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A1113 " --> pdb=" O VAL A1104 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 4.970A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.629A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.203A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.732A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.526A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 318 removed outlier: 5.681A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 323 through 328 removed outlier: 6.375A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASN B 540 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP B 586 " --> pdb=" O THR B 553 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 566 " --> pdb=" O ALA B 575 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.037A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.116A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 717 through 719 removed outlier: 3.510A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 717 through 719 removed outlier: 3.720A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.572A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1081 through 1083 removed outlier: 4.932A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.653A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.573A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.962A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 118 through 121 Processing sheet with id=AE1, first strand: chain 'C' and resid 191 through 197 removed outlier: 3.550A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.532A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.532A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.552A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.316A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.849A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1047 through 1050 removed outlier: 5.540A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.608A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.779A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2370 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: 5.39 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7824 1.35 - 1.47: 6690 1.47 - 1.60: 10744 1.60 - 1.72: 0 1.72 - 1.85: 129 Bond restraints: 25387 Sorted by residual: bond pdb=" C1 NAG X 2 " pdb=" O5 NAG X 2 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 1.333 1.378 -0.044 1.44e-02 4.82e+03 9.50e+00 bond pdb=" N GLY B 639 " pdb=" CA GLY B 639 " ideal model delta sigma weight residual 1.444 1.478 -0.034 1.19e-02 7.06e+03 7.98e+00 bond pdb=" N SER B 640 " pdb=" CA SER B 640 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.11e+00 bond pdb=" C PRO B 986 " pdb=" N PRO B 987 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.27e+00 ... (remaining 25382 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 33245 1.56 - 3.12: 1129 3.12 - 4.68: 142 4.68 - 6.24: 21 6.24 - 7.80: 13 Bond angle restraints: 34550 Sorted by residual: angle pdb=" CA GLY B 639 " pdb=" C GLY B 639 " pdb=" O GLY B 639 " ideal model delta sigma weight residual 121.30 117.29 4.01 9.80e-01 1.04e+00 1.68e+01 angle pdb=" N CYS C 525 " pdb=" CA CYS C 525 " pdb=" C CYS C 525 " ideal model delta sigma weight residual 107.88 113.03 -5.15 1.41e+00 5.03e-01 1.33e+01 angle pdb=" N ILE A 666 " pdb=" CA ILE A 666 " pdb=" C ILE A 666 " ideal model delta sigma weight residual 111.62 108.93 2.69 7.90e-01 1.60e+00 1.16e+01 angle pdb=" N THR C 124 " pdb=" CA THR C 124 " pdb=" C THR C 124 " ideal model delta sigma weight residual 113.43 109.18 4.25 1.26e+00 6.30e-01 1.14e+01 angle pdb=" CB LYS C 195 " pdb=" CG LYS C 195 " pdb=" CD LYS C 195 " ideal model delta sigma weight residual 111.30 118.66 -7.36 2.30e+00 1.89e-01 1.02e+01 ... (remaining 34545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.53: 14971 22.53 - 45.06: 927 45.06 - 67.59: 137 67.59 - 90.12: 47 90.12 - 112.65: 25 Dihedral angle restraints: 16107 sinusoidal: 7263 harmonic: 8844 Sorted by residual: 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 93.00 178.75 -85.75 1 1.00e+01 1.00e-02 8.89e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -164.13 78.13 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -158.49 72.49 1 1.00e+01 1.00e-02 6.71e+01 ... (remaining 16104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3932 0.097 - 0.195: 219 0.195 - 0.292: 7 0.292 - 0.390: 2 0.390 - 0.487: 2 Chirality restraints: 4162 Sorted by residual: chirality pdb=" C1 NAG C2002 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C2002 " pdb=" O5 NAG C2002 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" C1 NAG A2002 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A2002 " pdb=" O5 NAG A2002 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" C1 NAG B2001 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B2001 " pdb=" O5 NAG B2001 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 4159 not shown) Planarity restraints: 4410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO A 986 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO A 987 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B1056 " -0.026 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO B1057 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B1057 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B1057 " -0.022 5.00e-02 4.00e+02 ... (remaining 4407 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 310 2.64 - 3.20: 22556 3.20 - 3.77: 35274 3.77 - 4.33: 45895 4.33 - 4.90: 77158 Nonbonded interactions: 181193 Sorted by model distance: nonbonded pdb=" OG1 THR C 393 " pdb=" OE2 GLU C 516 " model vdw 2.071 3.040 nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.164 3.040 nonbonded pdb=" O THR A 998 " pdb=" NE2 GLN A1002 " model vdw 2.167 3.120 nonbonded pdb=" OG1 THR A 124 " pdb=" O6 NAG A2002 " model vdw 2.169 3.040 nonbonded pdb=" OG1 THR B 393 " pdb=" OE2 GLU B 516 " model vdw 2.187 3.040 ... (remaining 181188 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 621 or resid 635 through 827 or resid 855 throu \ gh 2005)) selection = (chain 'C' and (resid 27 through 621 or resid 635 through 827 or resid 855 throu \ gh 2005)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' 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' } 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: 3.570 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: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.800 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 25500 Z= 0.216 Angle : 0.701 16.526 34855 Z= 0.342 Chirality : 0.049 0.487 4162 Planarity : 0.004 0.052 4362 Dihedral : 14.905 112.654 10313 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.35 % Favored : 93.59 % Rotamer: Outliers : 0.04 % Allowed : 0.15 % Favored : 99.81 % 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: -1.11 (0.15), residues: 2993 helix: 1.44 (0.22), residues: 660 sheet: -0.65 (0.20), residues: 672 loop : -1.75 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 355 TYR 0.017 0.001 TYR B 91 PHE 0.021 0.001 PHE A 906 TRP 0.020 0.001 TRP A 353 HIS 0.008 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00460 (25387) covalent geometry : angle 0.65711 (34550) SS BOND : bond 0.00424 ( 34) SS BOND : angle 1.41098 ( 68) hydrogen bonds : bond 0.14068 ( 870) hydrogen bonds : angle 6.01179 ( 2370) link_BETA1-4 : bond 0.00613 ( 31) link_BETA1-4 : angle 3.08647 ( 93) link_NAG-ASN : bond 0.00367 ( 48) link_NAG-ASN : angle 2.90051 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: B 369 TYR cc_start: 0.8743 (t80) cc_final: 0.8493 (t80) REVERT: B 1029 MET cc_start: 0.8976 (tmm) cc_final: 0.8678 (tmm) REVERT: C 410 ILE cc_start: 0.9235 (mm) cc_final: 0.9027 (mt) outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.1407 time to fit residues: 30.2269 Evaluate side-chains 74 residues out of total 2657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.0170 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.5980 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B1088 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.105536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.068514 restraints weight = 69698.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.071420 restraints weight = 38755.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.073318 restraints weight = 27446.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.074563 restraints weight = 22155.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.075320 restraints weight = 19271.145| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25500 Z= 0.119 Angle : 0.638 12.262 34855 Z= 0.304 Chirality : 0.046 0.481 4162 Planarity : 0.004 0.049 4362 Dihedral : 9.916 99.972 4907 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.25 % Favored : 94.69 % Rotamer: Outliers : 0.34 % Allowed : 5.23 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.15), residues: 2993 helix: 1.41 (0.21), residues: 697 sheet: -0.46 (0.20), residues: 670 loop : -1.71 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 466 TYR 0.014 0.001 TYR B1067 PHE 0.019 0.001 PHE A 201 TRP 0.018 0.001 TRP A 353 HIS 0.011 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00257 (25387) covalent geometry : angle 0.60371 (34550) SS BOND : bond 0.00369 ( 34) SS BOND : angle 1.12183 ( 68) hydrogen bonds : bond 0.05236 ( 870) hydrogen bonds : angle 4.91128 ( 2370) link_BETA1-4 : bond 0.00674 ( 31) link_BETA1-4 : angle 2.52115 ( 93) link_NAG-ASN : bond 0.00435 ( 48) link_NAG-ASN : angle 2.54067 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1017 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7876 (tm-30) REVERT: B 740 MET cc_start: 0.8224 (mmm) cc_final: 0.8003 (mmt) REVERT: B 855 PHE cc_start: 0.7403 (m-80) cc_final: 0.6528 (m-10) REVERT: B 993 ILE cc_start: 0.8706 (mm) cc_final: 0.8482 (mm) REVERT: B 1029 MET cc_start: 0.9106 (tmm) cc_final: 0.8670 (tmm) REVERT: C 780 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8301 (tm-30) REVERT: C 981 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8835 (pp) REVERT: C 1029 MET cc_start: 0.9055 (tmm) cc_final: 0.8798 (tmm) outliers start: 9 outliers final: 6 residues processed: 103 average time/residue: 0.1340 time to fit residues: 24.5451 Evaluate side-chains 90 residues out of total 2657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 990 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 260 optimal weight: 0.3980 chunk 149 optimal weight: 4.9990 chunk 271 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 264 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 273 optimal weight: 4.9990 chunk 263 optimal weight: 0.9980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 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 = 0.3914 r_free = 0.3914 target = 0.104583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.067349 restraints weight = 69715.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.070184 restraints weight = 39273.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.072052 restraints weight = 28050.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.073282 restraints weight = 22706.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.074046 restraints weight = 19786.486| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25500 Z= 0.140 Angle : 0.624 11.717 34855 Z= 0.297 Chirality : 0.046 0.467 4162 Planarity : 0.004 0.048 4362 Dihedral : 8.591 95.111 4907 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.61 % Favored : 94.32 % Rotamer: Outliers : 0.49 % Allowed : 8.81 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.15), residues: 2993 helix: 1.41 (0.21), residues: 697 sheet: -0.46 (0.20), residues: 671 loop : -1.67 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 355 TYR 0.018 0.001 TYR A 91 PHE 0.036 0.001 PHE C 456 TRP 0.015 0.001 TRP A 353 HIS 0.007 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00323 (25387) covalent geometry : angle 0.58902 (34550) SS BOND : bond 0.00351 ( 34) SS BOND : angle 1.19042 ( 68) hydrogen bonds : bond 0.05321 ( 870) hydrogen bonds : angle 4.80992 ( 2370) link_BETA1-4 : bond 0.00621 ( 31) link_BETA1-4 : angle 2.53774 ( 93) link_NAG-ASN : bond 0.00358 ( 48) link_NAG-ASN : angle 2.50353 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1017 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7791 (tm-30) REVERT: B 523 THR cc_start: 0.8735 (p) cc_final: 0.8460 (t) REVERT: B 1029 MET cc_start: 0.9127 (tmm) cc_final: 0.8635 (tmm) REVERT: C 780 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8377 (tm-30) REVERT: C 981 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8851 (pp) outliers start: 13 outliers final: 6 residues processed: 100 average time/residue: 0.1296 time to fit residues: 23.1382 Evaluate side-chains 86 residues out of total 2657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 990 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 91 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 170 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 209 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 255 optimal weight: 0.0030 chunk 215 optimal weight: 0.8980 chunk 242 optimal weight: 0.2980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.105652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.068707 restraints weight = 68999.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.071632 restraints weight = 38470.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.073538 restraints weight = 27255.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.074783 restraints weight = 21987.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.075544 restraints weight = 19110.376| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25500 Z= 0.105 Angle : 0.595 11.509 34855 Z= 0.281 Chirality : 0.045 0.470 4162 Planarity : 0.003 0.047 4362 Dihedral : 7.942 90.645 4907 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.74 % Favored : 95.19 % Rotamer: Outliers : 0.60 % Allowed : 11.33 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.15), residues: 2993 helix: 1.50 (0.21), residues: 690 sheet: -0.29 (0.20), residues: 674 loop : -1.60 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 355 TYR 0.012 0.001 TYR A1067 PHE 0.020 0.001 PHE A 201 TRP 0.012 0.001 TRP A 353 HIS 0.003 0.000 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00224 (25387) covalent geometry : angle 0.56082 (34550) SS BOND : bond 0.00322 ( 34) SS BOND : angle 1.02632 ( 68) hydrogen bonds : bond 0.04759 ( 870) hydrogen bonds : angle 4.61702 ( 2370) link_BETA1-4 : bond 0.00646 ( 31) link_BETA1-4 : angle 2.49981 ( 93) link_NAG-ASN : bond 0.00404 ( 48) link_NAG-ASN : angle 2.38306 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1017 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7888 (tm-30) REVERT: B 490 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.6994 (t80) REVERT: B 523 THR cc_start: 0.8753 (p) cc_final: 0.8495 (t) REVERT: B 1029 MET cc_start: 0.9135 (tmm) cc_final: 0.8613 (tmm) REVERT: C 981 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8834 (pp) outliers start: 16 outliers final: 6 residues processed: 102 average time/residue: 0.1413 time to fit residues: 25.4372 Evaluate side-chains 89 residues out of total 2657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 990 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 238 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 270 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN ** C 422 ASN ** 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 = 0.3875 r_free = 0.3875 target = 0.102200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.065078 restraints weight = 70012.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.067680 restraints weight = 40937.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.069388 restraints weight = 29833.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.070510 restraints weight = 24500.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.071253 restraints weight = 21517.125| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25500 Z= 0.229 Angle : 0.689 11.282 34855 Z= 0.334 Chirality : 0.047 0.460 4162 Planarity : 0.004 0.051 4362 Dihedral : 7.871 91.887 4907 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.98 % Favored : 92.95 % Rotamer: Outliers : 0.94 % Allowed : 13.17 % Favored : 85.89 % 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: -1.09 (0.15), residues: 2993 helix: 1.21 (0.21), residues: 688 sheet: -0.45 (0.20), residues: 658 loop : -1.75 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 355 TYR 0.026 0.002 TYR A 91 PHE 0.036 0.002 PHE C 456 TRP 0.009 0.002 TRP A 353 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00539 (25387) covalent geometry : angle 0.65557 (34550) SS BOND : bond 0.00432 ( 34) SS BOND : angle 1.43102 ( 68) hydrogen bonds : bond 0.06213 ( 870) hydrogen bonds : angle 4.96991 ( 2370) link_BETA1-4 : bond 0.00572 ( 31) link_BETA1-4 : angle 2.54459 ( 93) link_NAG-ASN : bond 0.00351 ( 48) link_NAG-ASN : angle 2.59425 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 1017 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7989 (tm-30) REVERT: A 1029 MET cc_start: 0.9013 (tpp) cc_final: 0.8552 (tmm) REVERT: B 490 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.6942 (t80) REVERT: B 523 THR cc_start: 0.8820 (p) cc_final: 0.8580 (t) REVERT: B 697 MET cc_start: 0.7608 (ttm) cc_final: 0.7406 (ttm) REVERT: B 740 MET cc_start: 0.8289 (mmt) cc_final: 0.8055 (mmp) REVERT: B 1029 MET cc_start: 0.9161 (tmm) cc_final: 0.8563 (tmm) REVERT: C 410 ILE cc_start: 0.9200 (mm) cc_final: 0.8995 (mt) REVERT: C 981 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8836 (pp) outliers start: 25 outliers final: 13 residues processed: 105 average time/residue: 0.1292 time to fit residues: 24.1300 Evaluate side-chains 95 residues out of total 2657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 139 optimal weight: 1.9990 chunk 280 optimal weight: 0.3980 chunk 30 optimal weight: 4.9990 chunk 86 optimal weight: 0.3980 chunk 223 optimal weight: 0.1980 chunk 158 optimal weight: 0.8980 chunk 298 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 302 optimal weight: 0.6980 chunk 227 optimal weight: 0.9990 chunk 281 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** C 422 ASN ** 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 = 0.3918 r_free = 0.3918 target = 0.104851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.067918 restraints weight = 69374.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.070798 restraints weight = 38752.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.072682 restraints weight = 27484.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.073917 restraints weight = 22173.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.074719 restraints weight = 19277.744| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25500 Z= 0.108 Angle : 0.601 11.268 34855 Z= 0.286 Chirality : 0.045 0.464 4162 Planarity : 0.004 0.048 4362 Dihedral : 7.492 90.138 4907 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.68 % Favored : 95.26 % Rotamer: Outliers : 1.09 % Allowed : 14.38 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.15), residues: 2993 helix: 1.46 (0.21), residues: 687 sheet: -0.45 (0.20), residues: 689 loop : -1.60 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 102 TYR 0.014 0.001 TYR A1067 PHE 0.012 0.001 PHE A1121 TRP 0.029 0.001 TRP A 104 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00230 (25387) covalent geometry : angle 0.56755 (34550) SS BOND : bond 0.00346 ( 34) SS BOND : angle 1.09856 ( 68) hydrogen bonds : bond 0.04887 ( 870) hydrogen bonds : angle 4.58740 ( 2370) link_BETA1-4 : bond 0.00672 ( 31) link_BETA1-4 : angle 2.48500 ( 93) link_NAG-ASN : bond 0.00438 ( 48) link_NAG-ASN : angle 2.33418 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 1017 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7947 (tm-30) REVERT: A 1029 MET cc_start: 0.8902 (tpp) cc_final: 0.8456 (tmm) REVERT: B 490 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.7069 (t80) REVERT: B 523 THR cc_start: 0.8788 (p) cc_final: 0.8523 (t) REVERT: B 976 VAL cc_start: 0.9533 (OUTLIER) cc_final: 0.9317 (p) REVERT: B 1029 MET cc_start: 0.9163 (tmm) cc_final: 0.8615 (tmm) outliers start: 29 outliers final: 13 residues processed: 109 average time/residue: 0.1273 time to fit residues: 25.2984 Evaluate side-chains 95 residues out of total 2657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 250 optimal weight: 0.0000 chunk 63 optimal weight: 0.6980 chunk 210 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 265 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 chunk 233 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 109 optimal weight: 0.5980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.105095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.068114 restraints weight = 69365.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.071006 restraints weight = 38943.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.072886 restraints weight = 27643.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.074105 restraints weight = 22320.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.074932 restraints weight = 19462.665| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 25500 Z= 0.107 Angle : 0.590 10.931 34855 Z= 0.280 Chirality : 0.045 0.452 4162 Planarity : 0.003 0.047 4362 Dihedral : 7.191 83.501 4907 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.15 % Favored : 94.79 % Rotamer: Outliers : 0.94 % Allowed : 15.13 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.16), residues: 2993 helix: 1.47 (0.21), residues: 689 sheet: -0.36 (0.20), residues: 692 loop : -1.56 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 355 TYR 0.015 0.001 TYR A1067 PHE 0.021 0.001 PHE A 201 TRP 0.010 0.001 TRP C 633 HIS 0.001 0.000 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00234 (25387) covalent geometry : angle 0.55724 (34550) SS BOND : bond 0.00335 ( 34) SS BOND : angle 1.08380 ( 68) hydrogen bonds : bond 0.04712 ( 870) hydrogen bonds : angle 4.50071 ( 2370) link_BETA1-4 : bond 0.00673 ( 31) link_BETA1-4 : angle 2.48112 ( 93) link_NAG-ASN : bond 0.00362 ( 48) link_NAG-ASN : angle 2.29909 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: A 1017 GLU cc_start: 0.8236 (tm-30) cc_final: 0.8007 (tm-30) REVERT: A 1029 MET cc_start: 0.8919 (tpp) cc_final: 0.8486 (tmm) REVERT: B 490 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.6963 (t80) REVERT: B 523 THR cc_start: 0.8819 (p) cc_final: 0.8546 (t) REVERT: B 697 MET cc_start: 0.7616 (ttm) cc_final: 0.7368 (ttp) REVERT: B 976 VAL cc_start: 0.9528 (OUTLIER) cc_final: 0.9316 (p) REVERT: B 1029 MET cc_start: 0.9144 (tmm) cc_final: 0.8561 (tmm) outliers start: 25 outliers final: 14 residues processed: 104 average time/residue: 0.1267 time to fit residues: 23.9763 Evaluate side-chains 97 residues out of total 2657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 127 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 251 optimal weight: 0.2980 chunk 281 optimal weight: 1.9990 chunk 286 optimal weight: 6.9990 chunk 213 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 243 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 100 optimal weight: 0.0770 chunk 47 optimal weight: 4.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 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 = 0.3915 r_free = 0.3915 target = 0.104630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.067542 restraints weight = 69375.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.070402 restraints weight = 39150.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.072262 restraints weight = 27887.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.073468 restraints weight = 22585.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.074223 restraints weight = 19702.731| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25500 Z= 0.121 Angle : 0.595 10.933 34855 Z= 0.283 Chirality : 0.045 0.448 4162 Planarity : 0.003 0.046 4362 Dihedral : 7.031 77.430 4907 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.35 % Favored : 94.59 % Rotamer: Outliers : 0.83 % Allowed : 15.62 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.16), residues: 2993 helix: 1.46 (0.21), residues: 689 sheet: -0.33 (0.20), residues: 675 loop : -1.55 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 355 TYR 0.014 0.001 TYR A1067 PHE 0.037 0.001 PHE C 456 TRP 0.009 0.001 TRP C 633 HIS 0.002 0.000 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00275 (25387) covalent geometry : angle 0.56294 (34550) SS BOND : bond 0.00336 ( 34) SS BOND : angle 1.08090 ( 68) hydrogen bonds : bond 0.04802 ( 870) hydrogen bonds : angle 4.52096 ( 2370) link_BETA1-4 : bond 0.00621 ( 31) link_BETA1-4 : angle 2.48084 ( 93) link_NAG-ASN : bond 0.00339 ( 48) link_NAG-ASN : angle 2.28828 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 1017 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7991 (tm-30) REVERT: A 1029 MET cc_start: 0.8930 (tpp) cc_final: 0.8466 (tmm) REVERT: B 490 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.6987 (t80) REVERT: B 523 THR cc_start: 0.8819 (p) cc_final: 0.8549 (t) REVERT: B 697 MET cc_start: 0.7574 (ttm) cc_final: 0.7363 (ttp) REVERT: B 976 VAL cc_start: 0.9527 (OUTLIER) cc_final: 0.9314 (p) REVERT: B 1029 MET cc_start: 0.9156 (tmm) cc_final: 0.8549 (tmm) outliers start: 22 outliers final: 15 residues processed: 103 average time/residue: 0.1270 time to fit residues: 23.9026 Evaluate side-chains 97 residues out of total 2657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 56 optimal weight: 10.0000 chunk 288 optimal weight: 0.9990 chunk 189 optimal weight: 0.9990 chunk 283 optimal weight: 3.9990 chunk 100 optimal weight: 0.0980 chunk 35 optimal weight: 10.0000 chunk 237 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 279 optimal weight: 0.5980 chunk 280 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.105091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.068124 restraints weight = 69464.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.070995 restraints weight = 38993.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.072888 restraints weight = 27746.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.074143 restraints weight = 22395.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.074908 restraints weight = 19487.454| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 25500 Z= 0.107 Angle : 0.590 12.553 34855 Z= 0.278 Chirality : 0.045 0.443 4162 Planarity : 0.003 0.047 4362 Dihedral : 6.847 69.996 4907 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.01 % Favored : 94.92 % Rotamer: Outliers : 0.87 % Allowed : 15.92 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.16), residues: 2993 helix: 1.48 (0.21), residues: 689 sheet: -0.28 (0.20), residues: 675 loop : -1.52 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 355 TYR 0.014 0.001 TYR A1067 PHE 0.013 0.001 PHE A1121 TRP 0.009 0.001 TRP C 633 HIS 0.002 0.000 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00238 (25387) covalent geometry : angle 0.55756 (34550) SS BOND : bond 0.00324 ( 34) SS BOND : angle 1.02225 ( 68) hydrogen bonds : bond 0.04583 ( 870) hydrogen bonds : angle 4.45221 ( 2370) link_BETA1-4 : bond 0.00632 ( 31) link_BETA1-4 : angle 2.48392 ( 93) link_NAG-ASN : bond 0.00357 ( 48) link_NAG-ASN : angle 2.24905 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 1017 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7990 (tm-30) REVERT: A 1029 MET cc_start: 0.8903 (tpp) cc_final: 0.8461 (tmm) REVERT: B 490 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6922 (t80) REVERT: B 523 THR cc_start: 0.8849 (p) cc_final: 0.8580 (t) REVERT: B 697 MET cc_start: 0.7638 (ttm) cc_final: 0.7396 (ttp) REVERT: B 976 VAL cc_start: 0.9523 (OUTLIER) cc_final: 0.9308 (p) REVERT: B 1029 MET cc_start: 0.9176 (tmm) cc_final: 0.8956 (tmm) outliers start: 23 outliers final: 17 residues processed: 109 average time/residue: 0.1335 time to fit residues: 26.2085 Evaluate side-chains 99 residues out of total 2657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 3 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 204 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 235 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** C 422 ASN ** 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 = 0.3906 r_free = 0.3906 target = 0.104134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.066960 restraints weight = 69621.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.069772 restraints weight = 39518.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.071630 restraints weight = 28277.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.072739 restraints weight = 22910.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.073583 restraints weight = 20104.717| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25500 Z= 0.143 Angle : 0.621 14.176 34855 Z= 0.294 Chirality : 0.045 0.440 4162 Planarity : 0.004 0.046 4362 Dihedral : 6.808 62.995 4907 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.61 % Favored : 94.32 % Rotamer: Outliers : 0.75 % Allowed : 16.26 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.15), residues: 2993 helix: 1.46 (0.21), residues: 687 sheet: -0.33 (0.20), residues: 672 loop : -1.55 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 355 TYR 0.017 0.001 TYR A 91 PHE 0.026 0.001 PHE C 456 TRP 0.007 0.001 TRP C 633 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00331 (25387) covalent geometry : angle 0.58953 (34550) SS BOND : bond 0.00366 ( 34) SS BOND : angle 1.16227 ( 68) hydrogen bonds : bond 0.04921 ( 870) hydrogen bonds : angle 4.54550 ( 2370) link_BETA1-4 : bond 0.00598 ( 31) link_BETA1-4 : angle 2.50649 ( 93) link_NAG-ASN : bond 0.00316 ( 48) link_NAG-ASN : angle 2.28787 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 900 MET cc_start: 0.8048 (ptp) cc_final: 0.7764 (ptp) REVERT: A 1017 GLU cc_start: 0.8248 (tm-30) cc_final: 0.8010 (tm-30) REVERT: A 1029 MET cc_start: 0.8928 (tpp) cc_final: 0.8445 (tmm) REVERT: B 490 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6957 (t80) REVERT: B 523 THR cc_start: 0.8823 (p) cc_final: 0.8551 (t) REVERT: B 697 MET cc_start: 0.7640 (ttm) cc_final: 0.7392 (ttp) REVERT: B 976 VAL cc_start: 0.9528 (OUTLIER) cc_final: 0.9317 (p) REVERT: B 1029 MET cc_start: 0.9164 (tmm) cc_final: 0.8546 (tmm) outliers start: 20 outliers final: 17 residues processed: 99 average time/residue: 0.1320 time to fit residues: 23.7929 Evaluate side-chains 99 residues out of total 2657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 198 optimal weight: 0.2980 chunk 105 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 230 optimal weight: 0.0000 chunk 48 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 287 optimal weight: 0.0170 chunk 69 optimal weight: 0.8980 overall best weight: 0.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.105484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.068538 restraints weight = 69259.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.071429 restraints weight = 38854.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.073318 restraints weight = 27637.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.074503 restraints weight = 22314.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.075370 restraints weight = 19466.420| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 25500 Z= 0.103 Angle : 0.596 13.143 34855 Z= 0.280 Chirality : 0.045 0.440 4162 Planarity : 0.003 0.047 4362 Dihedral : 6.646 58.415 4907 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.68 % Favored : 95.26 % Rotamer: Outliers : 0.75 % Allowed : 16.37 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.16), residues: 2993 helix: 1.52 (0.21), residues: 690 sheet: -0.17 (0.20), residues: 672 loop : -1.51 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 355 TYR 0.014 0.001 TYR A1067 PHE 0.023 0.001 PHE A 201 TRP 0.009 0.001 TRP C 104 HIS 0.002 0.000 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00220 (25387) covalent geometry : angle 0.56485 (34550) SS BOND : bond 0.00334 ( 34) SS BOND : angle 1.00901 ( 68) hydrogen bonds : bond 0.04459 ( 870) hydrogen bonds : angle 4.41943 ( 2370) link_BETA1-4 : bond 0.00643 ( 31) link_BETA1-4 : angle 2.50518 ( 93) link_NAG-ASN : bond 0.00383 ( 48) link_NAG-ASN : angle 2.21322 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4737.98 seconds wall clock time: 82 minutes 13.72 seconds (4933.72 seconds total)